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@@ -33,3 +33,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.zip filter=lfs diff=lfs merge=lfs -text
 *.zst filter=lfs diff=lfs merge=lfs -text
 *tfevents* filter=lfs diff=lfs merge=lfs -text
+output/biomedbert_vector_db/faiss.index filter=lfs diff=lfs merge=lfs -text

README.md

@@ -1,20 +1,290 @@
 ---
-title: Knowledge Extraction From Pathology Reports
-emoji: 🚀
-colorFrom: red
-colorTo: red
-sdk: docker
-app_port: 8501
-tags:
-- streamlit
+title: Pathology RAG System
+emoji: 🔬
+colorFrom: blue
+colorTo: indigo
+sdk: streamlit
+app_file: app.py
 pinned: false
-short_description: Streamlit template space
-license: apache-2.0
 ---
 
-# Welcome to Streamlit!
+![Multimodal RAG Architecture](image.png)
+
+# Visual Architecture Diagram - Pathology Report Knowledge Extraction
+
+## System Architecture - Complete Flow
+
+```
+╔═══════════════════════════════════════════════════════════════════════════════╗
+║                     PATHOLOGY REPORT PROCESSING SYSTEM                        ║
+║                    RAG + Spark NLP + Vector Database                          ║
+╚═══════════════════════════════════════════════════════════════════════════════╝
+
+┌───────────────────────────────────────────────────────────────────────────────┐
+│                           1. DATA INGESTION                                   │
+└───────────────────────────────────────────────────────────────────────────────┘
+
+    📄 Pathology Reports (PDF)
+         │
+         ├─── Scanned PDFs ────────► OCR (Tesseract/EasyOCR)
+         │                                     │
+         └─── Digital PDFs ────────► PyMuPDF Text Extraction
+                                               │
+                                               ▼
+                                      📝 Raw Text Files
+                                               │
+                                               │
+┌──────────────────────────────────────────────┼─────────────────────────────────┐
+│                    2. SPARK NLP PROCESSING   │                                 │
+└──────────────────────────────────────────────┼─────────────────────────────────┘
+                                               │
+                    ┌──────────────────────────┴──────────────────────────┐
+                    │        Spark NLP Medical Pipeline                   │
+                    │                                                      │
+                    │  ┌────────────────────────────────────────────┐    │
+                    │  │  Stage 1: Document Assembly                │    │
+                    │  │  • DocumentAssembler                       │    │
+                    │  │  • SentenceDetector                        │    │
+                    │  │  • Tokenizer                               │    │
+                    │  └──────────────┬─────────────────────────────┘    │
+                    │                 ▼                                   │
+                    │  ┌────────────────────────────────────────────┐    │
+                    │  │  Stage 2: Entity Recognition (NER)         │    │
+                    │  │  • Medical NER (BioBERT/ClinicalBERT)     │    │
+                    │  │  • Extract: PROBLEM, TREATMENT, TEST,      │    │
+                    │  │            ANATOMY, LAB_VALUE              │    │
+                    │  └──────────────┬─────────────────────────────┘    │
+                    │                 ▼                                   │
+                    │  ┌────────────────────────────────────────────┐    │
+                    │  │  Stage 3: Assertion & Relations            │    │
+                    │  │  • AssertionDL (present/absent/possible)   │    │
+                    │  │  • RelationExtraction (entity links)       │    │
+                    │  └──────────────┬─────────────────────────────┘    │
+                    │                                                    │
+                    └─────────────────┼─────────────────────────────────┘
+                                      ▼
+                          📊 Structured Clinical Data
+                          {
+                            "entities": [...],
+                            "relations": [...],
+                            "assertions": [...],
+                            "metadata": {...}
+                          }
+                                      │
+                                      │
+┌─────────────────────────────────────┼───────────────────────────────────────┐
+│                  3. CHUNKING & ENRICHMENT                                    │
+└─────────────────────────────────────┼───────────────────────────────────────┘
+                                      │
+                    ┌─────────────────┴─────────────────┐
+                    │                                   │
+                    ▼                                   ▼
+          ┌──────────────────┐              ┌──────────────────┐
+          │ Section-Based    │              │ Semantic-Based   │
+          │ Chunking         │              │ Chunking         │
+          │                  │              │                  │
+          │ • Clinical       │              │ • 512-1024       │
+          │   History        │              │   tokens         │
+          │ • Findings       │              │ • 128 overlap    │
+          │ • Diagnosis      │              │ • Entity-aware   │
+          │ • Treatment      │              │                  │
+          └────────┬─────────┘              └────────┬─────────┘
+                   │                                 │
+                   └────────────┬────────────────────┘
+                                │
+                                ▼
+                    📦 Enriched Chunks with Metadata
+                    {
+                      "chunk_id": "...",
+                      "text": "...",
+                      "entities": [...],
+                      "section": "...",
+                      "report_date": "...",
+                      "report_type": "..."
+                    }
+                                │
+                                │
+┌───────────────────────────────┼───────────────────────────────────────────┐
+│               4. EMBEDDING GENERATION                                      │
+└───────────────────────────────┼───────────────────────────────────────────┘
+                                │
+                    ┌───────────┴───────────┐
+                    │                       │
+                    ▼                       ▼
+         ┌────────────────────┐   ┌────────────────────┐
+         │ Dense Embeddings   │   │ Sparse Embeddings  │
+         │                    │   │                    │
+         │ • BioBERT          │   │ • BM25             │
+         │ • ClinicalBERT     │   │ • TF-IDF           │
+         │ • PubMedBERT       │   │ • Keyword Index    │
+         │ • SapBERT          │   │                    │
+         │                    │   │                    │
+         │ 768-dim vectors    │   │ Sparse vectors     │
+         └────────┬───────────┘   └────────┬───────────┘
+                  │                        │
+                  └───────────┬────────────┘
+                              │
+                              ▼
+                    🔢 Hybrid Embeddings
+                              │
+                              │
+┌─────────────────────────────┼─────────────────────────────────────────────┐
+│               5. VECTOR DATABASE STORAGE                                   │
+└─────────────────────────────┼─────────────────────────────────────────────┘
+                              │
+              ┌───────────────┼───────────────┐
+              │               │               │
+              ▼               ▼               ▼
+      ┌──────────────┐ ┌──────────────┐ ┌──────────────┐
+      │  ChromaDB    │ │    FAISS     │ │  Pinecone    │
+      │              │ │              │ │              │
+      │ • Dev/Test   │ │ • Production │ │ • Cloud      │
+      │ • Easy setup │ │ • Fast       │ │ • Managed    │
+      │ • Metadata   │ │ • Scalable   │ │ • Enterprise │
+      └──────┬───────┘ └──────┬───────┘ └──────┬───────┘
+             │                │                │
+             └────────────────┼────────────────┘
+                              │
+                              ▼
+                  💾 Indexed Knowledge Base
+                  • Embeddings: 384-768 dims
+                  • Metadata: entities, dates, types
+                  • Relations: entity graphs
+                              │
+                              │
+┌─────────────────────────────┼─────────────────────────────────────────────┐
+│                     6. QUERY & RETRIEVAL (RAG)                             │
+└─────────────────────────────┼─────────────────────────────────────────────┘
+                              │
+         👤 User Query: "What are ER+ breast cancer markers?"
+                              │
+                              ▼
+              ┌───────────────────────────────┐
+              │   Query Processing            │
+              │   • Entity extraction         │
+              │   • Query expansion           │
+              │   • Generate embeddings       │
+              └───────────┬───────────────────┘
+                          │
+                          ▼
+              ┌───────────────────────────────┐
+              │   Hybrid Retrieval            │
+              │                               │
+              │   ┌─────────────────────┐    │
+              │   │ Dense Search        │    │
+              │   │ (Semantic)          │────┼──► Top 20 chunks
+              │   └─────────────────────┘    │
+              │                               │
+              │   ┌─────────────────────┐    │
+              │   │ Sparse Search       │    │
+              │   │ (BM25/Keywords)     │────┼──► Top 20 chunks
+              │   └─────────────────────┘    │
+              │                               │
+              │   ┌─────────────────────┐    │
+              │   │ Entity Filter       │    │
+              │   │ (Medical entities)  │────┼──► Filtered
+              │   └─────────────────────┘    │
+              └───────────┬───────────────────┘
+                          │
+                          ▼
+              ┌───────��───────────────────────┐
+              │   Reranking                   │
+              │   • Cross-encoder scoring     │
+              │   • Medical relevance         │
+              │   • Temporal filtering        │
+              └───────────┬───────────────────┘
+                          │
+                          ▼
+                  📚 Top 5-10 Relevant Chunks
+                          │
+                          │
+┌─────────────────────────┼───────────────────────────────────────────────┐
+│                 7. GENERATION (LLM)                                       │
+└─────────────────────────┼───────────────────────────────────────────────┘
+                          │
+                          ▼
+          ┌───────────────────────────────────┐
+          │   Prompt Construction             │
+          │                                   │
+          │   System: "You are a medical      │
+          │            expert assistant..."   │
+          │                                   │
+          │   Context: [Retrieved chunks]     │
+          │                                   │
+          │   Query: [User question]          │
+          │                                   │
+          │   Instructions: "Answer with      │
+          │                  citations..."    │
+          └───────────┬───────────────────────┘
+                      │
+                      ▼
+          ┌───────────────────────────────────┐
+          │   LLM (Claude/GPT-4/Med-PaLM)    │
+          │                                   │
+          │   • Medical reasoning             │
+          │   • Citation generation           │
+          │   • Accuracy validation           │
+          └───────────┬───────────────────────┘
+                      │
+                      ▼
+          ┌───────────────────────────────────┐
+          │   Post-processing                 │
+          │   • Format citations              │
+          │   • Fact checking                 │
+          │   • Safety validation             │
+          └───────────┬───────────────────────┘
+                      │
+                      ▼
+                  💬 Final Response
+                      │
+                      │
+┌─────────────────────┼─────────────────────────────────────────────────┐
+│             8. USER INTERFACE                                           │
+└─────────────────────┼─────────────────────────────────────────────────┘
+                      │
+        ┌─────────────┼─────────────┐
+        │             │             │
+        ▼             ▼             ▼
+   ┌────────┐   ┌─────────┐   ┌──────────┐
+   │  CLI   │   │ Web UI  │   │ REST API │
+   │        │   │         │   │          │
+   │ Python │   │Streamlit│   │ FastAPI  │
+   │ Script │   │ Gradio  │   │          │
+   └────────┘   └─────────┘   └──────────┘
+        │             │             │
+        └─────────────┼─────────────┘
+                      │
+                      ▼
+              📊 User Gets Answer
+              with Citations & Sources
+
+
+╔═══════════════════════════════════════════════════════════════════════════╗
+║                        SUPPORTING COMPONENTS                              ║
+╚═══════════════════════════════════════════════════════════════════════════╝
+
+┌─────────────────────┐  ┌─────────────────────┐  ┌────────────────────────┐
+│  Monitoring &       │  │  Knowledge Graph    │  │  Caching Layer         │
+│  Logging            │  │  (Optional)         │  │                        │
+│                     │  │                     │  │  • Query cache         │
+│  • MLflow           │  │  • Neo4j            │  │  • Embedding cache     │
+│  • W&B              │  │  • NetworkX         │  │  • LLM response cache  │
+│  • Prometheus       │  │  • Entity graphs    │  │  • Redis/Memcached     │
+└─────────────────────┘  └─────────────────────┘  └────────────────────────┘
+
+┌─────────────────────┐  ┌─────────────────────┐  ┌────────────────────────┐
+│  Security &         │  │  Evaluation         │  │  Data Pipeline         │
+│  Compliance         │  │  Metrics            │  │                        │
+│                     │  │                     │  │  • Apache Airflow      │
+│  • De-identification│  │  • Precision@k      │  │  • Spark jobs          │
+│  • HIPAA compliance │  │  • Medical accuracy │  │  • Batch processing    │
+│  • Access control   │  │  • Latency          │  │  • ETL workflows       │
+└─────────────────────┘  └─────────────────────┘  └────────────────────────┘
+
+═══════════════════════════════════════════════════════════════════════════
+                            END-TO-END FLOW
+═══════════════════════════════════════════════════════════════════════════
+
+
 
-Edit `/src/streamlit_app.py` to customize this app to your heart's desire. :heart:
 
-If you have any questions, checkout our [documentation](https://docs.streamlit.io) and [community
-forums](https://discuss.streamlit.io).

app.py

@@ -0,0 +1,164 @@
+#!/usr/bin/env python3
+"""
+Pathology RAG System - Streamlit Version
+Query existing FAISS database
+"""
+
+import os
+import sys
+from pathlib import Path
+from datetime import datetime
+
+import streamlit as st
+
+# Force CPU
+os.environ["CUDA_VISIBLE_DEVICES"] = ""
+
+# Add src folder
+sys.path.append("src")
+
+DB_PATH = "output/biomedbert_vector_db"
+
+if not Path(DB_PATH).exists():
+    st.error("Vector database not found. Upload output/biomedbert_vector_db.")
+    st.stop()
+
+# Import RAG pipeline
+try:
+    from retriever import CompleteRAGPipeline
+except ImportError as e:
+    st.error(f"Import error: {e}")
+    st.stop()
+
+
+# -----------------------------
+# Load Pipeline (cached)
+# -----------------------------
+
+@st.cache_resource
+def load_pipeline():
+    # Cache busted to pick up the new ask method return dictionary
+    pipeline = CompleteRAGPipeline(
+        faiss_db_path=DB_PATH,
+        embedding_model="microsoft/BiomedNLP-BiomedBERT-base-uncased-abstract-fulltext",
+    )
+
+    return pipeline
+
+
+pipeline = load_pipeline()
+
+
+# -----------------------------
+# Page Config
+# -----------------------------
+
+st.set_page_config(
+    page_title="Pathology RAG",
+    layout="wide"
+)
+
+st.title("🔬 Pathology Report Analysis System")
+
+st.markdown(
+"""
+AI-powered search and question answering over pathology reports  
+Vector database powered by **BiomedBERT + FAISS**
+"""
+)
+
+
+# -----------------------------
+# Session State
+# -----------------------------
+
+if "query_count" not in st.session_state:
+    st.session_state.query_count = 0
+
+
+# -----------------------------
+# Sidebar
+# -----------------------------
+
+st.sidebar.header("System Info")
+
+st.sidebar.write(f"Queries: {st.session_state.query_count}")
+
+st.sidebar.write("Embedding Model:")
+st.sidebar.write("BiomedBERT")
+
+st.sidebar.write("Vector DB:")
+st.sidebar.write("FAISS")
+
+
+# -----------------------------
+# Query Input
+# -----------------------------
+
+st.header("🔎 Ask a Question")
+
+question = st.text_area(
+    "Enter your medical query",
+    placeholder="What are common findings in breast cancer pathology?",
+)
+
+num_sources = st.slider(
+    "Number of sources",
+    min_value=1,
+    max_value=10,
+    value=5
+)
+
+
+# -----------------------------
+# Search Button
+# -----------------------------
+
+if st.button("Search"):
+
+    if question.strip() == "":
+        st.warning("Please enter a question.")
+
+    else:
+
+        with st.spinner("Running RAG pipeline..."):
+
+            st.session_state.query_count += 1
+
+            result = pipeline.ask(
+                question,
+                top_k=num_sources
+            )
+
+        answer = result["answer"]
+
+        st.subheader("Answer")
+
+        st.markdown(answer)
+
+
+        # Metadata
+        st.subheader("Query Info")
+
+        st.write({
+            "query_number": st.session_state.query_count,
+            "timestamp": datetime.now().strftime("%Y-%m-%d %H:%M:%S"),
+            "sources_used": result["num_sources"]
+        })
+
+
+        # Sources
+        st.subheader("Sources")
+
+        sources = result["sources"]
+
+        if not sources:
+            st.write("No sources retrieved.")
+
+        for i, source in enumerate(sources, 1):
+
+            chunk = source["chunk"]
+
+            with st.expander(f"Source {i} | {chunk['filename']}"):
+
+                st.write(chunk["text"][:600])

output/biomedbert_vector_db/faiss.index

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:13e528783241822262d42f011636618870f54d84c8cbbaffdf7a21fa92dd0d2f
+size 30584877

output/biomedbert_vector_db/metadata.pkl

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:1138cbbb3cd4e2cec0f626bb88d412b95e22a0cc77c4d291cb35f5757a86c925
+size 10202202

output/biomedbert_vector_db/stats.json

@@ -0,0 +1,5 @@
+{
+  "files_processed": 2257,
+  "total_chunks": 9956,
+  "timestamp": "2026-04-01T16:03:19.178128"
+}

output/text/00103fa2-43e4-4c6a-babb-d8b46612399e.txt

@@ -0,0 +1,3 @@
+
+--- Page 1 ---
+UUID:C8BBFFAA-4A45-44D3-921B-6F2BD8DB5B19 TCGA-XS-A8T3-01A-PR Redacted IcD-0-3 8072]3 QruyNbS C 53.oy Nature of material: Cervix tJ 1|Z 4f14 ANATOMOPATHOLOGIC RESULT MACROSCOPY Specimen consists of the uterus and left fallopian tube, weighing 559.0 grams. The tube measures 9.0 cm in length and diameter ranges between 6.0 and 1.5 cm. To the cuts the wall is thin, measuring 0.1 cm, the light is dilated and filled with hemorrhagic content. The uterus measures 13.5 cm in its longitudinal axis, 8.0 cm in anteroposterior diameter and 8.5 cm in bicorneal distance. The cervix measures 3.7 cm in diameter and is surrounded by the vaginal dome, measuring between 0.7 and 1.2 cm. It is observed hard and ulcerated lesion with poorly defined edges and granular background, measuring 3.4 x 3.0 cm, involving all quadrants of the cervix. To the cuts, the myometrium measures 7.8 cm at the bottom, which is thicker, and it has multiple round, firm and whitish lesions, with crisscrossing beams. The endometrium measures 0.4 cm. MICROSCOPY Dispensable description.. DIAGNOSTIC Product of hysterectomy and left salpingectomy: -Invasive squamous cell carcinoma, non-keratinizing, moderately differentiated measuring 3.4 x 3.0 cm in major axis and infiltrating the stroma until 1.38 cm in depth and 2.8 cm in horizontal extent, without compromising uterine isthmus or circumferential and vaginal resection margins.. - Presence of extensive component by squamous cell carcinoma in situ.. - Presence of neoplastic lymphatic embolization. - Uterine leiomyomas. - Endometriosis in parametrium bilaterally and in the left fallopian tube. - Dysfunctional endometrium with moderate stromal edema. - Pathological staging: pT1b1, pN1 (TNM 7th). - For lymph node biopsy, see biopsy number  in this service.

output/text/0010ce59-fd1e-4a45-8753-a224164fb818.txt

@@ -0,0 +1,6 @@
+
+--- Page 1 ---
+page 1 / 2 Department of Cancer Pathology copy No. Date: Examination: Histopathological examination Examination No.: Cost of diagnostic procedure Internal invoice No. Age: ender: F pesel: xXx Patient: XXX 1cs-0-3 Material: Total organ resection -- left breast ad axillary tissues Caci oma, nf {tatv7 duct,Nos 85oxf3 Sih:bus# N0s c5o.9 p~ q1a|1 Unit in charge: (  Physician in charge: Material received on: : Material collected on: Expected time of examination: up to 8 working days Clinical diagnosis: Examination performed on: Macroscopic description: Left breast'sized 24 x 19.5 x 5 cm removed with axillary tissues sized 10 x 7 x 2.5 cm and a skin flap of 24 x 12 cm. Tumour sized 1.9 x 1.3 x 1.4 found in the subaurolar part, located 5.2 cm from the upper boundary, 2.8 cm from the base and 0 cm from the  skin. Metastatic lymph nodes 2 cm in length. Microscopic description:. Carcinoma ductale invasivum - NHG2 (3 + 2 + 1 / 6 mitoses/10 HPF - visual area 0.55 mm) Foci of carcinoma ductaie in situ Dcis detected within the tumour (cribrate and solid type with high nuclear atypia with comedo necrosis, 5% of the tumour). Mamilla sine laesionibus. Glandular tissue showing lesions of the type mastopathia fibrosa. AXILLARY LYMPH NODES  Metastases carcinomatosae in lymphonodis (No ix/xv). Infiltratio capsulae lymphonodis et telae perinodalis. Histopathological diagnosis: Carcinoma ductale invasivum et ductale in situ mammae sinistrae. Invasive ductal and in situ ductal carclrioma of the feft breast Metastases carcinomatosae in lymphonodis axillae (No Ix/xv). Cancer metastases of the axillary lymph nodes (No Ix/xv). (NHG2, pTIc, pN2a). UUID:53ED4388-8CD2-4925-81A9-9C4792C83566 TCGA-D8-A1Y0-01A-PR Redacted Hef1
+
+--- Page 2 ---
+page 2 / 2 Compliance validated by: Examination performed on: Results of immunohistochemical examination: Estrogen receptors found in over 75% of neoplastic cell nuclei. Progesterone receptors found in over 75% of neoplastic cell nuclei. HER2 protein stained with HercepTestTM by DAKO.  Negative reaction in invasive cancerous cells ( Score = 1+ ) CONTACT YOUR DOCTOR WITH THIS REPORT!

output/text/00157a93-7d77-41d8-ac9c-6317c9ae38fe.txt

@@ -0,0 +1,3 @@
+
+--- Page 1 ---
+Jcs-0 - 3 Curcinonn mf1tnaHnz ductul,nsos 850t/3 Sih: BUsotj LbQ C50.5 1/21n h Pish Sit: Brst, Nos c5o.9 CqcF Diagnosis: Right-sided breast excision material with a poorly differentiated inyasive ductal breast. carcinoma measuring about 4.3 cm with invasion of the lymph vessels and a minimum margin. of 3 mm at 6 o'clock and 10 mm at 12 o'clock and 1.5 cm or more at 3 and 9 o'clock. No intraductal tumor component. Tumor classification: M-8500/3, G 3, pT 2, pN 3a (14/28), pMx, stage III c. R 0. 40FA-823A-E608ABFEF591 Redacted

output/text/001fee13-0e0d-464d-8b18-5641d51c86db.txt

@@ -0,0 +1,6 @@
+
+--- Page 1 ---
+SPECIMENS: A. RIGHT COLON DIAGNOSIS: A. RIGHT COLON, RIGHT HEMICOLECTOMY: - EXOPHYTIC CIRCUMFERENTIAL ULCERATED INVASIVE MODERATE TO POORLY DIFEERENTIATED ADENOCARCINOMA OF CECUM. PROXIMAL ASCENDING COLON WITH EXTENSION TO ILEOCECAL VALVE, WITH FULL MUSCLE WALL THICKNESS INVASION, EXTENSION TO SUB- SEROSAL FAT., METASTASIS TO SIX OF THIRTY-SIX (6/36) PERICOLIC LYMPH NODES (WITH PERINODAL FAT EXTENSION). - SIZE OF TUMOR- 8 X 4 X1 CM. - TUBULOVILLOUS ADENOMA (1.2 X 1.1 CM). - VERMIFORM APPENDIX - NEGATIVE FOR TUMOR - PROXIMAL, DISTAL AND RADIAL MARGINS OF RESECTION - NEGATIVEE FOR TUMOR. COLORECTAL CANCER TEMPLATE Specimen Type: Right hemicolectomy Tumor Site: Cecum,proximal ascending coln. Tumor Configuration: Exophytic (polypoid), Infiltrative, Ulcerating Tumor Size: 8.0 x 4.0 x 1.0 cm Histologic Type: Adenocarcinoma Histologic Grade: G3 Extent of Invasion:  Subserosa Margins:  Margins uninvolved by invasive carcinoma  Venous/Lymphatic Invasion: Present Perineural Invasion: Present Additional Pathologic Findings: Adenoma Extent of Resection: R0 Positive (6/36) Lymph Nodes:  Implants: Absent EGFR Expression: Pending Pathologic Stage: pT3 N2 MX ADDENDUM: Additional report: Results of immunostain: EGFR ( section with tumor,#A5) - negative immunoreactivity. SPECIMEN(S): A. RIGHT COLON GROSS DESCRIPTION: A. RIGHT COLON TERMINAL ILEUM: Received fresh labeled with the patient's name, unit number and "right colon terminal ileum' is a 28.5x8.5x4 cm. right hemicolectomy specimen. The ileum is 8 cm. long and 7 cm. in circumference, the colon is 20.5 cm. Iong, 8.5 cm. in circumference and the attached appendix is 5.8 cm. long and 0.9 cm. in diameter. The serosal surface of the specimen is tan, smooth and multiple firm lymph nodes are palpated throughout the adherent pericolonic fat at the cecum. The specimen when opened shows a circumferential exophytic centrally ulcerated tumor with raised indurated peripheral borders occupying proximal ascending colon,cecum, and extending to involved the iliocecal valve,measuring 8x4x1.0 cm.
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+Tumor 14.5 cm from distal,and 5.5cm from proximal margin.Cut sections show tan white granular surface.and tumor seen infiltrating muscle wall and grossly appears to extend to subjacent subserosal fat. The rest of colonic mucosa shows a flattened appearance .with a small polyp along hepatic flexure measuring 1.2x1.1 cm. Dissection of the adherent pericolonic fat shows multiple lymph nodes,the Iargest measuring 2x1.1x0.9 cm. Appendix is grossly free of tumor. Multiple sections submitted as follows in 30 cassettes labeled A1-A17.  Block summary: A1: margin A2: apex A3,A4,A5,A6: tumor and tandom section from ileum to colon A7,A8: tumor A9-A11: tumor deep section A12: polyp A13: three lymph nodes ileum. A14: three lymph nodes ileum A15 lymph nodes cecum colon A16: lymph nodes cecum colon A17: two lymph nodes distal colon A19-21: lymph nodes distal colon A26-30: sections of tumor, A29 and A30 are random sections

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+UUID:654A67F7-8755-4BF6-9674-69ADA7C976DA TCGA-TM-A84H-01A-PR Redacted Repor Final Updatec Page 2 DOCTOR DOC. ADDRESS COLL. DATE DATE RECEIVED WARD CONSULTANT ISTOPATHOLOGY REPORT COPY TO: SUPPLEMENTARY AND FINAL REPORT SPECIMEN: A. Right frontal tumour. B. Right frontal tumour. C Tumour. Further tissue sections of the glioma have been. examined, additional immunohistochemical studies performed, and Fish results finalized. Examination: of the additional sections of the glioma, which is now been examined in its entirety, reveals similar microscopic appearances to those initially report.  Variable cytoarchitectural patterns are evident, ranging from sparsely cellular microcystic, through to microscopic nodular areas where the neoplastic cells aggregate closely, and have a variably pleomorphic and hyperchromatic nuclei, minimal cytoplasm, and demonstrates some nuclear angulation and irregularity. No areas of vascular endothelial proliferation or palisading necrosis have been identified. Maximal mitotie counts within the hypercellular areas, seven mitotic figures per 10 high power fields (field area 0.196 mm squaredl. The proliferation index, as judged by immunohistochemical staining for the proliferation marker Mrs I is variable.  Low-grade and sometimes microcystic areas typically have low MIs 1 indices, with relatively raxe nuclear labelling, but the small hypercellular foci demonstrate elevated labelling. Immunohistochemical staining for p53 protein demonstrates no convincing nuclear positivity.  Synaptophysin staining is evident in many of the neoplastic cells, particularly in hypercellular foci, and takes the form of granular cytoplasmic 0 positivity, sometimes with perinuclear dot like exenteration. There is no convincing positivity for NeuN, which highlights scattered mononuclear neuronal cells, which do not demonstrate abnormal clustering or cytologic features such as binucleation. Neurofilament highlights this non-neoplastic population, together with an entrapped network of processes of background neuropii. Representative formalin fixed paraffin embedded tissue sections were submitted 9382/3 for FIsh (fluorescence in situ. hybridization] studies to assess lp, 19q and The results of the studies (which have been reported separately) demonstrated no loss of Ip and no loss of 19q, and Ecrr amplification was not detected. C71.0 In summary, considering these results and additional findings, this diffuse glioma is perhaps best regarded as a diffuse wHo Grade IIl mixed oligo- astrocytoma, conctusion: Right frontal tumor. wHo Grade IIl mixed oligo-astrocytoma, lacking ip and 19q deletions, and demonstrating no evidence Egrr amplification. Comment: Grading of oligoastrocytomas is a problematic area in surgical neuropathology. There is no specific grading scheme for oligoastrocytoma in the most recent wHo Classification of Tumors of the CNs. In grading oligoastrocytoma, many authorities now adopt the same grading scheme as used for oligodendroglioma. . The minimum criteria for a diagnosis of who Grade III anaplastic glioma in this setting are not well defined. Many authorities regard mitotic activity [greater than 5 mitotic figures per 10 high power fields] as a
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+valuable parameter of anaplasia in the absence of endothelial proliferation, palisading necrosis, or frankly anaplastic cytology and hypercellularity. In this case, overt features of anaplasia are not evident, but the maximal mitotic count exceeds 5 mitotic figures per 10 high power fields, and in hypercellular foci the MIs 1 determined proliferation index is relatively high. As such, the findings are int amount to a wHo grade III oligoastrocytoma. PATHOLOrr em. DATED: ELECTRONICALLY VALIDATED: END OF REPORT FOR Page 2 DOCTOR Doc. ADDRESS COLL. DATE DATE RECEIVED CONSULTANT HISTOPATHOLOGY REPORI COPY TO: SPECIMEN: A. Right frontal tumour. B. Right frontal tumour. C. Tumour. CLINICAL: Low grade frontal glioma.. MACROSCOPIC: A.  One piece of grey-white tissue approximately 6 x 6mm. A second smaller piece 2 x 2mm. Larger piece submitted for frozen sections and imprint cytology. A INTRA-OPERATIVE ASSESSMENT - FROZEN SECTION / IMPRINT CYTOLOGY: Glial neoplasm, grade 2-3.. Result phoned to B.  Multiple irregular fragments of tan coloured tissue with areas of haemorrhage and myxoid change. Specimen is sectioned and reveals a white and grey matter differentiation.  Several pieces of brain tissue. The largest measures 5Omm x 30mn x 30mm. Tissue is serially sectioned and reveals a creamy cut surface with areas showing myxoid change and haemorrhage. Centrally, the specimen is very friable and the tissue has a soft consistency.. MICROSCOPIC: A. C.  The specimens have been thoroughly sampled and show extensive malignancy.  In some areas it shows an oedematous appearance with a "fried egg' pattern and there is infiltration into grey matter with peri-neuronal satellitosis. The cells have round to oval slightly irregular nuclei with granular chromatin and inconspicuous nucleoli. Mini-gemistocytes are also seen. The background appears fibrillary. Elsewhere the tumour is more cellular and arranged either in sheets or in alternating hyper and hypocellular areas. The cells have larger, more pleomorphic nuclei, coarsely granular chromatin and inconspicuous nucleoli. 'Mini-gemistocytes are still present.. The background appears myxoid and there is microcystic change containing mucoid material. Scattered mitotic figures are noted.. There is no endothelial proliferation or necrosis identified. CONCLUSION:
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+A. - C. Right frontal tumour: Glial series tumour with oligodendroglial features. The cellularity, atypia and mitotic activity are consistent with an anaplastic oligodendroglioma (who grade IIl), cytogenetic. studies are proceding to confirm this and a supplementary report will be issued. REGISTRAR: PATHOLOGIST: DATED: as ELECTRONICALLY VALIDATED: END OF REPORT FOR

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+Diagnosis: Resected ileocolic material displaying in the colon ascendens, located 2 cm distal to the ileocecal valve, an adenocarcinoma of colorectal type measuring a maximum of 4 cm in diameter, ulcerated, moderately differentiated and with infiltration of the perifocal adipose tissue. Tumor-free lymph nodes in this region. Tumor-free small and large intestine resection margins. Tumor-free mesenteric resection margin. Tumor-free appendix. Tumor-. free omental adipose tissue. Tumor stage therefore pT3, pN0 (0/39) pMX; G2, L0, V0, local R0

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+IGDo 3 UUID:5A59F9F1-9F37-468D-B120-B12C92E2C474 TCGA-VR-AA4D-01A-PR Redacted Site: Espnagus, olstal thud C15.5 Q0s3|5/14 Collect date: (MM/DD/YYYY) PATHOLOGY REPORT: PRIMARY SITE: Esophagus (Distal) 1-"Product of esophagogastrectomy"':. Moderately differentiated adenocarcinoma with papillary areas infiltrative up to submucosa. Presence of lymphatic invasion. Perineural infiltration not detected.. Infiltrative growth pattern. Absence of necrosis. Discrete peritumoral inflammatory infiltrate. Surgical margins free of neoplastic compromise. 2-"Lymphadenectomy according to standardization"': Metastatic adenocarcinoma in 6 of 25 identified lymph nodes (6/25), with no capsular compromise, distributed as follows:. 1/2 right cardiac; 2/7 left cardiac, 0/13 lesser curvature; 3/3 left gastric artery; 0/0 celiac trunk; 0/0 inferior para-esophageal. 3- "Greater omentum": Free of neoplastic compromise. 4-"Esophageal margin": Free of neoplastic compromise. 194

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+UUID:9A8F7726-D97C-44DE-B72F-6BF0FC2078F8 TCGA-LL-A73Y-01A-PR Redacted RUN DATE: PAGE 1 RUN TIME: RUN USER: r PATIENT: ACCT #: LOC: AGE/SX :  ROOM: REG DR: DOB: BED: STATUS : SPEC #: RECD: STATUS: COLL: TIME IN FORMALIN: "hrs. COLD ISCHEMA TIME: mins. CLINICAL INFORMATION: Pre-Op Diagnosis: Remarks: Specimen(s): A. Right sentinel node B. Right breast for tissue banking Ecd-6.3 scnima, d yiltetis ductNDS U 8s$oL3 ICROSCPIC IIAGNOSIS S.iti  Buast4oS CsP9 A. ONE LYMPH NODE, RIGHT SENTINEL NODE. LYMPHADENECTOMY: IMMUNOCHEMICAL STAINS B. RIGHT BREAST. TOTAL MASTECTOMY: INFILTRATING DUCTAL CARCINOMA MODIFIED NOTTINGHAM HISTOLOGIC GRADE 3 OF 3: NUCLEAR SCORE 3 OF 3. TUBULAR FORMATION SCORE 3 OF 3. MITOTIC SCORE 2 OF 3 (5 MITOTIC FIGURES PER SQUARE MILLIMETER) NO DUCTAL CARCINOMA IN SITU IDENTIFIED INVASIVE TUMOR MEASURES 17 MM SURGICAL MARGINS FREE OF TUMOR WITH NEAREST MARGIN 7 MM FROM TUMOR. THE DEEP MARGIN SEE COMMENT FOR SYNOPTIC REPORT COMMENT(S) SURGICAL PATHOLOGY CANCER CASE SUMMARY - APPROVED BY COLLEGE OF AMERICAN PATHOLOGISTS PROCEDURE : Total mastectomy LYMPH NODE SAMPLING: Sentinel lymph node(s) SPECIMEN LATERALITY: Right TUMOR SIZE: Greatest dimension of largest focus of invasion:. 17 mm HISTOLOGIC GRADE (NOTTINGHAM HISTOLOGIC SCORE) : Glandular/tubular differentiation: score 3. Nuclear pleomorphism: score 3 Mitotic rate: score 2 Overall grade: grade 3 TUMOR FOCALITY: Single focus of invasive carcinoma. DUCTAL CARCINOMA IN SITU: No DcIs is present ** CONTINUED ON NEXT PAGE **
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+RUN DATE: PAGE 2 RUN TIME: RUN USER: SPEC #: PATIENT : (Continued) COmmenT(S) (Continued) MARGINS : Invasive carcinoma: Margins uninvolved by invasive carcinoma Distance from closest margin: 7 mm, deep LYMPH NODES: Number of sentinel lymph nodes examined: Number of lymph nodes with macrometastases: 0 Number of lymph nodes with micrometastases: PATHOLOGIC STAGING: Primary tumor: pT1c Regional lymph nodes: pN0 (i-) Distant metastases: Not applicable ANCILLARY STUDIES: Estrogen receptor: Results: negative (<1% of tumor cells with nuclear positivity) Progesterone receptor: Results: negative (<1% of tumor cells with nuclear positivity) HER-3: Immunoperoxidase studies: Results: negative (score 0) GROSS DESCRIPTION: The specimen is received in two parts. Both parts are received labeled with the patient's name. A. Received in formalin. labeled with the patient's name and "right sentinel node" is a 3.5. x 2.5 x 2.0 cm portion of yellow. lobulated adipose. The adipose is trimmed to have a. flattened. 2.6 x 2.0 x 0.6 cm nodular. fatty lymph node. The node is sectioned perpendicular to the long axis to be entirely submitted per sentinel lymph node protocol cassettes Al-A3. B. Received fresh for tissue banking. labeled with the patient's name and "right breast" is a 962 gram. 23.0 x 20.0 x 4.5 cm fibrofatty breast consistent with simple mastectomy specimen. There is a suture designating the region of the axilla and an overlying 12.5 x 4.5 cm black-brown skin ellipse. The skin ellipse has a central. 5.0 x 4.5 cm areola which extends to the skin margins and a central 1.3 cm erect nipple. The deep margin is predominantly smooth and intact with a focal. minor. inferior medial area of disruption. The deep margin will be inked blue and the breast is serially sectioned to have a diffusely fatty parenchyma. The upper inner quadrant has a 1.7 x 1.0 x 0.8 cm tumor mass. The mass. is 2.5 cm from the superior peripheral margin. The . is 17 cm from the inferior peripheral margin. is approximately 4 cm from the medial peripheral margin and at least 16.5 cm from ths lateral peripheral margin. The tumor comes to within 0.7 cm of the deep margin. The remainder of the breast has glistening, yellow adipose with diffuse. delicate and focal scant dense-white fibrous tissue. There is a central area of possible fibrocystic change. The white fibrous tissue makes up between 15 and 20% of the parenchyma and is more pronounced towards the medial aspect of the breast. No additional indurated lesions or tumor-like masses are identified. Representative sections are sampled as labeled: B1 perpendicular section of nipple B2 section of tumor adjacent to tumor collected for tissue banking ** CONTINUED ON NEXT PAGE ** lw g/3 3
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+RUN DATE: PAGE 3 RUN TIME: RUN USER: (Continued) SPEC #: GROSS DESCRIPTION: (Continued) B3-B5 sections of tumor to deep margin B6 representative sections of upper outer quadrant. B7 representative sections of lower outer quadrant. B8 representative sections of upper inner quadrant (quadrant near tumor) B9 representative sections of lower inner quadrant sampled. INTRAOPERATIVE CONSULTATION: IMMEDIATE GROSS EVALUATION RIGHT BREAST: INVASIVE CARCINOMA. PROCESSED FOR TUMOR BANKING SURGICAL MARGINS FREE OF TUMOR PHOTO DOCUMENTATION Image Image Signed (signature on file) ** END OF REPORT **

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+page 1 / 1 Department of Cancer Pathology. Examination: Histopathological examination Internal invoice No. Cost of diagnostic procedure Examination No.: Patient: XXX PESEL: XXX Age: Gender: Material: 1. Multiple organ resection - sigmoid colon Unit in charge:  Physician in charge: Material collected on: Material received on Expected time of examination: Clinical diagnosis: Sigmoid colon with tumour Examination performed on: Macroscopic description: A 18.3 cm length of the large intestine with a piece of mesentery sized 19 x 9 x 4 cm. Tumour sized 5.6 x 6.3 x 1.7 found in the mucosa. The lesion surrounds 1o0% of the intestine circumference, is removed by 9.8 cm from the proximal incision line, and 7.2 cm from the distal incision line. Microscopic description: Adenocarcinoma tubulopapillare (GI).. Infiltratio carcinomatosa telae adiposae pericolicae.  Incision lines free of neoplastic lesions. Lymphonodulitis reactiva (NO viII).. Histopathological diagnosis: Adenocarcinoma tubulopapillare coli. Tubulopapillar adenocarcinoma of the colon. (GI, Dukes B, Astler - Coller B2, pT3, pNO). Compliance validated by: CONTACT YOUR DOCTOR WITH THIS REPORT!

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+UUID:019F3900-7479-4CDC-8C82-45A27910E782 1cs-0-3 TCGA-A7-A0C-01A-PR Redacted Carcioma mfiltrstig oluct; Nos 850of3 SPECIMEN A. Left axillary sentinel lymph node B. Left breast biopsy. CLINICAL NOTES CLINICAL HISTORY: A -year-old white female with left breast cancer. FROZEN SECTION DIAGNOSIS AFs: Left axillary sentinel node, excision - One lymph node with no metastasis identified.. GrOss DEscRIpTIon A. Container A is labeled with the patient's name, medical record number and "left axillary sentinel node". The specimen consists of a single partially fatty replaced lymph node measuring 1.3 x 1 x 0.6 cm. AFs,bisected. B. Container B is labeled with the patient's name, medical record number and "left breast biopsy, long anterior, short superior." The specimen consists of a single piece of fibrous adipose tissue oriented by two sutures and measuring 6.5 cm in medial to lateral, 3.5 cm from superior to inferior and 3 cm from anterior to posterior. The specimen margins are inked as follows: Blue -- anterior; black -- posterior; yellow -- lateral; orange medial; red -- superior; green -- inferior. The specimen is serially sectioned. On cut section, there is a firm tan fibrotic-appearing tumor mass measuring 2.2 x 1.5 x 1.8 cm. The mass appears to extend to the posterior margin of resection. A portion is submitted for tissue procurement. The remainder of the tissue is submitted in blocks 1-15. MICROSCOPIC DESCRIPTION A. Sections of the left axillary sentinel lymph node demonstrate i lymph node with no evidence of metastasis. The lymph node was examined and multilevel sectioning with H&E stain as well as immunohistochemistry for pankeratin. B. The following template applies to the left breast biopsy: Invasive Carcinoma: Present. Histologic type: Infiltrating ductal carcinoma Histologic grade: Overall grade: 3 Architectural score: 3 Nuclear score: 3 Mitotic score: 2
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+Greatest dimension (pT): 2.2 cm. (pT2) Specimen margins: Positive. Invasive carcinoma extended to the green ink involving the. inferior margin. Vessel invasion: Not identified.. Calcification: Present Ductal carcinoma in situ: Present. Histologic pattern: Solid and cribriform. Nuclear grade: 2-3 Central necrosis: Focally present. *Dcis of total tumor: 25% Extensive intraductal component (present/absent): Present Specimen margins: Close. In situ carcinoma is less than 1 mm from the anterior, posterior, medial and inferior margins. Calcification: Present Description of non-tumorous breast: Proliferative changes.. Comments: None. MICROSCOPIC DESCRIPTION Prognostic markers:  Previously performed. 4x2, 20 DIAGNOSIS A. Left axillary sentinel lymph node, resection:. No evidence of metastasis in one lymph node (0/1).. B. Left breast, excisional biopsy:. Infiltrating ductal carcinoma, grade 3, 2.2 cm. extending to the inferior margin. Extensive ductal carcinoma in situ, solid and cribriforming. subtypes, nuclear grade 2-3, less than 1 mm from multiple margins. M.D, (Electronic Signature). - End Of Report

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+with right colon mass and Specimens Submitted: I: Sp: Colon, right; hemicolectomy. DIAGNOSIS: 1. Sp: Colon, xight; hemicolectomy: Tumor Type: Adenocarcinoma Histologic Grade: Moderately differentiated Tumox Location: Ascending colon Tumor Size: Length is 5.5 cm width is 6.5 cm Tumor Budding: Absent Increased Tumor Infiltrating Lymphocytes: Absent Precursor Leslone: Not identified Deepest Tumor Invasion: Subserosal adipose tissue and/or mesentexic fat Gross Tumor Perforation: Not identified Lymphovascular Invasion: Identified Large Venous Invaslon: Not Identified Perineuxal Invasion: Not identified Surgical Margins: Free of tumor Polyps/Mucosa Dysplasia (away from the carcinoma): Tubular adenoma; number: 2 Hyperplastic polyp; number: 1 Non-Neoplastic Bowel: Unremarkable t* Continued on next page ** $
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+2 of 3 Appendix Fibrous obliteration of the lumen Lymph Nodes: Number with metastasis: 1 Total number examined: 24. Tumor deposits in pericolorectal soft tissue: Identieied Tumor Staging (Acc 7th Edition): pT3 (Tumor invades through the muscularis propria into pexicolorectal tissues) Lymph Node Stage (Awcc 7th Edition): N1 (Metastasig in 1-3 regional lymph nodes) PENDING K-RAS. I ATTEST THAT THE ABOVE DIAGNOSIS IS BASED UPON MY PERSONAL EXAMINATION OF THE SLIDES (AND/OR OTHER MATERIAL), AND THAT I HAVE REVIEWED AND APPROVED THIS REPORT. Result Special Stain Comment KRAS Gross Description: 1).The specimen is received freah, labeled "Right hemicolectomy colon' and consists of a segment of terminal ileun, cecum with attached appendix and. ascending colon. The terminal ileum measuxes 7.5 cm in length and 3.5 cm in circumference at the proximal resected margin.  The remaining colon measures. 19 in length with a circumference of 8 cm at the distal resected margin. The attached appendix measures 6.5 cm in length and averages 0.7 cm in. diameter. The appendiceal and intestinal serosa is pink tan and smooth.. Focally hemorrhagic lobulated yellow tan adipose tissue spans the length ot the specimen measuring up to 5' cm in thickness. The gpecimen is opened to. reveal a circumferential, centrally ulcerative, fungating, brown tan tumor measuring 5.5 cm in length, 6.5 cm in width, and 2.0 cm in height. On cut section of the tunox, it measures 2.5 cm in maximun depth and abuts the. black inked radial margin..  The tumor is located 6.3 cm from the ileocecal valve and 6 cm from the distal resected margin. Alao identified, 4.0 cm from. the ileocecal valve and 4.2 cm from the main tumor mass, there is a brown-tan polypoid structure measuring 1.8 x 0.8 x 0.7 cm.  The remaining mucosa shows brown-tan folded appearance and several polypoid areas measuring up to 0.4 x 0.3 cm in greatest dimensions, which are entirely Submitted. The apecimen is submitted fox lymph node dissection. The attached adipose tissue is thoroughly examined and all identified lymph nodes are aubmitted. Representative sections of the specimen are submitted. Continued on next page.
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+Pag Summary of sections: PM - proximal margin shave DM - distal margin shave T - tumor (box 11 and 12, 13 and 14 are full-thickness section of tumor with underlying cause of lymph node, bisected) APP - appendix representative sections RS -representative sectione LN - lymph nodes LPOL-largest polypoid area POL-polypoid areas Summary of Sections: Part 1: SP: Colon, right; hemic ectomy Block Sect. Site PCs app 2 m r dm LN 18 N m4 md mj 1po1 pm po1 1 rg 6 r ** End of Report ** $
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+Specimeng Submitted: 1: DM SUBMITTED 1O UNSTAINED SLIDES AND 1 H&E, RIGHT COLON Test Performed:. KRAs Gene Exon 2 mutation analyais (codons 12 and 13) DNA quality: good. Methodology: PCR was performed to amplify exon 2 of the KRAs gene from genomic DNA prepared from the submitted tigaue. The pcr product was analyzed on an ABI DIAGNOSTIC INTERPRETATION: Negative for KRAs exon 2 mutation.. Technical sensitivity: This asaay'cannot detect a xRAs exon 2 mutation if the proportion of tumor cells in the sample studied is less than 25%. 1. This result cannot be used as sole evidence for or against cancer and has to be interpreted in the context of all available clinical and pathological information. 2. This test was developed and its performance characteristics determined by the Laboratory of Diagnostic Molecular Pathology. It has not been cleared or approved by the. U.S. Food and Drug. Administration (Fba). The FDa has determined that such clearance is not necessary. This test is used for clinical purposes.. Pursuant to the requirements of CLia : 88,. oux laboratory has established the accuracy and precision of this test. This test has been approved by as a laboratory specific assay.. I ATTEST THAT THE ABOVE DIAGNOSTS IS BASED UPON MY PERSONAL EXAMINATION OF ** Continued on next page **.
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+Page 2 of 3 THE SLIDES (AND/OR OTHER MATERIAL), AND THAT I HAVE REVIEWED AND APPROVED THIS REPORT. Procedures/Addenda Addendum Date Ordered:. Date Complete: Date Reported Addendum Diagnosis NONE OF THESE MOTATIONS WERE DETECTED IN THE TUMOR. CLINICAL PANEL Gene Codon BRAF V600 EGFR L858 INVESTIGATIONAL PANEL Gene Codon Gene Codon Gene Codon AKT1 E17 EGFR L861 NRAS G12 BRAF G469 ERBB2 L755 NRAS G13 BRAF D594 ERBB2 D769 NRAS Q61 EGFR E709 ERBB2 V777 PIK3CA R88 EGFR G719 KRAS Q61 PIK3CA N345 EGFR D761 KRAS K117 PIK3CA C420 EGFR S768 KRAS A146 PIK3CA E542 EGFR R776 MEKL Q56 PIK3CA E545 EGFR T790 MEK1 K57 PIK3CA M1043 EGFR T854 MEKL D67 PIK3CA H1047 Diagnoatic sensitivity: This finding does not exclude the poasibility of other mutations. Technical sensitivity: This test may not detect certain mutations if the proportion of tunor cells in the sample studied is less than 10%.. Test Performed:d Sequenom masa-spectrometry genotyping for specific mutations in 8 genes:. AKT1, BRAF, EGFR, ERBB2, KRAS, MEK1 (MAP2KI), NRAS, and PIK3CA Methodology: The specific mutations are detected by amplification of the corresponding. exons by polymerase chain reaction (pcr), followed by a single base. extension at the site of the point mutation. The single base extension product is detected by tandem mass-spectrometry on a Sequenom MassArray Spectrometer. Addendum Comment PLATE# P10-42 ** Continued on next page **
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+Page 3 of 3 This result cannot be used as sole evidence for or against cancer and has to be interpreted in the context of all available clinical and pathological. information. This test was developed, and ita performance characteristics detexmined, by. the It has not been cleared or approved by the U.S. Food and Drug Administration (FDA). The FDA has determined that such clearance is not necessary. This test is used for clinical purposes our laboratory has established the accuracy and precision of this test. The results of the inveetigational panel are for investigational use only.. ** End of Report **

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+UUID:53881871-C36B-4622-BFC6-4DA363507B263 TCGA-AC-A7VB-01A-PR Redacted Referrinn Physician:. DOB: Age: Gender:F Ref#: Hoso#: Provider Group : Date of Service: Date Received: ase Date Reported: FINAL SURGICAL PATHOLOGy REPORT Diagnosis: A. - f. rIght breast And AxIlLary Lymph noDes, mastectomy, Sentinel LYMPH NODE BIOPSIES, AND AXILLARY LYMPH NODE DISSECTION: - Multifocal invasive ductal carcinoma, Nottingham grades 2-3. See comment. - Largest tumor nodule: 1.5 cm in diameter (6 o'clock aspect). - Two smaller nodules: 0.6 and 0.8 cm (7-8 o'clock aspect). - Ductal carcinoma in situ (DciS), high nuclear grade, solid type. - DCIS comprises less than 10% of biopsy tissue volume, and is associated with all three invasive tumor nodules. - Mastectomy margins are free of tumor.. - Carcinoma is 3 cm from the inferior margin and is at least 6 cm from all other margins.. - Metastatic carcinoma in three of fifteen lymph nodes (3/15). - Largest metastatic focus: 0.9 cm in diameter. - Extranodal extension present.. - Positive lymph nodes are sentinel lymph nodes #2, #3, and #4 PATHOLOGIC TUMOR STAGING SYNOPSIS: Type and grade (invasive): Invasive ductal carcinoma, Nottingham grade 2-3. Type and grade (in situ): Dcis, high-nuclear grade.. LQD o 3 Primary tumor: pT1c(m). Regional Iymph nodes: pN1c. 'arersmo,iryiltatiy oluct NoS Distant metastasis: Not applicable.. 8s00/3 Stage: IIA. Lymphovascular invasion: Indeterminate.. c 50.9 Margin status: Negative.. Q4I id/4ll3 COMMENT: The three foci of invasive carcinoma have similar histologic features, although the tumor grade is somewhat variable in the largest tumor nodule, where there is a variable rate of mitosis, and nuclear pleomorphism ranging from intermediate to high-grade. The smaller tumor nodules contain high-grade malignant Case #: Page 1 Printed: This report continues... (FiNAL) MR No. Acct No. - Patient Name  Pathology - Page 1/6. Page 1 Doc#1
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+Patient: Case #: FINAL SURGICAL PATHOLOGY REPORT epithelial cells arranged in solid sheets with frequent mitoses, compatible with Nottingham grade 3. There is enough morphologic similarity between three nodules to suggest that they have a common origin. Intradepartmental consultation: concurs with this impression. Invasive Breast Cancer Tumor Staging Information AJCC Cancer Staging Handbook, 7th Ed.. and CAP Protocol (revised June 2012). Previous pathology specimens: Page 2 Case #: 'his report continues... (FINAL) Printed: Patient Name - MR No. - 'age 2 Doc# 1 Pathology - Page 2/6
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+Patient: Case #: SPECIMEN IDENTIFICATION Procedure/specimen type: Modified radical mastectomy. Laterality: Right. Lymph node sampling: Sentinel lymph node biopsies followed by lymph node dissection. INVASIVE CARCINOMA TUMOR CHARACTERISTICS Histologic type: Invasive ductal carcinoma (multifocal). Tumor sites: 6:00-8:00. Tumor size: Largest tumor nodule 1.5 cm.. Tumor focality: Multifocal. Histologic grade (Nottingham Score): 2-3 of 3. Tubule formation: 3 of 3. Nuclear pleomorphism: 2-3 of 3. Mitotic rate: 2-3 of 3 (variable mitotic rate). Lymphovascular invasion: Indeterminate. Macroscopic and microscopic extent of tumor: No skin or chest wall invasion identified. DUCTAL CARCINOMA INSITU (DCIS): Present in association with three invasive tumor  nodules. MARGINS Invasive carcinoma: Negative. Ductal carcinoma in situ: Negative. LYMPH NODES Total lymph nodes examined 15. Number of lymph nodes involved 3. Size of largest metastatic deposit: 0.9 cm. Extranodal extension: Present. PATHOLOGIC STAGING: Primary Tumor (pT): pT1c(m). Regional lymph nodes (pN): pN1a. Distant metastasis (pM): Not applicable. AJCC Stage: IIA. ANCILLARY STUDIES: Performed by jn 2 previous biopsies (additional HER2 studies pending, to be reported in an addendum). Estrogen receptor: 85-96% positive cells, strong intensity. Progesterone receptor: 0% positive cells. HER2: Additional studies pending, to be reported in an addendum. Case # Page 3 Printed: This report continues... (FINAL) MR No. Acct No. . Patient Name - Pathology - Page 3/6 Page 3 Doc# 1
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+Patient: Case #: FINAL SURGICAL PATHOLOGY REPORT Variable, previously reported 7-69%. Ki-67: Source of Specimen: A. Sentinel lymph node;#1-- right axillary B. Sentinel lymph node;#2-- right axillary right axillary C. Sentinel lymph node;#3-- D. Sentinel lymph node;#4-- right axillary E. Breast surgical;right F. Axillary nodes right Clinical History/Operative Dx:. Right breast cancer. Intraoperative Diagnosis:. A. Sentinel node #1 - diagnosis: Negative for carcinoma. B. Sentinel node #2 - diagnosis: Rare atypical cells, suspicious for carcinoma. (Defer to. permanents). and  - diagnosis: Positive for carcinoma. D. Sentinel node #4 The intraoperative interpretation(s) was/were performed and rendered at. Gross Description:  right axilla, touch prep. Initially received in the fresh. A. Part A is designated as sentinel node #1 state four frozen section/touch prep evaluation is a 1.0 x 0.8 x 0.6 cm piece of red-tan soft tissue. Examination reveals a 0.7 x 0.6 x 0.5 cm lymph node. The cut surfaces are fatty and rubbery, pink and tan. Two touch imprint slides are prepared for microscopic evaluation. The lymph node is entirely. Page 4 Case #: This report continues... (FINAL) Printed: Acct No. : Patient Name - MR No. age 4 Doc# 1 Pathology - Page 4/6
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+Patient: Case #: FINAL SURGICAL PATHOLOGY REPORT submitted for routine histology in A1 with a sentinel node protocol performed. B. Part B is sentinel node #2 . Initially received in the fresh state for touch prep/frozen section evaluation is a 1.5 x 1.2 x 1. 0 cm yellow-tan portion of tissue. Examination reveals a 0.8 x 0.6 x 0.6 cm Iymph node. Sectioning demonstrates a rubbery, pink and tan cut surfaces. Two touch imprint slides are submitted for microscopic evaluation. The Iymph node is entirely submitted for routine histology in B1 with a sentinel node protocol performed. C. Part C designated as sentinel node #3. right axillary. Received in formalin is a 1.5 x 1.5 x 0.7 cm fragment of fat. Examination reveals two possible apparent lymph nodes, 0.8 x 0.6 x 0.4 cm each. The Iymph node is serially sectioned and entirely submitted for microscopic evaluation in C1 with a sentinel Iymph node protocol performed. D. Part D is designated as sentinel node #4 right axillary. Initially received in the fresh state for. frozen section/touch imprint evaluation is a 1.5 x 1.2 x 1.0 cm yellow-green portion of fatty soft tissue. representative section is submitted for frozen section evaluation. The residual frozen tissue is submitted in D1 for permanent sections and the touch imprint aspect of the lymph node is submitted in D2 for permanent sections with a sentinel lymph node protocol performed E. Received fresh labeled *right breast.* Sutures present for orientation purposes. A portion of tumor is submitted for Laterality: Right. Specimen: Mastectomy. Size of mastectomy: (M-L x S-I x A-P): 23.5 x 19 x 5 cm. Axillary tail: Not present. Skin: 24 x 18 cm, pigmented skin.Nipple/areola: Yes, center of skin. Specimen weight: 971 grams. Ink code: Blue -- superior-anterior, orange -- inferior-anterior, black - deep Slabs: Total # 11, M-1=1, L-S= 11. Nipple in slab #6. Time of resection: Time placed into formalin: Time out of formalin:. Lesion 1: Biopsy site present. Size: 1.5 x 1.4 x 0.8 cm, stellate, gray-white, firm mass. Location: 6:00. Involves slabs # 3-4. Distance to nearest margin(s): 3 cm from inferior margin, 6 cm from deep margin. Lesion #2: Biopsy site present. Size: 0.8 x 0.5 x 0.5 cm. Location: 7:00. Involves slabs #2-3. Distance to nearest margin(s): 6 cm from inferior. Case #: Page 5 Printed: This report continues... (FINAL) MR No. - Acct No. - Patient Name - Pathology - Page 5/6. - Page 5 Doc# 1
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+Patient: Case #: FINAL SURGICAL PATHOLOGY REPORT Lesion #3: No biopsy site present. Size: 0.6 x 0.6 x 0.5 cm. Location: 7:00. Involves slabs #4. Distance to nearest margin(s): 5 cm from inferior. Non-lesional breast: Fibrofatty breast tissue. Cassette summary:  E1) smallest 7:00 tumor, previously biopsied (portion of the small tumor submitted for E2-E4) largest 6:00 lesion, E5) central breast tissue, E6-E7) lateral breast tissue, E8) nipple/subareolar breast tissue, E9) representative breast tissue, E10-E11) fibrous tissue medial to largest tumor, E12) representative medial breast tissue, E13) mass #3, 7:00, E14-E15) central posterior breast tissue. F. Part F is which axillary nodes, right. Received in formalin is an 83 gram partially tattered portion of yellow-tan fatty soft tissue, 13.0 x 9.0 x 2.6 cm. Examination reveals eleven lymph nodes ranging from 0.2 cm to 1.9 x 1.4 x 1.2 cm in greatest dimension. The lymph nodes are entirely submitted for microscopic evaluation. Cassette summary: 4/28 F1) four lymph nodes,. F2) four lymph nodes,. F3) one lymph node, bisected, F4) one lymph node, bisected, F5-F6) largest lymph node, serially sectioned but Microscopic Description: A. - C. Immunohistochemical stain: CK OsCAR, showing focal metastatic carcinoma in specimens B and C. D. Immunohistochemical stain: CK OSCAR, highlighting metastatic carcinoma. HER2 - results pending, to be reported in an addendum. E. Immunohistochemical stain: HER2, to be reported in an addendum. F. Microscopic sections have been examined. The microscopic findings are retlected in the diagnosis rendered. Case #: Page 6 Printed: END OF REPORT (FINAL) MR No. - Acct No. 'atient Name - Pathology - Page 6/6 uge 6 Doc#1

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+Pathology Report. DIAGNOSIS (A) LEFT KIDNEY: CHROMOPHOBE RENAL CELL CARCINOMA, FUHRMAN'S NUCLEAR GRADE 3. (SEE COMMENT) TUMOR MEASURES 5.O CM IN MAXIMUM DIMENSION. FOCAL LYMPHATIC/VASCULAR INVASION IDENTIFIED.S Multilocular cyst. (4.0 cm) Margins of resection free of tumor.. COMMENT Immunoperoxidase studies demonstrate the tumor cells to be positive for CK7 and negative for CD10 and Vimentin, supporting the diagnosis of Chromophobe renal cell carcinoma. The tumor has a pushing border but does not invade the sinus adipose tissue or perinephric fat. The renal vein is free of tumor.. GROSS DESCRIPTION (A) LEFT KIDNEY - A nephrectomy specimen (15.0 x 10.0 x 8.0 cm) including the kidney (10.0 x 6.0 x 5.0 cm) and attached ureter (9.0 cm in length). Located in the mid-portion of the kidney there is a orange-brown homogeneous tumor measuring 5 x 4 x 4 cm. The tumor appears grossly to be confined to the kidney. No invasion of the renal vein is identified. Located in the inferior pole of the kidney (0.5 cm from the main mass) is a large multilocular cyst (4.0 x 3.0 x 3.0 cm) containing clear fluid. The cyst has a thin capsule and smooth lining.. SECTION CODE: A1, vascular and ureteric resection margin, en face;. A2-A7, tumor with adjacent kidney; A8, A9, tumor with adjacent renal sinus; A10-A14, renal cysts with adjacent renal parenchyma and small portion of tumor in cassette A10; A15, renal pelvis; A16, normal kidney.. SQ/msm CLINICAL HISTORY Left renal mass. SNOMED CODES

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+UUID: 5049C91E-F48B-4AA7-BE64-8371681893790 TCGA-OL-A5DA-01A-PR Reda Sample # LcD o-3 Carcinoma, Is bular inf, /traIn. FINAL PATHOLOGIC DIAGNOSIS 85q0/3 Sentinel node biopsy and partial mastectomy, S,te : Path-Brast UOQ A. Right axillary sentinel node: - Single lymph node, no tumor (0/1) C50.4 B. Right breast partial mastectomy: C$cF B Brash N6s - Invasive lobular carcinoma, SBR grade II, with focal necrosis. C 50.9 - Focal atypical ductal hyperplasia and atypical columnar cell change. - Uninvolved breast parenchyma with apocrine metaplasia. Breast Pathologic Parameters 1. Invasive carcinoma: A. Combined gross and microscopic measurement: 3.2cm B. Composite histologic (modified SBR) grade II - Architecture: 3 - Nuclear grade: 2 - Mitotic count: 1 C. Associated ductal carcinoma in situ (DCIS): Absent 2. Excisional biopsy margins: Free of tumor - Invasive carcinoma 1mm from superior (closest) margin (slide B14) - Additional margins greater than 2mm away 3. Blood vessel and lymphatic invasion: Absent 4. Axillary lymph nodes: Negative for tumor 5. Special studies (see - Expression of ER in 68% of invasive tumor nuclei - Expression of PR in 66% of invasive tumor nuclei - Her2/neu antigen (FISH): Non-amplified (ratio: 1) 6. pTNM: pT2, NO(sn), MX Clinical History: This patient is a.  -year-old female with a right breast mass. The patient self-palpated a breast mass in the right upper outer quadrant in  was sent for diagnostic mammography and ultrasound which revealed a worrisome mass approximately 2.5 cm in size. An ultrasound-guided core biopsy and clip placement was done. This was read as 3invasive mammary carcinoma with lobular features4 by The patient underwent a breast MRI on the which demonstrated an irregularly shaped, posteriorly positioned mass at 11 o'clock in the right breast measuring 4.5 x 2.5 cm. The
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+left breast and bilateral axillae were normal. The patient undergoes right sentinel lymph node biopsy and right breast partial mastectomy with needle localization. Comment The tumor cells are negative for E-cadherin consistent with a lobular phenotype. AE1/AE3 stain is negative on the sentinel node.. Specimens Received: A: Right axillary sentinel lymph node B: Right Breast Partial Mastectomy Gross Description: The specimen is received in two containers each labeled with the patient's name and medical record number. A. Part A is additionally designated 31 right axillary sentinel node #14. Received fresh for frozen diagnosis is a 0.9 x 0.7 x 0.6 cm lymph node which is bisected and entirely frozen and read as 3no evidence of metastatic tumor4 per The remnant of frozen tissue is entirely submitted in cassette A1FS. B. Part B is additionally designated 32. right breast partial mastectomy4. Received fresh on an AccuGrid with accompanying radiograph is a 185.5 gm partial mastectomy specimen. The specimen bears two needle localization wires and a double long stitch as well as double short stitch for orientation. The overall measurements are as follows: superior to inferior 9.8 cm, medial to lateral 9.5 cm, anterior to posterior 3.7 cm. The requisition designates the double long. stitch as lateral margin and short stitch as superior margin. The accompanying radiograph demonstrates an irregularly shaped stellate mass within the partial mastectomy specimen overlying quadrant C2, C3, D3 and D2. There is a needle localization wire which enters at A3 and terminates at E1. There is a second needle localization wire which enters A5 and terminates at E4. The mass is in between these two wires. Thereis a single clip in quadrant D2.. The specimen is inked as follows: anterior-black, posterior-red, lateral-violet. medial-yellow, superior-blue and inferior-green. The specimen is serially sectioned from lateral to medial into nine slices to demonstrate an irregularly shaped, firm, white-tan mass present in slices #4 through #8. Needle. localization wires terminate in slices #3 and #8. The clip is not identified
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+The dimensions of the mass are 2.8 x 2.4 x 1.5 cm. The mass is present 0.2 cm from the anterior margin, 2.7 cm from the inferior margin, 1.6 cm from the superior margin, and greater than 2 cm from both lateral and medial margins. The remainder of the specimen demonstrates grossly unremarkable breast parenchyma consisting of lobular, soft, yellow-tan tissue with intervening white fibrous septa. Representative sections are submitted as follows:. B1,B2: lateral margin, serially sectioned, entirely submitted B3,B4: medial margin, serially sectioned, entirely submitted. B5: closest approach of mass to anterior margin, slice #5 B6: closest approach to superior margin, slice #6. B7: closest approach of mass to inferior margin, slice #6 B8: mass, representative section slice #6. B9: additional representative section of mass, slice #7 B10: representative section of tissue at termination of localization wire, slice #3 B11,B12: tissue at needle localization wire termination, slice #8. B13,B14: representative sections of nodular tan-white breast parenchyma slice #9 B15,B16: representative sections of nodular tan-white breast parenchyma, slice #10 B17: representative section of unremarkable breast parenchyma, slice #8 B18: representative section of unremarkable breast parenchyma, slice #12 Intraoperative Consult Diagnosis: A1FS. Right axillary sentinel lymph node: No evidence of metastatic tumor.

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+/Cs 0-3 Sits: brust nos c50.9 8/74  Final Diagnosis Breast, right, excision: Infiltrating lobular carcinoma, Nottingham I (of III) forming a 1.6 x 1.5 x 1.3 cm mass (AJcc pTlc). The carcinoma shows ductular involvement. No angiolymphatic involvement is present. The surgical resection margins, including the separately submitted margins, are negative for tumor. Lymph nodes, right sentinel, excision: Negative for tumor. embedded sentinel lymph node tissue and confirms the H&E impression. The infiltrating breast carcinoma is positive for estrogen receptor and negative for progesterone receptor. UUID:95DC80AB-C070-4613-8C11-A124AEDF9754 TCGA-AR-A2LE-01A-PR Redacted

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+ FINAL DIAGNOSIS: TCGA-AZ-4682 Parts 1, 2 AND 3: SIGMOID COLON, COLECTOMY -- A.  INVASIVE MODERATELY DIFFERENTIATED ADENOCARCINOMA (3.0 CM) THROUGH MUSCULARIS Propria into.perirectal fat.  NO ANGIOLYMPHATICINVASION IDENTIFIED. C.  SURGICAL RESECTION MARGINS FREE OF TUMOR. D.  Three pericolonic Lymph nodes, free Of tumor (0/3). E. pATHOLOGIC STAGE pT3 N0 M1. HYPERPLASTIC.POLYPS. Part 4: Liver, biopsy -- MICROSCOPIC: SYNOPTIC DATA - PRIMARY COLON AND RECTAL TUMORS SPECImen TyPe: . Rectal/rectosigmoid colon (low anterior resection) SPECIMEN LENGTH: 32.0.cm : Rectosigmoid TuMOR SITE: TUMOR CONFIGURATION. Uicerating TUMOR SIZE: Greatest dimension: 3.0 cm INTACTNESS OF MESORECTUM:  Not applicable HISTOLOgIC TyPE: Adenocarcinoma HISTOLOGIC GRADE: .:. Low-grade (well to moderately differentiated) PATHOLOGIC STAGING (pTNM):. pT3 pN0 Number of nodes examined: 3 Number of nodes involved: 0 pM1 MARGINS: Proxima! margin uninvolved by invasive carcinoma Dista! margin uninvolved by invasive carcinoma Circumferential (radial) margin uninvolved by invasive carcinoma. Mesenteric margin cannot be assessed ANGIOLYMPHATIC INVASION: Absent PERINEURAL INVASION: Absent TUMORAL LYMPHOCYTIC RESPONSE: Mild to moderate Other polyps (type[s]):Hyperplastic polyps ADDITIONAL PATHOLOGIC FINDINGS:

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+/es.0-3 Caucinome.mfi1tnsHny dutl, Nos 8500f3 Sr+ : buast, Nos C 50.9 3 page 1 / 1 Department of Cancer Pathologye copy No. Date: Examination: Histopathological examination. Internal invoice No. Cost of diagnostic proceduree Examination No.: Patient: XXX PESEL: XXX Age: Gender: F Material: Multiple organ resection -- left breast. Unit in charge:  Physician in charge: Material collected on: Material received on Expected time of examination: up to 8 working days. Clinical diagnosis: Examination performed or.. Results of immunohistochemical examination: No estrogen receptors found in the neoplastic cell nuclei. No progesterone receptors found in the neoplastic cell nuclei. HER2  protein stained with HercepTestTM by DAKo. Negative reaction in invasive cancerous cells (Score = 1+ ) Compliance validated by: Examination performed or Macroscopic description: Right breast sized 26 x 19 x 5 cm removed along with axillary tissues sized 10 x 8 x 2 cm and a skin flap of 27 x 11 cm. Tumour sized 2.1 x 2.2 x 0.8 cm on the border of the lower inner quadrants, placed 1.5 cm from the lower edge, 0.1 cm from the base. and 2.0 cm from the skin. Microscopic description: Carcinoma ductale invasivum NHG3 (3 + 3 + 2: 15 mitoses/10 HPF - visual area of 0.57 mm). Glandular tissue off the tumour showing lesions of the type mastopathia fibrosa et cystica, hyperplasia ductalis simplex (UDH). Axillary lymph nodes: Sinus histiocytosis lymphonodorum (No XI). Histopathological diagnosis: Carcinoma ductale invasivum mammae dextrae. Invasive ductal carcinoma of the right'breast. (NHG3, pT2, pN0). Compliance validated b CONTACT YOUR DOCTOR WITH THIS REPORT! UUID: 1560F753-D83A-4934-9618-1E18CE46C845 TCGA-D8-A13L-01A-PR Redacted 3f+r/x

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+Department of Pathology UUID:FFA18E29-2CC3-48F3-A7F2-88FC092E5606 TCGA-P4-A5E7-01A-PR Redacted Tissue Source Site (TsS) #: Patholgy Accession No: Patient ID: Normal Sample ID: Pathology Report LCD-O-3 ******* MODIFIED REPORT - REVIEW ADDENDUM SECTION ****** COMMENT celi 8Q6c13 This addendum report is issued to comment on the type of papillary renal cell carcinoma,. as it was not mentioned in the original report. There is no other change in diagnosis. 8ite C64.9 After review of the H&E slides, this tumor is designated as type 2 papillary renal cell H1/io113 carcinoma. DIAGNOSIS (A) LEFT PARTIAL NEPHRECTOMY PAPILLARY RENAL CELL CARCINOMA, FUHRMAN'S NUCLEAR GRADE 3. TUMOR CONFINED TO KIDNEY. TUMOR MEASURES 4.5 CM IN MAXIMUM DIMENSION. Margins of resection free of tumor. (B) LEFT PARTIAL NEPHRECTOMY II: Renal parenchyma with focal glomerulosclerosis, no tumor present. (See comment) (C) ADRENAL BIOPSY: Adrenal cortical tissue. (See comment) COMMENT The specimen designated left partial nephrectomy (specimen B), consists of a fragment of renal parenchyma with focal glomerulosclerosis. Multiple additional deeper sections were examined.. The specimen designated adrenal biopsy (specimen C), consists of a fragment of adrenal cortical tissue. No metastatic carcinoma is identified. Correlation with the clinical findings is suggested. GROSS DESCRIPTION (A) LEFT PARTIAL NEPHRECTOMY - DEEP MARGIN - INK FROZEN SECTION INKED MARGIN - A partial nephrectomy specimen with attached perinephric fat (9.0 x 8.0 x 2.0 cm overall). The portion of kidney is approximately 5.0  5.0 x 2.0 cm and is marked with blue surgical ink along part of the parenchymal resection margin. A 4.5 x 4.0 x 1.9 cm friable orange-brown and focally hemorrhagic tumor mass is present within the kidney parenchyma. The tumor is less than 0.2 cm from the nearest parenchymal margin. No gross extension into perinephric fat is noted. The surrounding renal parenchyma is light tan and unremarkable. INK CODE: Black - parenchymal resection margin; blue - surgically marked parenchymal margin. SECTION CODE: A1, A2, frozen sections of parenchymal margin; A3-A6, tumor with margin; A7-A9, tumor with surrounding adipose and normal kidney; A10, tumor with blue surgical ink; A11-A16, additional tumor section. *FS/DX: REPRESENTATIVE MARGIN FREE OF TUMOR. (B) LEFT PARTIAL NEPHRECTOMY #2 - A 0.9 x 0.5 x 0.4 cm portion of renal parenchyma. The apparent cortical surface displays a 0.3 x 0.3 tan area of vague nodularity. The apparent parenchymal margin is tan and unremarkable. The cut surface does not show grossly invasive tumor.
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+Department of Pathology. Tissue Source Site (TSs) #: Patholgy Accession No: Patient ID: Normal Sample ID: Tumor Sample ID: INK CODE: Blue-apparent cortical surface, orange-apparent  parenchymal margin.e SECTION CODE: B, entire left partial nephrectomy. (C) ADRENAL BIOPSY, RULE OUT METASTASIS - A single portion of soft, yellow tissue (1.2 x 0.5 x 0.3 cm) is submitted entirely for frozen section in C. *FS/DX: ADRENAL CORTICAL TISSUE, NO METASTATIC CARCINOMA. CLINICAL HISTORYS None given. SNOMED CODES T-71000, M-Y7343 "'Some tests reported here may have been developed and performance. characteristics determined by . These tests have not been specifically cleared or approved by the U.S. Food and Drug Administration."

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+SPECIMENS: A. RIGHT COLON AMENDMENT REASON This case was amended to correct a formatting error. No other changes were made to this report. SPECIMEN(S): A. RIGHT COLON GROSS DESCRIPTION: A. RIGHT COLON Received without fixative, labeled "right colon", is an ilealcolectomy specimen including one segment of. 6-cm long ileum, 3.5-cm cecum with attached 6-cm long appendix, 30-cm long colon, with attached mesenteric fat. The colon is approximately 3.5 cm in diameter. Both resection margins are stapled closed. After removal of the stapled line, the specimen is opened and reveals one polypoid ulcerated colonic lesion measures 2.2 x 1.5-cm and elevated above the colonic mucosa to 0.7 cm. This lesion is. 11-cm to the colonic resection margin and 19-cm to ileal resection margin. The lesion appears to be superficial and does not involve the colonic wall. Three additional polypoid areas are present and each measuring 1.2, 1.5 and 2-cm in greatest dimension and are located 3.5, 4.5, and 8.0-cm to the colonic resection margin. The uninvolved colonic mucosa and ileal mucosa are unremarkable. The appendix is. 6-cm in length and 0.5-cm in diameter and is grossly unremarkable. Multiple possible lymph nodes are. present in the mesentery fat. Representative sections are submitted as follows:. A1. Distal colonic resection margin A2. Proximal ileal resection margin A3-A4: Full thickness of ulcerated polypoid lesion with attached mesenteric fat (inked black), bisected A5. Additional section of ulcerated polypoid lesion A6. Sections from polypoid area, 8.0-cm to the colonic resection margin A7. Sections from polypoid area, 4.5-cm to the colonic resection margin A8. Sections from polypoid area, 3.5-cm to the colonic resection margin A9. Sections of ileum. A10. Sections of cecum and appendix A11. Ileocecal valve A12-A14: Random sections of uninvolved colon A15-A27: Multiple possible lymph nodes A28: Tip of appendix DIAGNOSIS: A. COLON AND TERMINAL ILEUM, RIGHT HEMICOLECTOMY:  INFILTRATING MODERATELY DIFFERENTIATED ADENOCARCINOMA ARISING IN A SERRATED ADENOMA (2.2-CM) - SURGICAL MARGINS ARE NOT INVOLVED  - METASTATIC CARCINOMA INVOLVING THREE LYMPH NODES (3/44) SYNOPTIC REPORT - COLON & RECTUM Specimens Involved Specimens: A: RIGHT COLON Specimen Type: Right hemicolectomy Tumor Site: Cecum Tumor Configuration: Exophytic (polypoid) Tumor size: 2.2cm Additional dimensions 1.5cm x 0.7cm WHO Classification Adenocarcinoma 8140/3 Histologic Grade: G2: Moderately differentiated Extent of Invasion: Muscularis propria Margins: Margin(s) uninvolved by invasive carcinoma (Proximal, Distal, Radial) Distance of invasive carcinoma from closest margin: 11cm Margin: distal Venous/Lymphatic Invasion: Absent
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+Perineural Invasion:  Absent Additional Pathologic Findings: three hyperplastic polyps Extent of Resection: R0: Complete resection with grossly and microscopically negative margins Lymph Nodes: Positive 3 / 44 Extranodal extension: Absent Implants: Absent Pathological Staging (pTNM): pT 2 N 1 M x Comment(s): The tumor has a minor mucinous component with occasional, rare signet ring cells present... Immunohistochemical studies were performed in blocks A3/A4-see below- to confirm presence of metastatic disease and assess depth of invasion. Further studies to assess microsatellite instability will. be reported as an addendum. SUMMARY OF IMMUNOHISTOCHEMISTRY/SPECIAL STAINS Material: Block A3 Population: Tumor Cells Stain/Marker:Result:Comment: CYTOKERATIN AE1/3 Positive Material: Block A4 Population: Tumor Cells Stain/Marker:Result: Comment: CYTOKERATIN AE1/3 Positive The interpretation of the above immunohistochemistry stain or stains is guided by published results in. the medical literature, provided package information from the manufacturer and by internal review of staining performance and assay validation within the Immunohistochemistry Laboratory of. The use of. one or more reagents in the above tests is regulated as an analyte specific reagent (AsR). These tests. were developed and their performance characteristic determined by the Department of Pathology Laboratory at. They have not been cleared or approved by the U.S. Food and Drug Administration.. The FDA has determined that such clearance or approval is not necessary. Special stains and/or immunohistochemical stains were performed with appropriately stained positive. and negative controls. CLINICAL HISTORY: None given PRE-OPERATIVE DIAGNOSIS: Colon cancer ADDENDUM: SUMMARY OF IMMUNOHISTOCHEMISTRY/SPECIAL STAINS Material: Specimen A Population: Tumor Cells
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+Stain/Marker:Result: Comment: MLH1 Positive MSH2 Positive PMS2 Negative MSH6 Positive The interpretation of the above immunohistochemistry stain or stains is guided by published results in the medical literature, provided package information from the manufacturer and by internal review of staining performance and assay validation within the Immunohistochemistry Laboratory of the. The use of one or more reagents in the above tests is regulated as an analyte specific reagent (ASR). These tests were developed and their performance characteristic determined by the Department of Pathology Laboratory. They have not been cleared or approved by the U.S. Food and Drug Administration. The FDA has determined that such clearance or approval is not necessary. Special stains and/or immunohistochemical stains were performed with appropriately stained positive and negative controls.  INTERPRETATION: No PMS2 proteins identified by immunohistochemistry. The results of microsatellite instability testing will be issued in a separate report.

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+P.15/33 SsiS; tAxiLLARY SENTIneL LympH NODe #1, BIOpSy - one lymph node with metastatic carcinoma measuring 1.5 mm in greatest Dimension (1/1).  NO exTracApsulAr ExTension Is identifieD. Part 2: Right sreast at 9 O'clock, segmental mastectomy . A.  mUL TIfOCAl JNyASIVe DUctAL CArciNQMA. nOTTInghAm GrADE 2 (nUCLEAr GrADe 3, TUBULE Score 3, mitotic activity score 1. total 8core 7/9). e.  mAIn TUmOR MASs MEAsURe8 2.2 Cm AND iS ASSOciATed WITh BIOPSy SITe CHAnGES. C. A 2.S MM SATELLITE nODUEE OF INVASIVE TUMOR IS PRESENT NEAR THE LATERAL ASPECT OF THE Specimen, Away from the main tumor mass. D. THiro tumOR FOcUS iS SEen in PaRT 3 (soc comment). E. LYMPHOVASCULAR SPACE INVASION IS IOENTIFIED. F.  PERINEURAL INVASION IS.IDENTIFIED. G. TUMOR NODULES.CONTAIN CENTRAL FIBROSIS WITH PSEUDO DECiDUALIZEd STROmAL HYPERPI.ASIA (pash) LiKe StrOmal ReactiOn. H. DuctaL CARcInOmA In SiTU (DCIS). nUcLEAR GrADe 3 wITh COmEDOnecROSiS And CALCIFICATIONS:  MARGINS ARE NEGATIVE FOR NEOPLASM (INCLUDING BOTH TUMORS IN PART 1); INVASIVE CARCINOMA WAS CLOSEST TO THE ANTERIOR MARGiN (3 mM) AND INTRAVASCULAR TUmOR WAS CLOSEST TO THE SUPERIOR MARGIN (2 Mm). Changes consIstent with previous BiOp8y Site. K. tUmOr PreViOUsLy repORted tO BE POsITiVE fOR eR AnD PR, AnD nEgAtIVe fOr hEr-2/nEu PATHOLOGIC 8TAGE: pT2 pN2a pMX. Part 3: Right axillary contents, Di8section : A. Satellite.noDule Of invasive ductal Carcinoma And Ductal Carcinoma In Situ .  SimILAR in APPEArAnCe tO TUmOR SEen In PArt 2 (9.5 mm). B.  SEVEN LYMPH NODES, POSITIVEFOR METASTATIC AOENOCARCINOMA MEASURING UP TO AppROXImATELY 6 Mm EACH (7/13). C. ExtracapsuLar Ex'tensIonis Present and measures Less thAn 1 mm. D. EXTeNSIVe intRAVASCULAK iumUR. CASE SYNOPSIS: 1cs-o-3  SYNOPTIC - PRIMARY iNVASIVE CARCINOMA OF BREASt LATERALITY: Cnicii oms, nifilr#ny ductl,Nts 85oo/3 PROCEDURE: Right  Sagmental Si#:buust, Nos C5v.9 3/131n d- LOCATION: Uppur nuter quadrant SIZE OF TumOR: Lower outor quadrant MULTICENTRICITY/MULTIFOCALITY OF INVASIVE FOCI: Maxirmiurn Qimcnsion invasive componcnt: 2.2 cm Tumor Aggregate size: Yes TUmOR TYPE (invasive component): Sum of the sizos of multiple invasive tumors: 3.4 cm NOTTINGHAM SCORE: Ductal adenocarcinoma, NOS Nuclear grade: 3 Tubulo formatlon: 3 Total Nottinyham srnre: 7 UUID:E4CBDC29-63E2-4CF0-B02F-16CA9C69F26E ANGIOLYMPHATIC INVASION: Nottinyham grade (1, 2. 3): 2 TCGA-BH-A0DS-01A-PR DERMAL LYMPhATIC INVASION: Yes Redacted CALCIFICATION: Not applicahlc Tumor type, in situ: Yes, malignant zones Cribriform SURGICAL mARGINS INVOLVED BY INVASIVE COMPONENT: Comedo No SURG MARGINS INVOLVED BY IN SITU COMPONENT: Distance of invasive tumor lo closest maryin: 2 mm No LYMPH NODES POSITIVE: Diytance of in situ discaxe to dosest margin: 6 mm LymPh nODeS ExAMINED: B METHOD(S) OF LYMPH NODE EXAMINATION: 14 Sentinel nOde metAstasis: H/E stain  SIZE OF NODAL METASTASES: Yes Lymph nOde metA8tASis(-es) wiTh ExtracapsuLAR ExTensiOn: Diameter of largest lymph node metastasis: 6 mm t stage, Pathologic: Ycs N Stage. pathologIC: pT2 m stage, pathologic: pN2a ESTROGeN RECEPTOrS: pMX PROGeSTERONe RecEptORS: posilive HER2/NEU: positivn rimary Tum HPAA Disc Zoro ur 1+ rior Malignan sual/Synch se is{Li 33

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+1cs-0-3 CaLcinvma, metap|asft,N0s 8575f3 UUID:46A75AD3-BAD1-4A16-873E-0099BD10FA8C Sit; srnst, NOS TCGA-A7-A26F-01A-PR Redacted C 50.9 4/27/11 DEPARTMENT OF PATHOLOGY AND LABORATORY MEDICINE Date Coll SPECIMEN A. Left axillary sentinel lymph node B. Left breast CLINICAL NOTES CLINICAL HISTORY: A -year-old with left breast metaplastic cancer. FROZEN SECTION DIAGNOSIS AFs Left axillary sentinel node, excision: No evidence of metastasis in 1 node (0/1) GROSS DESCRIPTION A. Received in a container labeled with the patient's name, medical record number and "left axillary sentinel lymph node". The specimen container holds a single soft tan lymph node measuring 1.5 x 1 x 0.5 cm. AS block Asf, bisected. B. Container B is labeled with the patient's name, medical record number and "left breast". The specimen consists of an excisional biopsy oriented by two sutures and measuring 3.5 cm. from anterior to posterior, 3.8 cm. from superior to inferior and 2.5 cm. from medial to lateral. The specimen margins are inked as follows: blue-interior, black-posterior, red-superior, green-inferior, yellow-medial, orange-lateral. serially sectioned and there is a firm, tan stellate lesion The specimen is measuring 1.8 x 1.5 x 1.5 cm., located extending in the direction of the inferior margin of resection and appearing to involve the inferior margin. Asb1-b20. MICROSCOPIC DESCRIPTION A. There is no evidence of metastasis in one left axillary sentinel lymph node. The node is examined by multilevel sectioning with H&E staining, as well as for immunohistochemistry for pankeratin. B. Invasive Carcinoma: Present. Histologic type: metaplastic. Histologic grade: Overall grade: 3 Architectural score: Nuclear score: 3 Mitotic score: 3 Greatest dimension (pT): 1.8 cm (pT1) Specimen margins: Positive. Vessel invasion:  Invasive carcinoma involves inferior margin over a distance of greater than 1 cm. Vessel invasion: foci suspicious. Calcification: Present. Ductal carcinoma in situ: Present. Histologic pattern:  Solid. Nuclear grade: 3 Central necrosis: Present.
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+% Dcis subtotal tumor: Less than 10%.. Absent. Extensive intraductal component:. Specimen margins: Negative. Calcification: Present. Description of non-tumorous breast:. Unremarkable. Comments: None. Previously FISh for HER-2 was reported as Prognostic markers: equivocal and a block is sent at the request of. repeat HER-2 by FISH. DIAGNOSISS Left axillary sentinel lymph node, resection: A. B. Left breast, excisional biopsy:. Poorly differentiated carcinoma with metaplastic features, grade 3, 1.8 cm Invasive carcinoma extends to involve the inferior margin of resection.  Ductal carcinoma in situ, solid and comedo subtypes,. nuclear grade 3 with necrosis, margins negative.. ctronic Signature) -End Of Report Case is (circie)

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+Clinical Diagnosis & History: Right renal mass. Specimens Submitted: 1:SP:Right kidney,ureter and bladder cuff nephrouterectomy 2:SP:Retroperitoneal lipoma,rightexcision 3:SP:Lymph nodes.paracavalexcision 4:SP:Lymph nodes,right common iliacexcision 5:SP:Lymph nodes,precaval and interaortocavalexcision 6:SP:Lymph nodes, suprahilar,and adrenal gland,right excision DIAGNOSIS: SP:Right kidney,ureter and bladder cuff; nephrouterectomy Tumor Type: Renal cell carcinoma-Chromophobe type Tumor Size: Greatest diameter is 3.2 cm. Local Invasion (for renal cortical types): Involves renal sinus fat Renal Vein Invasion: Not identified Small vessel angiolymphatic invasion is also not identified Surgical Margins: Free of tumor Non-Neoplastic Kidney: Mild arteriosclerotic changes and benign cortical cysts Adrenal Gland Not identified Lymph Nodes: Not identified Staging for renal cell carcinoma/oncocytoma: pT3a Tumor invades the adrenal gland or perinephric tissues but not beyond Gerota's fascia Comment:Benign pelvi-calyceal system and ureter 2.SP:Soft tissue, retroperitoneumright;excision Mature adipose tissue,4.6cm. Page 1 of4
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+SURGICAL PATHOLOGYREPORT No atypia identified. Comment: This part of the specimen was seen in consultation with who concurs. 3. SPLymph nodes,paracaval;excision Lymph Nodes: Not involved Number of nodes examined:4 4. SP:Lymph nodes,right common iliac;excision Lymph Nodes: Not involved Number of nodes examined:2 5.SP:Lymph nodes,precaval and interaortocaval; excision Lymph Nodes Not involved Number of nodes examined:7 6.SP:Suprahilar nodes and right adrenalgland;excision Benign adrenal gland. No lymph nodes identified. IATTEST THAT THE ABOVE DIAGNOSIS IS BASED UPON MY PERSONAL EXAMINATION OF THE SLIDES (AND/OR OTHER MATERIAL).AND THAT IHAVE REVIEWEDANDAPPROVEDTHISREPORT. Special Studies: Result SpecialStain Comment RECUT RECUT RECUT Gross Description: 1).The specimen is received in fresh state for intraoperative consultation, labeled as"right kidney,ureter, and bladder cuffand it consists of a total nephrectomy specimen weighing in total 502 g.The specimen surface is inked.No adrenal gland is identified. Kidney measures 11x 6.0 x 3.9 cm,and the segment of ureter measures 19 cm in length and 0.8 cm in circumference.The distal end of the ureter may actually represent "bladder cuff.Sectioning reveals a well-circumscribed brown soft cortical mass measuring 3.2 x 3.2 x2.9 cm in the lower medial aspect of the specimen.The majority of the tumor is in close contact with sinus fat, but frank invasion is grossly not identified. Grossly evident venous invasion is not seen. Perirenal fat is uninvolved. Background renal parenchyma shows mildly thinned cortex (0.7 cm) with sharp cortical medullary junction. Pelvic mucosa and ureteral mucosa appears grossly unremarkable.No possible lymph nodes are identified in the perirenal fat.The specimen is photographed. TPS is taken. Summary of sections: FSC--frozen section control tumor) UM- ureter margin Page 2of4
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+SURGICAL PATHOLOGY REPORT VM--vascular margins TSF-tumor with sinus fat T-tumor BG--background renal parenchyma P--pelvic mucosa U--ureteral mucosa 2).The specimen is received in formalin, labeled as" right retroperitoneal lipoma",and it consists of a partially encapsulated nodule of adipose tissue measuring 4.6 x 2.3 x2.0 cm.Sectioning reveals grossly unremarkable adipose tissue without fibrosis or hemorrhage. Representative sections are submitted. Summary of sections: U--undesignated 3).The specimen is received in formalin,labeled as paracaval lymph nodes",and it consists of multiple possible lymph nodes measuring up to 1.0 cm.Entire lymph nodes are submitted. Summary of sections: LN-- lymph nodes 4). The specimen is received in formalin, labeled as "right common iliac lymph nodes",and it consists of a single possible lymph node measuring 0.6 cm.Entire lymph node is submitted Summary of sections LN-- lymph node Akihiko Yoshida,M.D. 5).The specimen is received in formalin, labeled as precaval and inter-aortocaval lymph node",and it consists of multiple possible lymph nodes measuring up to 3.5 cm.The largest lymph node is trisected. Entire lymph nodes are submitted. Summary of sections: TLN--trisected lymph node LN--lymph nodes Akihiko Yoshida,M.D 6).The specimen is received in formalin, labeled as "suprahilar nodes and right adrenal gland",and it consists of an adrenal gland and surrounding adipose tissue.Adrenal gland measures 7.0 x 3.5 x 1.6 cm and weighs 10.5 g after the removal of fat. Section reveals grossly unremarkable adrenal tissue. Surrounding adipose tissue does not contain grossly evident lymph nodes. Representative sections are submitted. Summary of sections: AD--adrenal F-adipose tissue, slightly fibrotic area Summary of Sections: Part 1:SP:Right kidney, ureter and bladder cuff; nephrouterectomy Block Sect.Site PCs 2 bg 2 1 fsc 1 1 1 1 1 6 tsf 6 1 u 1 1 um 1 Page3of4
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+SURGICAL PATHOLOGY REPORT 1 vm 1 Part 2:SP:Retroperitoneal lipoma,rightexcision Block Sect.Site PCs 5 u 5 Part 3:SP:Lymph nodes,paracaval;excision Block Sect.Site PCs 1 In 1 Part 4: SP:Lymph nodes,right common iliac;excision Block Sect. Site PCs 1 In 1 Part 5: SP:Lymph nodes,precaval and interaortocaval;excision Block Sect. Site PCs 1 In 1 2 tIn 2 Part 6: SP:Lymph nodes,suprahilar,and adrenal gland,rightexcision Block Sect.Site PCs 1 ad 1 1 f 1 Intraoperative Consultation: Note: The diagnoses given in this section pertain only to the tissue sample examined at the time of the intraoperative consultation. FROZEN SECTION DIAGNOSIS:SP:Right kidney,ureter and bladder cuff RENAL CORTICAL NEOPLASM. PERMANENT DIAGNOSIS: SAME Page4of4 END OFREPORT

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+Diagnosis: Colon resection material 8 cm in length includes an extensively ulcerated, colorectal type of adenocarcinoma of almost circular growth extending 3 cm lengthwise and situated in the center of the preparation with infiltration of the pericolic fatty tissue and five regional lymph node metastases. No evidence of penetration of the overlying serosa. Tumor-free colon resection margins. Tumor stage: pT3 pN2 (5/12) pM1 (clinical liver metastases); G2, L1, V0, locally R0). 2.: Inflammation-free small intestine or Meckel's diverticulum without evidence of tissue heterotopy.

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+UUID:7BA4658F-3343-4176-BDCD-620A1001A032 TCGA-D8-A73U-01A-PR Redacted Patient: XXX Age: Gender: F Unit in charge: orcnoind, syyistiativg lsbulor  Physician in charge: $52013 Clinical diagnosis (suspicion) Cancer of the left breast Nos Date of admission: S C5b.9 10/s/3 Material: 1) Material: Left breast. Method of collection: total organ resection. Histopathological diagnosis: Examination performed on:  Invasive lobular carcinoma of the left breast (NHG2, pT2). (8520/3 T-34030)* * codes according to ICD-O-3 or SNOMED Macroscopic description: Left breast, sized 21.2 x 12.3 x 5.4 cm, removed without axillary tissues and with a skin flap of 18.2 x 8.3 cm. Weight: 436g. Tumour sized 4x2,2x1,6cm found on the boundary of upper quadrants, placed 2.8 cm from the upper boundary, 1.4cm from the base and 1.0cm from the skin.. Microscopic description: Invasive ductal carcinoma (classical type) -- NHG 2 (3+2+1: 0 mitoses/ 10 HPF -- visual area: 0.55mm: 0.55mm). The  nipple without pathological lesions. Glandular tissue showing parenchyma atrophy. Assistant: Pathologist: Edited by Results of intraoperative examination:. Examination performed on:. Estrogen receptors found in 75% of neoplastic cell nuclei. Progesterone receptors found in 75% of neoplastic cell nuclei. HER2 protein stained with. HER-2/neu (4B5) Rabbit Monoclonal Antibody. Negative reaction in invasive cancerous cells ( Score = 1+). The expression of proliferating nuclear antigen Ki 67 in 15 % cellular nuclei.. Assistant: Pathologist: Edited by CONTACT YOUR DOCTOR WITH THIS REPORT! i.8/ rmary Tun

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+SPECIMEN A. Sigmoid colon, upper rectum and adherent posterior bladder wall and small intestines B. Appendix CLINICAL NOTES PRE-OP DIAGNOSIS: Rectal cancer. GROSS DESCRIPTION A. Received fresh subsequently fixed in formalin labeled "sigmoid, upper rectum with adherent posterior bladder. wall and small intestines". The specimen consists of a rectosigmoid colon with adherent portions of small bowel and possible portion of. bladder. A segment of small bowel was 12 cm long, stapled at both ends, which are arbitrarily inked blue and black. A portion of colon is 46 cm long. Both ends are stapled, inked blue and the. opposite is opened and is inked black. There is also a small portion of possible bladder, which is 7 x 5 cm. This is smooth to slightly velvety and the margin of this is inked blue. Orientation. cannot be determined.  One end away from the tumor is inked blue. The opposite end close to the tumor is inked black. The specimen is opened to show a large fungating mass, which is 12 x 11.5 x 3.5 cm. This comes within 2.5 cm of the black inked margin. This tumor is centrally necrotic and goes through the wall of the colon, into the. surrounding fat and through the wall of the small bowel into the mucosa of the small bowel. The remainder of the mucosa of small bowel is pink-tan smooth glistening with normal slightly dilated poles having an average circumference of 6.5 cm and the mucosal alteration of tumor is 3.5 x 3.5 cm. This comes within equidistant luminal margins of the small bowel. The tumor also comes through the wall into the fat and possibly involves the mucosa of the portion of bladder. This is velvety, coming within 0.5 cm of the nearest peripheral margin. The remainder of the mucosa of the specimen is pink-tan smooth glistening with an average. circumference of 9.5 cm. The tumor comes within 1.5 cm of being circumferential and shows a markedly necrotic central focus. Lymph nodes are grossly identified. Representative sections of the specimen are submitted as follows: BLOCK SUMMARY: 1 - Representative luminal margins of small bowel,. 2  representative section of small bowel tumor, 3-4 - representative section of bladder to tumor, 5 - representative luminal margins of. the colon, 6 - representative section of tumor to normal, 7 and 8. representative sections of tumor to fat, 9-12 - have six possible
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+lymph nodes have four possible lymph nodes each. RS-15. B. Received in formalin labelled "appendix" is a 6.3 x 0.7 cm appendix which is partially covered with pink-tan smooth glistening serosa and yellow lobular fat.  The specimen is sectioned to show an intact wall with. an average thickness of 0.4 cm. The lumen ranges from pinpoint to 0.4 cm and shows possible diverticula present. No other discrete gross lesions are identified. The entire specimen with the exception of the fat is. submitted in t settes. As-2 (fat retained), proximal end. inked. As-2. MICROSCOPIC DESCRIPTION A. Microscopic exam of the resection shows:. Histologic type: Adenocarcinoma, not otherwise specified Histologic grade: Moderately differentiated. Primary tumor(pT): Tumor invades through the entire colonic wall and through the entire adhesed small intestinal wall into the lumen of the small intestine. The tumor also invades into the muscularis propria of the bladder wall (pT4b).. Proximal margin: Negative for tumor.. Distal margin: Negative for tumor.. Circumferential (radial) margin: Negative for tumor although not truly applicable given the resection of the adhered additional Organs. Distance of tumor from closest margin: 2.5 from one of the colonic margins Vascular invasion: Not identified. Regional lymph nodes (pN): 30 lymph nodes are dissected from the specimen and they are all negative for metastatic (pno). Non-lymph node pericolonic tumor: Present in the soft tissue adhesing the small intestine and the bladder to the upper rectal/sigmoid colon resection. No discrete additional nodules of
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+pericolonic tumor seen. Distant metastasis (pM): Cannot evaluate pMx. Other findings: There is significant necrosis of the tumor in the central areas. B. Microscopic examination of the appendix reveals a benign mucocele at the tip. No dysplasia or malignancy is identified. There is focal fibrous obliteration of the tip. including obliteration of the diverticulum. There is acute serositis and ahdesions. 5x1, 2x1, 3260F DIAGNOSIS A. Sigmoid colon, upper rectum and adherent posterior bladder wall and small intestines, resection: Invasive moderately differentiated adenocarcinoma. Tumor invades through the entire colonic wall and through the. entire adhesed small intestinal wall into the mucosa of the. small intestine. Tumor invades into the muscularis propria. of the bladder (pT4b). Thirty lymph nodes are negative for metastatic tumor (0/30). (pNO). Resection margins are negative for tumor. B. Appendix, excision: Hyperplastic mucinous epithelium consistent with benign mucocele. . Resection margins are negative. Serosal adhesions. --- End Of Report ---

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+/cs-0-3 8500/3 Carcinoma, mifiltrstny duct, N0s Site : srsst, nos c50. 9 4/20 OC#:. TSS #: Procurement Date: Laterality:Right, upper inner quadrant Path RepOrt:BREAST TISSUE CHECKLiST Specimen type: Lumpectomy Specimen size: Not specified Tumor site: Breast Tumor size: 1.5 x 0 x 2 cm Grossly evident lesion: Yes Histologic type: Infiltrating ductal carcinoma Histologic grade: Poorly differentiated Tumor extent: Not specified Lymph nodes: 0/10 positive for metastasis (Axillary 0/10) Extracapsular invasion of the lymph nodes: Not specified Margins: Uninvolved Nottingham Histologic Score Tubule formation: Not specified Nuclear pleomorphism: Not specified Mitotic count (25x): Not specified Mitotic count (40x): Not specified Total Nottingham Score: Score cannot be determined Evidence of neo-adjuvant treatment: Not specified Additional pathologic findings: Not specified UUID:742A4812-9EB1-4348-996E-3F1AD7FA3E5D Comments: None TCGA-E9-A243-01A-PR Redacted

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+Patient Name Accession #: Med. Rec. #: Date of Procedure DO8. Date of Receipt Gendor: Date of Report: Ret. Physician: Account #f. Patient Address: Billing Type. Additional Copy to. Ref. Source: Clinical Diagnosis & History: Right renal mass. Specimens Submitted: 1: SP: Kidney, right, partial nephrecton 2: SP:Kidney, Deep surgical margin #2. DIAGNOSIS: 1 SP: Kidney, right, partial nephrectomy(fs)(am): Tunor Type: Renal cell carcinoma - Unclassitied type The tunor has papillary. tubular, and solid foaturos.High grade. Tumor Size Greatest diameter is 1 6 cm Local Invasion (lor renal corlical typos): Involves ronal sinus fatd Renal Vein Invasion: Not idontified Surgical Margins: Free of tumor Non-Neoplaslic Kidney:. Unremarkable Adrenal Gland: Not identified Lymph Nodos: Not identified Staging for renal cell carcinoa/oncocytoma pT3 Tumor extends into major voins or invades the adrenal gland or pornephric tissues, but not boyond  fascia Comment: While this tumor does not fit into one of our well described entities, I favor it being ol distal nephron origin 2."Deep surgical margin#2",  excision: Benign renal parenchyma. No tunor idontified. Page 1 of 3
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+SURGICAL PATHOLOGY REPORT TATTEST THAT THE ABOVE DIAGNOSIS IS BASED UPON MY PERSONAL EXAMINATION OF THE SLIDES (AND/OR OTHER MATERIAL), AND THAT I HAVE REVIEWEDANDAPPROVEDTHISREPORT Special Studies:. Rosull Special Stain Comment CA-1X. NEG CONT IMM RECUT RECUT RECUT RECUT CK7 RACEMASE MIB-1 (Ki-67) Gross Description. ed "right renal tumor.It consists of a 2.8 x 2.8 x 2.5 cm wedge shapod portion of kidney with a suture marking the deep margin. The margin is inked black and the margin at stitch pink -yellow. The specimen is serialy seclioned to reveai white yellow mass measuring 1.6 X 1.5 X 1.1 cm. The tumor from the resection margin (with stitch. yellow ink) is 0.3 cm and within 0.1 cm to the closest the black inked margin.  A representative section of the nearest margin is submitted for frozen section diagnosis. Representalively submitted. Portions of the tumor are submilled for TPS. Summary of sections:. FSC - frozen seclion control. T - tumor M - margin RS - representalive sections. 2).The specimen is received in formalin. labeled "Deep surgical margin number two" and consists of a 0.7 x 0.6 x 0 3 cm fragment of tan soft tissue. Entirely submitted. Summary of sections: U - undosignaled. Summary of Sections:. Part 1: SP: Kidney, right, partial nephrectomy Block Sect. Site PCs fsc 1 1 m 1 2 rs 2 1 1 Part 2: SP:Kidney, Deop surgical margin #2, excisio Block pCs Sect. Site 1 u 1 Intraoperative Consultation:d Nole: The diagnoses given in this section pertain only to the tissue sample examined at the lime of the intraoperative consultation. 1) FROZEN SECTION DIAGNOSIS: MARGIN AT STITCH IS BENIGN. CARCINOMA, NOT CLEAR CELL Page 2 of 3
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+PERMANENT DIAGNOSIS Page 3 of 3 END OF REPORT

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+TCGA-AN-A0XR-01A-PR Redacted TSS Patient ID Case #: DOB: Sex: Female Ethnicity (Race): Cancer Sample  Diagnosis: Breast Cancer Histological description: Infiltrative ductal carcinoma Date of Procurement:. Anatomic Site: Breast Tumor location: Primary Tissue Specification: Tumor Specimen Matrix: Tissue Specimen Format: OCT Container: block Type of Procurement: surgery Grade: 2 T Stage: 2 N Stage: 2b M Stage: 0 Treatnent: none Treatment Details: n/a. Norma! Sample Anatomic Site: Blood Sample Type: Normal Type of Procurement: blood draw Matrix: Blood Specimen Format: frozen Container: tube Date of Procurement: 1cs-0 -3 csrcinwma infiIt^eAny ctuct; Nos 85oc/3 Site: breast, Nos. C50.? hu 10 /21/ 1/8+f1t

output/text/026bb285-537e-4a6f-96d9-9f9ec8fa45e0.txt

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+ UUID: 89A67051-898A-4E2A-A874-E0165F274E630 TCGA-A1-A0SG-01A-PR Redacted Jcs-0-3 Circinoma,m fiHtnatig micropopillery.nitraducAl 8507f3 Site: brast Nos C50.7. Final Pathologic Diagnosis: A. Right axillary sentinel lymph node #1, count = 35oo, dissection: Metastatic. adenocarcinoma in one of two lymph nodes (1/2).. B. Right axillary sentinel lymph node #2, count = 500, dissection: No tumor in two. Iymph nodes (0/2). C. Right breast, partial mastectomy:. 1. Invasive micropapillary carcinoma, 2.1 cm, associated with microcalcifications; see. comment. 2. Atypical lobular hyperplasia.. 3. Fibroadenoma. 4. Microcalcifications in benign ducts D. Sentinel lymph node #3, count - 350, dissection: No tumor in two lymph nodes (0/2). Note: Breast Tumor Synoptic Comment - Laterality: Right. - Invasive tumor type: Invasive micropapillary carcinoma. - Invasive tumor size: 2.1 cm maximum diameter. The tumor is present in slices 4, 5, 9, and 10; however the tumor has been banked from slices 6, 7, and 8. Therefore, the tumor extends through seven consecutive slices, each with a width of approximately 0.3 cm, for a total maximum diameter of 2.1 cm. - Invasive tumor grade (modified Bloom-Richardson): 2 Nuclear grade: 3, 3 points. Mitotic count: < 10 mitotic figures/10 HPF, 1 point.. Tubule/papilla formation: Definite tubule formation in <10%, 3 points.. Page 1 of'4
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+Surgical Pathology - Working Draft Total points and SBR grade - 7 points, grade 2 - Lymphatic-vascular invasion: None identified. - Perineural invasion: None identified. - Resection margins for invasive tumor: - Deep margin: Negative (1 cm). - Medial margin: Negative (0.9 cm).. - Lateral margin: Negative (0.6 cm).. - Anterior/superior margin: Negative (0.5 cm). - Anterior/inferior margin: Negative (greater than 1 cm). - Ductal carcinoma in situ (DCis) type: None identified. - Microcalcifications: Present involving both benign ducts and invasive carcinoma.. - Lobular carcinoma in situ (LCiS): None identified. - Lymph node status: - Number of positive lymph nodes: 1. - Total number sampled: 6. - Diameter of largest metastasis: 2.1 mm. - Extranodal extension: Absent. - AJCC/UICC stage: pT2N1aMX. - Nontumorous breast tissue: Atypical lobular hyperplasia, fibroadenoma, and sclerosing adenosis. - Additional comments: We reviewed the original frozen section slides and concur with the frozen section diagnosis rendered. The metastatic tumor in Part A was only present in the additionally submitted sections of the lymph node (slide A2). Level sections on A2-A4 confirms the diagnosis. Select slides from part C were shown at the the faculty in attendance concurred with the above diagnosis of micropapillary type ot invasive carcinoma. Dr.. has reviewed A2 and concurs with the diagnosis. An immunohistochemical test for estrogen and progesterone receptors was performed on block C9. The test for estrogen receptors is positive. There is 3+ nuclear staining in >95% of tumor cells. The test for progesterone receptors is positive. There is 3+ nuclear staining in >95% of tumor cells. Result of HER2/neu test: This carcinoma is negative for HER2/neu oncoprotein over-expression. An immunohistochemical assay was performed on block C9 using the CB11 monoclonal antibody to HER2/neu oncoprotein. The staining intensity of this carcinoma was 1 on a scale of 0-3.. Carcinomas with staining intensity scores of O or I are considered negative for over-expression of HER2/neu oncoprotein. Those with a staining intensity score of 2 are considered indeterminate. We and others have observed that many carcinomas with staining intensity scores of 2 do not show gene amplification. All carcinomas with staining intensity scores of 2 are therefore submitted for FISH testing. The results of the FISH test are issued directly from the molecular cytogenetics laboratory. Carcinomas with staining intensity scores of 3 are considered positive for over-expression of HER2/neu oncoprotein. Tumors in this category show an excellent correlation betwcen the results of immunohistochemical and FiSH testing, and almost always show gene amplification. Slide A2 was shown at the departmental Consensus Conference, and the faculty in attendance concurred with the above diagnosis.. Intraoperative Consult Diagnosis FS1 (A) Right axillary SLN #1, biopsy: Negative for carcinoma. (Dr.. Clinical History The patient is a year-old woman with right breast carcinoma. Paee 2 of 4
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+Surgical Pathology  Working Draft Gross Description The specimen is received in four parts, each labeled with the patient's name and medical record number.. Part A is received fresh and labeled It consists of one pink-yellow, soft, fatty tissue that measures 3.1 x 2.5 x 0.8 cm. The specimen is strained and two candidate Iymph. nodes are found, the smallest is inked blue and submitted with a representative section of the largest. submitted for frozen diagnosis #1, thereafter submitted in cassette A1. The remnant of the largest lymph. node is transected and entirely submitted in cassettes A2-A3, and the remnant of the yellow fatty tissue is. submitted in cassette A4. Part B, additionally labeled consists of a single fragment of yellow, fibrofatty tissue measuring 2 x 1.8 x 0.4 cm. The specimen is entirely submitted in cassette B1.. Part C, additionally labeled  consists of a right breast specimen oriented with a short superior and a long stitch lateral. The specimen measures 3.2 cm from anterior to posterior,. 5 cm from medial to lateral and 6.5 cm from superior to inferior. The resection margins are inked as follows for microscopic evaluation: anterior superior in blue, anterior inferior in green and posterior in black. The specimen is serially sectioned from medial to lateral into twelve slices. There is gray-white, fibrous tissue in the superior half of the specimen in slices 3-11, measuring 2.4 x 2 x 1.5 cm. White fibrous tissue extends from this area to the anterior inferior aspect in slices 5-8. The gray-white fibrous tissue appears extend to the inked margin in the posterior superior aspect of slices 3 and 4, and appears to be O.5 cm from the anterior superior inked margins in slices 5 and 9. Representative sections are submitted as follows: Cassette C1: Representative medial margin, slice 1, bread-loafed.. Cassette C2: Representative section of slice 3. Cassettes C3-C5: Slice 4. Cassette C6: Representative section of slice 5. Cassette C7: Representative section of slice 6. Cassette C8: Representative section of slice 8. Cassette C9: Representative section of slice 9. Cassettes C10-C11: Representative sections of slice 10 Cassette C12: Representative section of slice 11. Cassette C13: Representative lateral margin, slice 12, bread-loafed.. Part D, additionally labeled consists of a single, yellow, fibrofatty tissue fragment. measuring 2.5 x 1.5 x 0.4 cm. The specimen is entirely submitted in cassette D1. The immunoperoxidase stain(s) reported above were developed and their performance characteristics determined by the They have not been cleared or approved by the U. S. Food and Drug Administration. The FDA has determined that such clearance or approval is not necessary. These tests are used for clinical purposes. They should not be regarded. as investigational or for research. This laboratory is certified under the Clinical Laboratory Improvement Amendments of 1988 (*CLlA") as qualified to perform high-complexity clinical testing.. Signed Fee Codes: Other Specimens - pecimen Class: Status: Signed Out Accessioned: Signed Out: Specimen(s) Received: Right axillary contents Final Diagnosis Axilla, right, "contents," excision: 1. Scar tissue, fat necrosis and suture with giant cell reaction. No malignancy is. identified. Page 3 of 4
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+Surgical Pathology - : Working Draft 2. No metastatic tumor identified in five lymph nodes. (0/5). Specimen Class: Status: Signed Out Accessioned: Signed Out: Specimen(s) Received: Final Diagnosis Review of irom : Breast, right, 10 o'clock, core biopsies: Infiltrating ductal carcinoma, SBR Grade 2; see comment. FND OF RFPORT Paxe 4 0f4

output/text/026be35a-4528-4a87-9d09-29a50116d942.txt

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+Patlent Name: Accession #: Med, Roc. #: Date of Procedure: DOB: Date of Receipt: Gender: Date of Report: Ref. Physkcian: Account #: Pallent Address: Blling Type: Additional Copy to: Rel. Source: Other Related Data: Biiling Type: Financial Number: Clinical Diagnosis & History: Left renal mass. Specimens.Submitted: 1: SP: Left kidnay and adrena DIAGNOSIS: 1} KIDNEY AND ADRENAL, GLAND, LEFT NEPHRECTOMY AND ADRENALECTOMY : - RENAL CEIL. CARCINOMA, PAPILLARY TYPE, WITH FOCAL SPINDLE CEIL (SARCOMATOID) GROKTI AND EXTENSIVE NECROSIS. THE TOMOR GREATEST DIAMETER IS 1O.O CM. THE TUMOR EXTENDS THROUGH THE RENAL CAPSULS BUT IS CONFINED WITHIN GEROTA'S FASCIA. NO INVASION OF THE RENAL VEIN IS IDENTIFISD. ALL SURGICA MARGINS ARE FREE OE TUMOR. THE NON-NEOPLASTIC KIONEY IS UNREMARKABIE. THE ADRENAL GLAND IS UNREMARKABLE. I ATTEST THAT THE ABOVE DIAGNO$K$ IS BA$ED UPON MY PERSONAL EXAMINATION OF THE SLIDES (ANDIOR OTHER MATERIAL), AND THAT I HAVE. REVIEWED AND APPROVEO THIS REPORT. Gross Descrintion: .} The specimen is received fxesh labelled "Jeft kidney and. adrenal". It consists of a kidney with attached adrenal gland, alnost entirely covered by adipose tissue, which totally weighs 720 grams. The kidney measures 14 cm in superior-inferior, 10 am antexior - posterior, and 9.5 cm medial to lateral. The adrenal gland measures 4.5 x 2 x 0.7 cn, and on cut. section is unremarkable. The surgical maxgins of the vein and of the ureter are shaved off. The kidney is bisected to reveal an almost entirely nacrotic mass, which is located in the cortical portion of the specinen.  The mass measures 10 x 6 x 5 cm, and is centrally, diffusely occupied by brown necrotie tissue. In the Page 1 0f 2
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+Deriohera. pottro., tie Kass wosis's of soft, yetlow to ion. rod The mass aggears tncepsula.cd ard well damarnsted excep in she moet ouoorior portion wher. it appears to intiltrate the Sorrina adipoee tieote. The xternsl surfao tosete w +aae ao ir is anlenr if rassd. kidr.ey parehm.yu. Luror. The aninvolved kioney apcoors mnrannrkable. kotrmmtatiyt snnticns are subnittod. Homary ef Rert.onr: 1....! JK arremarhrrie kidney Hiaso statn Kosults/tsuonts: NinroranreHane Reru.I Comurer." .:::: ::.: :.. A: .id : : 1:7 1 r .! : M +* : Page 2 of 2 END OF REPORT

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+Accession #: Date of Procedure: Date of Receipt: Date of Report: Account #: Billing Type: Additlonal Copy to: TCGA-BP-4977 Clinical Diagnosis & History: ith left upper pole renal mass.. Specimens Submitted:. 1: KIDNEY, LEFT UPPER POLE, PARTIAL NEPHRECTOMY 2: "DEEP MARGIN COLLECTING SYSTEM ON SINUS FAT." BIOPSY DIAGNOSIS: 1. Kidney, Left upper pole, partial nephrectomy Tumor Type: Renal cell carcinoma - Conventional (clear cell) type Fuhrman Nuclear Grade: Nuclear grade III/IV Tumor Size: Greatest diameter is 4.5 cm. Local Invasion (for renal cortical types):. Not Identified Renat Vein Invasion: Not present for evaluation.. Surgical Margins: Free of tumor Non-Neoplastic Kidney: Multlple papillary adenomas are present.. Adrenal Gland:. Not Identified Lymph Nodes: Not identified Staging for renal cell carcinoma/oncocytoma:. pT1 Tumor <=: 7.0 cm in greatest dimension limited to the kidney. 2. "DEEP MARGIN COLLECTING SYSTEM ON SINUS FAT," BIOPSY - Benign urothelial mucosa with chronic inflammation.. - Benign renal parenchyma.. Page t of 2
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+Note: has reviewed select slides in Part 1 of this case and concurs with the diagnoses.. TATTEST THAT THE ABOVE DIAGNOSIS IS BASED UPON MY PERSONAL EXAMINATION OF THE SLIDES (AND/OR OTHER MATERIAL), AND THAT I HAVE REVIEWED ANO APPROVED THIS REPORT. Gross Description: 1.)The specimen is received fresh and is labeled "Left upper pole parlial nephrectomy peritumoral fat". It consists of 3 11.5 x 7.2 x 5.6 cm wedge shaped porlion of kidney with overlying perinephric fat. The kidney measures 6.5 x 5.5 x 4.6 cm. There is a suture marking the deep margin. The margin is inked black and the specimen is serially sectioned to reveal a well-circumscribed yellow tumor with ereos of hemorrhage and focal areas of cystification, measuring 4.5 cm in greatest dimension. The tumor is confined by  the renal capsule. The clearance trom the resection margin is 0.2 cm. The remainder of the specimen consists of renal parenchyma with a white well defined 0.4 cm subcapsular lesion, located 0.9 cm away from the main tumor.  Representatively submitted. Portions of the tumor are submitled for TPS.. Summary of sections:. T - tumor M - margin  RS - representative sections 2.) The specimen is received in formalin, labeled "deep margin collecting system on sinus fat", and consists of one irregularly shaped fragment of white-tan soft tissue with attached yellow lobulated adipose tissue, measuring 1.7 x 1.2 x 0.2 cm. Entirely submitted. Summary of sections:. U -- undesignated. Summary of Sections: Part 1:  KIDNEY, LEFt UPPER POLE, PARTIAL NEPHRECTOMY Block Sect. Site PCs 1 m 1 rs 1 4 t 4 Part 2:"DEEP MARGiN COLLECTING SYSTEM ON SINUS FAT," BIOPSY Block Sect. Site pCs 1 u 1 Page 2 of 2 END OF REPORT

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+page 1 / 1 Department of Cancer Pathology. copy No. Date: Examination: Histopathological examination. Internal invoice No. Value of diagnostic procedure Examination No.: Patient: XXX PESeL: XXX Age: Gender: F 1cs-0-3 Material: 1. Multiple organ resection -- left breast with axillary tissues Unit in charge: Csvcinoma b fisnuHmg dvct,N0s 85o0f'3 Physician in charge: Sits! bUast, Nos C50.9 ih 4f1sf1 Material collected on: Material received on: ' Expected time of examination: up to 8 working days Clinical diagnosis: Cancer of the left breast. . Examination performed on: Macroscopic description:. Left breast sizdd 16.8 x 15.3 x 5.2 cm removed along with axillary tissues sized 10 x 6 x 5 cm and a 16.2 x 9.8 cm skin flap and a. fragment of the muscle sized 4 x 3 cm. Weight 620 g.. Tumour sized 3.5 x 3 x 3 cm found in the inner upper quadrant, 1 cm from the inner boundary, 0.2 cm from the base and 0.8 cm from the skin.. Microscopic description: Carcinoma ductale invasivum - NHG3 (3+3+3/36 mitoses/10 HPF - visual area: 0.55mm' Mamilla sine laesionibus. UUID:3DB4F9E-C918-4913-93E8-F18FF22CBA7C TCGA-D8-A1XK-01A-PR Redacted Glandular tissue with lesions of the type mastopathia fibrosa and cystica. Invasive lesions 0.1 cm away from the base. Axillary lymph nodes: Metastases carcinomatosae in Iymphonodis (No t/xv). Histopathological diagnosis: Carcinoma invasivum mammae sinistrae. invasive ductal carcinoma of the left breast  Metastases carcinomatosae in lymphonodis axillae (NHG3, pT2, pN1a). Cancer metastases in axillary lymph nodes.. Compliance validated b: Examination performed on: Results of immunohistochemical examination: No estrogen receptors found in neoplastic cell nuclei. No progesterone receptors found in neoplastic cell nuclei.. HER2 protein stained with HercepTestTM by DAKO. Negative reaction in invasive carcinoma cells ( Score = 0 ). Compliance validated by:1 CONTACT YOUR DOCTOR WITH THIS.M

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+A description for each data field can be found in the 'Data description' worksheet (yellow tab). Sample Collection Details  Histology ar Sample Number  Sample Sample Site of Site of Year of Age at  Sample Days to Type  PreparatioTissue  Primary Sample  Sample Comments Procedure n (Event) Collection Collection Date (yrs) TUMOUR FF RENL BUFFY FF RENL
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+nd staging Days to Type of Site of Tumour  Histology Grade/  Pathologic Diagnosis Procedure  Primary Size (cm) Differentiat al T. (Histology) ion RESECT Right kidney Papillary renal ca., eosinophilic type x T2,NOS 14.5 RESECT  Right kidney 14.5 Papillary renal ca., eosinophilic type x T2,NOS
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+Pathologic Clinical M  Histology Comments Slide URL aI N NX  MO Furhman grade IlI. Extensive chronic pyelonephritis. NX MO Furhman grade lII. Extensive chronic pyelonephritis.

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+AlU t1o13 Collection Date: FINAL DIAGNOSIS: Renal mass, Left, partial Nephrectomy -- A.  renal CeLl CarcinOmA, with fEatures Of both papiLLAry (PapilLARy Type 2) AnD Clear CELl Pu TS8. clea cll festuies (CONVENTIONAL) TYPES (ses comment). CARCINOMA MEASURES 1.7 cm IN GREATEST DImENSION. : 5% B. CARCINOMA IS CONFINED TO THe KIDNEy. c FUHRMAN NUCLEAR GRADE IS 3 OF 4. D. E. ALL SURGICAL MARGINS OF RESECTION ARE NEGATIVE FOR CARCINOMA. F.  NO LyMPHOVASCULAR INVASION IS SEEN G LimIteD bacKgrOund RENal Parenchyma with mODerate mIxed And fOCaLLy XANTHOGRANULOMATOUS INFLAMMATION, INCLUDING HEMOSIDERIN-LADEN MACROPHAGES. H. PATHOLOGIC TNM STAGE (AJCC 7th EDITION): pT1a NX MX. COMMENT: Histologic sectlons show a malignant neoplasm composed of architecturally-crowded papillae of eosinophillc ceils with. abundant stromal macrophages. Moreover, focl of cytologically malignant cells with distinct clear cell features are also. identlfied in the periphery of thls lesion. Results of paraffin section immunohistochemical analysis aiso highlight both cell populations (see microscoplc description), thereby supporting the above rendered diagnosis. CASE SYNOPSIS: SyNOPTIC DATA - PRImARy KiDNEy TUmOrS UUID:F0882D8F-D5D3-4DCC-9E7B-EE6D6557128D Redacted TCGA-B1-A656-01A-PR SpeCImen TypE: Partial nephrectomy LATERALITY: Left TUMOR SITE: Not specified FOCALITY: Unifocal TUMOR SIZE: Greatest dimension: 1.7 cm Additional dimensions: 1.5 x 1.5 cm. macroscopic extent Of tumor: Tumor limited to kidney HIstologic type: Papillary renal cell carcinoma. HISTOLOGIC GRADE (Fuhrman Nuclear Grade): G3 PATHOLOGIC STAGING (pTNM): pT1a pNX Number of regional lymph nodes examined: 0 pMX MARGINS:  Margins uninvotved by invasive carcinoma ADRENAL GLAND: Not present LYMPH-VASCULAR INVASION (LVI): Absent/not identified KiDnEy-REsidual TUmor (r):  RO

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+UUID: F9C1971C-5BE2-4722-9A6C-CF4A4AD04352 TCGA-OR-A537-01A-PR Redacted Patient Name: Sex: Female Macroscopy Two vessels containing a material immersed in tormaldehyde solution, described as following: 1. product of en-bloc resection of the right kidney and an adrenal mass, weighting 503 g and measuring. 18 x 12 x 7 cm, previously sectioned. The tumor mass measures 12 x 7.5 x 7 cm (and weights 503 g) The cut surface is characterized by a partially encapsulated mass, intiltrating the surrounding fatty tissue, very close to the surgical margins. The tumor mass is multilobulated, brownish-yellow colored. with necrotic areas. The normal adrenal tissue is not clearly distinguishable. The right kidney is. attached to the mass, but no signs of invasion are seen. The surgical margins were stained with green indian ink. 2. Hepatic margin, consisting of two brownish fragments, measuring 2 x 1 x 0.4 cm. Conclusion: Product of right nephrectomy and right adrenal mass resection: Adrenocortical carcinoma with the following features: IcDO-3 Largest diameter -- 12 cm. Carcinorro, adnnol Nuclear grade (Fuhrman) -- 4 83703 Corticis Diffuse architectural pattern - present Site? BAtrenas g land. :Clear cells in < 25% of the neoplasm -- present cortee 0 474.Z .Areas on necrosis - present AtO y/80f1 3 .Mitotic count -- 3 in 50 H.P.F. Atypical mitosis - present  Capsular invasion - present  Venous invasion -- present

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+SPECIMENS: CARD CASE COMMENT: FIRST PATHOLOGY DATE FIRST PATHOLOGY REPORT: PRIMARY PATHOLOGIST: 2 DIAGNOSIS-1 M9593 MALIGNANT LYMPHOMA, NOS SPECIMEN-1 T07 SPLEEN
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+CHAI AD ONRNAVAA  RANGH ) to PARHICLAATE XYES ONO TSIARAFFIN ....4h1o. HARRIATE AMPLE. LWES 43. MFLASTIC AVERAGE: UNEVALUAELE O CRURERIIG CRIL COUNT DNOT APPLICAnLE  MYELOMLAST8 A PnOMYELOCYTE3 D) MEGAKAAYODLASTS CTMONOULASTS : PROMONIXYTES (JIYMPHHODLASTS + LYNPHOCYTES CLONES:YES Ono _  not eyaluable AS A  OF ALL NUCLEATEO CELLS (ANC) 0 t0 C] 1030 -5 55 EOSINOPHILIA: Onone QSPAnSE ) MAAKEO PER HPF (AM x tiNr) 010  1030 30-100 > 100 OASOPHILIA: ONONE SPARSE OMARKEO NOnMAL OA DTAPLAOTICHRMOPOIEGIS NOt EVALUAOL (Cylo/ngy unAyallntle) M:e natio: .... CEUURARITY low NORMAL HIQH Dyspl.  PLASMA CELLS INCAEASED QOECHEASED QRANULOCYIES. Q0 D1 04 Oy EOSINOPHILS INCREASEO QOECAEASED ERYTHROIDS. 00 D2. Oy dR BASOPHILS CINCREASED DDECnEASED MONOCYTES: 01 05 Oy DN HISTIOCYTES OINCREASED QOECREASED LYMPHIOCYTES: 00 00 04 5 IRON (IF EYALUABLE INCREASEO ODECAEASED MEGAKAAYOCKTES/HPF: 2.2 OTHER. OINCREASEO QDECREASED RANGE: MEAN FMYRLOFIOnOGIS. NOT EVALUABLE (spociAl staIns unavallablo) TINALTRATESOTHER THANNOTEOAROYEUNDSRLEUKEMICA CELLCOUNT: HAEPAS/GIEMSA DRetIcULin STAin  COLLAGEN STAIN ANONE sheets ONODULES ONUMOER: / Hpf: total no. QRADE OPARATRABECULAR Ointenstitial O 1  NO INCREASE IN RC TICULIN OLYMPHOID PIASMACYTIC CARCINOMA O? * FOCAL INCREASE IN RETICULIN AEACTIVE ONEOPLASTIC BOADERLINE O3 + DIFFUSE INCREA$E iN RETICULIN PROPORTION OF SEGTION INFILTRATED:E Dother . O 4  DIFFUSE INCREASe IN RETICULIN AND COLLAGEN S  COLIAGEN CONSPICUOUS,ARCHITECTURE DISTORTION 3 RIGHT ILtAC CREST % AVERAGE:  S6 : GRAOE 5a PLUS NEW DONE FORMATION (OSTEOSCLEROSIS) LEFT ILIAC CAEST % ASPIRATE: KMARROWIAPRINTASHIEARDIFICOUNT % % ONOTAYAILADLE N 'MOnoalAsts,+fy: NEUTRO, Eos. BASO 0,6. rr MYEL OSLASTS MONOCYTES . CELLSCOUNTED 1.0 PROMYELOCYTES NUC. ERYTHROID 21.2 mk.inc. 5.0 0.2 PLATELETS MYELOCYTES LYMPHORLASTS: H+ree. MEGAKARYOCYTES .inc. 9.4 0.4 METAMYELOCYTES LMPHOCYTES5 R MEGAKARYOBLASTS 28.6 0.6 STASS PLASMA CELL'S 0.6 21.6 AUEA nOOS SEGMEnTED Histiocytes 02 ETHERAPY :.:  HCEOR 12.5 SIDEAOBLASTS H08 - ONO DCp ORT TRANSP. 8.65 OTHEn. WBO x 10L  x 10/L Last date: CYTOCHEMICAL CELLS: % PX $8 CAE ANBE ANAE AP TAAP PAS OtheR SCORE( TOTAL: Onot: AVAILADLE DlAdnosiax(eroysns Bdeirabbreylated keys) ORDERLY GRANULOPOIESIS AND BRXTHROPOIESIS.  MODERATE MEGAKARYOCYTIC HYPERPLASIA. NEGATIVE FOR LYMTHOMA. CELLULARITY SSZ. LYMPHOCYTES S.4X. RIGHT AND LEFT ILIAC CRKET BtOFSt$T,SECTIONS, IMPRIHTS AND SMEARS IMMUNO PHENOTYPE: SIgnED. FEA SIGNED. PATHOLOGY FILe

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+SURGICAL PATHOLOGY Case Number : Redacted Diagnosis: A: Pancreas, bile duct margin, biopsy - No tumor seen. B: Pancreas pancreatic duct margin, biopsy - No tumor seen C: Superior pancreatic lymph node, biopsy - One lymph node with no malignancy identified (0/1) D: Aortocaval lymph node, biopsy - One lymph node with no malignancy identified (0/1) E: Pancreas, duodenum, pancreaticoduodenectomy. Tumor Histologic Type: adenocarcinoma. Histologic grade: moderately differentiated Tumor size: 3.5 cm Icd-o-3 Extent of invasion: adenocarcinomg, Nos Peripancreatic soft tissues: present Duodenum: identified. 8l40|3 Ampulla: identified Sik: Pancregs, huad Lymphatic Invasion: not identified. cQ5,o Venous Invasion: not identified 81a3|ia ep Perineural Invasion: present Margins:. Pancreatic neck: negative. Bile duct: negative Posterior pancreatic surface (deep radial margin): negative (<1 mm) Peripancreatic soft tissues: negative (<l mm). Proximal (gastric): negative Distal (duodenal): negative Regional lymph nodes:. Total number with metastasis: 0
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+Total number examined: 8 (including specimens A and B) AJCC PATHOLOGIC TNM STAGE: pT3 pNO pMx Note: This pathologic stage assessment is based on information available at the time of this report, and is subject to change pending'clinical review and additional information.. Intraoperative Consult Diagnosis: An intraoperative consultation is requested by FSAl: Pancreas, bile duct margin, biopsy - No tumor seen FsBl: Pancreas, pancreatic duct margin, biopsy. - No tumor seen'. Frozen Section Pathologist:, Clinical History: The patient is a :year-old with pancreatic head cancer. Gross Description: Specimen A is received fresh in the frozen section room appropriated labeled "bile duct margin for frozen section" and consists of a 2.2 x 0.6 x 0.6 cm red/tan soft tissue fragment with no lumen. The specimen is entirely submitted for frozen section and resubmitted in block FsAl,. Specimen B is received fresh in the frozen section room appropriately labeled "pancreatic duct margin for frozen section" and consists of a 1.0 x 0.8 x 0.3 cm red/tan soft tissue fragment. The specimen is entirely submitted for frozen section and resubmitted in block Fsbl, Specimen c is labeled as "superior pancreatic lymph node, biopsy". Received is a single pink/tan soft tissue fragment with focal erythematous areas and cautery, 1.2 x 0.8 x 0.5 cm. The specimen is serially sectioned and the entire specimen is submitted in block C1, Specimen D is labeled as "aortocaval lymph node, biopsy" and consists of a white to pink/tan soft tissue fragment 2.2 x 0.9 x 0.7 cm, with focal erythematous areas and cautery. The specimen
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+is serially sectioned and submitted in block D1,. Specimen E is labeled "Whipple specimen." Specimen fixation: formalin Specimen type: Whipple. Organs received (Whipple Specimen): stomach (3.5 cm long x up to. 6.5 cm in circumference), head of pancreas (4 x 3 x 1.5 cm),. duodenum (15 cm long x up to 6.7 cm in circumference), common. bile duct (3.6 cm long x 1.7 cm in circumference proximally) Orientation: common bile duct-yellow, pancreatic body. margin-blue, uncinate-black, peripancreatic soft tissue-green Tumor location: head. Tumor dimensions: 3.5 x 3.0 x 2.5 cm Gross appearance of tumor: solid, firm, variegated, tan/white; There is minimal amount of normal pancreas present.. Extent of invasion:. Confined / non-confined to the pancreas: confined Involvement of the ampulla: absent Involvement of the duodenum: absent Involvement of the bile duct: possibly into wall Involvement of adjacent vessels: n/a. Spleen (if applicable): n/a Gallbladder (if applicable): n/a. Stomach (if applicable): uninvolved Surgical margins:. Pancreatic body: negative (0.2 cm) Uncinate (Retroperitoneal): negative (<0.1 cm).
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+Common Bile duct: negative (0.2 cm) Proximal margin (stomach): negative (3.5 cm) Distal margin (duodenum): negative (9.3 cm) Peripancreatic soft tissues: positive Lymph nodes: multiple lymph node candidates are identified ranging in size from 0.5 up to 2.0 cm Other remarkable findings: none Digital photograph taken: no Tissue submitted for special investigation: no Block summary: El, E2 - proximal (stomach) margin, en face E3 - distal (duodenum) margin, en face E4 - pancreatic body margin, en face E5 - uncinate margin with closest approach of tumor, perpendicular E6 - closest approach to common bile duct margin, perpendicular, full thickness, bisected. E7 - remaining common bile duct margin, en face E8-e9 - mass with relationship to common bile duct and duodenum, one section, bisected. E10 - tumor with pancreatic duct El1-E12 - tumor with relationship to ampulla E13 - two lymph node candidates, one inked black and both bisected E14-El5 - largest lymph node candidate, serially sectioned E16 - two lymph node candidates E17 - one lymph node candidate, bisected

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+Department of Cancer Pathology. copy No. Date: Examination: Histopathological examination (cito) Internal invoice No. Cost of diagnostic procedure Examination No.: Patient: XXX pesel: XXx Age: Gender: F Material: Multiple organ resection - left breast and axillary tissues ICs-0-3 cavCiOmn hf1f^txy dut,n0s 85vtf3 Unit in charge: Physician in charge: ref. No. Material collected on: Material received on: Expected time of examination: 5 working days Clinical diagnosis: Examination performed on:. Macroscopic description: Left breast, sized 22 x 18 x 9 cm, removed with axillary tissues sized 10 x 11 x 5 cm and with a skin flap of 23 x 19 cm. Nipple retracted, skin resembling orange peel.. Tumour sized 6.0 x 6.0 x 3.5 found on the border of upper quadrants, located 3.0 cm from the upper boundary, 1.5 cm from the base and 0 cm from the skin. Lymph nodes 1.8 cm in length.. Microscopic description: Carcinoma ductale invasivum - NHG3 (3 + 2 + 3 / 35 mitoses/10 HPF - visual area 0.55 mm). Mamilla sine laesionibus. Glandular tissue showing lesions of the type mastopathia fibrosa et cystica. AXILLARY LYMPH NODES: Metastases carcinomatosae in lymphonodo (No I/xxi). Infiltratio capsulae lymphonodi et telae perinodalis. Histopathological diagnosis: Carcinoma ductale invasivum mammae sinistrae. invasive ductal carcinoma of the left breast.  Metastases carcinomatosae in lymphonodo (No I/xxi) (NHG3, pT3, pNla). Cancer metastases in the lymph nodes (No I/XxI) UUID:18198706-8844-452A-8F58-8880A239717C TCGA-D8-A1Y1-01A-PR Redacted
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+e 2 / 2 Results of immunohistochemical examination: Estrogen receptors found in 10-75% of neoplastic cell nuclei. Progesterone receptors found in over 75% of neoplastic cell nuclei. HER2 protein stained with Ventana's Pathway HER-2/neu (4B5) rabbit antibody. Negative reaction in invasive cancerous cells (Score=3+). C'ompl CONTACT YOUR DOCTOR WITH THIS REPORT!

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+ID03 'srceome, drsttelial NoS 8/2013 UUID:0B1A1E8B-78FD-43B8-A6B1-2E7EB251FD52 TCGA-4Z-AA87-01A-PR Redacted Sete: MadserNos C67.J Ht~ 3/18/14 Collect date: (MM/DD/YYYY) PATHOLOGY REPORT: PRIMARY SITE: Bladder 1 - "Left ureteral margin, paraffin from preoperative exam: Free of neoplastic involvement.. 2 - "Right ureteral margin, paraffin from preoperative exam: Free of neoplastic involvement. 3 - "Prostate + bladder'': High-grade urothelial carcinoma of the bladder characterized as follows: Measure of neoplasia in its major axis: 6.5 cm.. Ulceration present. Extensive areas of necrosis. Involvement of: bladder. all prostate right seminal vesicle and fibroadipous peri-visceral connective tissue. Neural infiltration present. Lymphatic vascular invasion doubtful.. Sanguineous vascular invasion not detected. Surgical margins free of neoplastic involvement.. 4 - "Left lymphadenectomy": Free of neoplastic involvement (0/3) 5 - "Right lymphadenectomy": Free of neoplastic involvement (0/2). bv 12f2of13 criterk

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+Surgical Pathology Histopathological Examination Pre-Op Diagnosis : Right Renal Mass On Native Kidney.Right Hydronephrosis Of Transplanted Kidney Order Physician. Specimens : Kidney, Right. Frozen Diagnosis. Report : GROSS EXAMINATION: The specimen is received fresh in a container labeled with the name of the patient and labeled as kidney, right. The specimen consists of a kidney and attached perinephric fat. The kidney measures 6 x 3.8 x 2.2 cm and weighs 47 g. The ureter and vascular margins of resection are submitted in block 1. The renal sinus/hilar margin is submitted in block 2. Sectioning shows an oval tan mass in the mid lateral aspect which measures 3.1 cm in greatest dimension. The mass. bulges against the capsule but is not grossly adherent to the capsule. A section of capsule overlying the mass is submitted in block 3. The mass does not grossly involve the. renal sinus. Sections of the mass are submitted in blocks 4-7. The pelves and calyces are not grossly dilated. The cortex averages 0.l cm. A random section of kidney is submitted in block 8. Sectioning through the attached fat shows no lymph nodes or adrenal tissue. This case was reviewed with DIAGNOSIS BASED ON GROSS AND MICROSCOPIC EXAMINATION: Kidney, right, nephrectomy:  Papillary renal cell carcinoma, type I, Fuhrman grade 2, 3.1 cm, confined to kidney with negative margins (see cancer case summary checklist below). KIDnEy: Nephrectomy, Partial or Radical (Version 3.l.0.0) PROcEuRE: Radical nephrectomy SPECIMEN LATERALITY: Right THIS CONFIDENTIAL AND PRIVILEGED DOCUMENT/INFORMATION IS PROTECTED BY FEDERAL AND STATE LAW.  UNAUTHORIZED DISCLOSURE, DISSEMINATION OR DUPLICATION IS PROHIBITED Page 1 of 2
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+TUMOR SITE: Middle TUMOR SIZE: Greatest dimension: 3.1 cm TUMOR FOCALITY: Unifocal MACROSCOPIC EXTENT OF TUMOR: TumOr limited to kidney HIsToLogic TypE: Papillary renal cell carcinoma, type I SARCOMATOID FEATURES: Not identified HISTOLOGIC GRADE (FUHRMAN NUCLEAR GRADE): Grade 2: NuClei slightly irregular, approximately 15 microns, nucleoli evident. MICROSCOPIC TUMOR EXTENSION: Tumor limited to kidney. MARGINS:  Margins uninvolved by invasive carcinoma. LYMPH-VASCULAR INVASION: Not identified. PATHOLOGIC STAGING (pTNM): Primary Tumor (pT): pTla: Tumor 4 cm or less in greatest dimension, limited to kidney. Regional Lymph Nodes (pN): pNx: Cannot be assessed, no nodes submitted or found. Distant Metastasis (pM): Not applicable. PATHOLOGIC FINDINGS IN NONNEOPLASTIC KIDNEY:  End stage renal renal disease with numerous sclerotic glomeruli,. thyroidization of tubules, fibrosis, and chronic inflammation.. COMMENT: This case was delayed to perform a panel of immunostains which shows the tumor cells to be positive for ck7, EMA, pankeratin, vimentin, CDl0, Rcc, pAx8, and P504S. They are negative for wTl. Positive and negative controls stained appropriately. Based on the histologic appearance and immunoprofile, this neoplasm is best interpreted as papillary renal cell carcinoma, type I. A fragment of tumor is associated with the edge of the soft tissue on the section of the ureteral and vascular margins. Multiple step sections are examined. Based on the very peripheral location of the tumor with no macroscopic evidence of involvement of the medulla or renal sinus, this tumor focus is best interpreted as a knife carry-over or a floater. Intradepartmental consultation obtained. Results communicated to

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+ UUID:BF3E21AE-D9DC-4011-908A-32C6C1FE10FB 1C D-O-3 TCGA-BC-A8YO-01A-PR Redacted Caru +nn', die ratee. Welar NDS S1703 SURGICAL PATHOLOGY Siti dlur Cx5.0 Case Number : yJ y13|4 Diagnosis: A: Gallbladder, cholecystectomy. - Benign gallbladder with no significant pathologic abnormality - No carcinoma identified B: Liver and adherent ascending colon and retroperitoneal soft tissue, segments 5 and 6, partial hepatectomy and en block resection Histologic tumor type/subtype: hepatocellular carcinoma. Histologic grade: Grade 3 (Edmondson and Steiner). Number of tumors: 1 primary lesion with multiple subcentimeter satellite lesions Tumor size: 1l cm Tumor location: Segments 5 and 6. Tumor necrosis: present (involves approximately 20% of microscopically examined tumor). Worst tumor differentiation: grade 3 (Edmondson and Steiner) Vascular invasion: present, macrovascular. Perineural invasion: not identified. Capsular invasion: Present Margins: uninvolved by carcinoma; tumor is 8 mm from the closest. inked retroperitoneal soft tissue margin and 1.7 cm from the hepatic resection margin (colonic and vascular en face margins negative for tumor) Lymph nodes: 1l benign lymph nodes present within pericolonic adipose tissue (0/11) Satellite lesions: present (multiple subcentimeter lesions). Background liver: chronic hepatitis, etiology unknown, grade 1,. stage 2 (see comment).
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+Other extrahepatic spread: present, tumor focally extends through the capsule/visceral peritoneum to involve fibrous adhesions (no microscopic evidence of tumor involvement within underlying colon and soft tissue) Additional findings: - Eleven benign colonic lymph nodes (0/11) AJCc Pathologic TNM stage: pT4 pNx NoTE: This pathologic stage assessment is based on information. available at the time of this report, and is subject to change pending clinical review and additional information.. C: Bowel, ileum, resection - Benign small bowel with fibrous serosal adhesions, acute. serositis, and serosal hemorrhage with hemosiderin laden macrophages - No carcinoma identified Comment: Microscopic examination of non-neoplastic liver reveals fibrotic portal tracts with mild bile ductular proliferation and an. associated chronic lymphocytic infiltrate consisting almost entirely of lymphocytes. No prominent plasma cell infiltrate is identified.. No piecemeal necrosis is identified. There is mixed macrovesicular and microvesicular steatosis involving less than 5% of the hepatic parenchyma and no features are present to suggest involvement by. steatohepatitis. A trichrome stain highlights areas of periportal fibrosis with no evidence of bridging fibrosis or cirrhosis. A reticulin stain also highlights periportal fibrosis but shows an otherwise normal hepatic. plate thickness. A DpAs stain shows no evidence of alpha-1- antitrypsin deficiency (no DpAs positive globules identified within hepatocytes). An iron stain shows a mild increase in hepatic. iron (grade 1 of 4). The findings are consistent with chronic hepatitis, grade l, stage 2. The differential diagnosis includes viral hepatitis and autoimmune hepatitis. Correlation with clinical history and laboratory studies is recommended to determine the. etiology of the chronic hepatitis. Clinical History: The patient is a -year-old female with a clinical diagnosis of. HCC.
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+Gross Description: Specimen A is received with one appropriately labeled container additionally labeled "gallbladder".. Previously opened or disrupted: No. Measurements: 4.6 x 3.1 x 0.9 cm External surface: Yellow/green, smooth and glistening Luminal contents: Green viscous fluid Stones present: No Mucosa: Green and velvety Wall thickness: 1 mm Other comments: No Block #: Al - Cystic duct margin and representative section Tissue remains in formalin. Specimen B is received in formalin appropriately labeled "segments 5 and 6". Specimen Type: Segmentectomy and right hemicolectomy Specimen Weight: 745 grams Measurement: 12.5 x 11 x 7 cm segment of liver with attached right hemicolectomy consisting of 3 cm of terminal ileum and 14 cm of cecum and ascending colon. Orientation: Anatomical. The liver resection margin is inked blue. Capsule: There is a 14.5 cm yellow bulging defect with adherent mesenteric fat and colon. Where the tumor is adherent to the mesentery, the surface margin is inked green. The remainder of the capsule is tan/brown and smooth. Beneath the capsular defect there is an 11 x 9 x 6.5 cm white to tan nodular partially circumscribed mass with multiple adjacent budding nodules. Mass: Further sectioning reveals a blood vessel that is plugged with tumor thrombus. Additionally, the mass extends through the capsule to within 1.1 cm of the green inked mesenteric margin. Where the mass is adherent to the bowel, it appears to extend to but not grossly invade the capsule. The tumor is 1.7 cm from the blue inked hepatic resection margin, and widely free of the distal margin. Adjacent liver tissue: Tan/brown and unremarkable. The colonic mucosa is pink/tan with normal folding. The appendix is surgically absent.. Major portal vein/ hepatic vein: Gallbladder: See specimen A. Block Summary: B1 - Closest blue inked resection margin, perpendicular B2 - Proximal colonic margin, en face
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+B3 - Distal colonic margin, en face. B4 - Tumor in relationship to the capsule and adjacent uninvolved tissue B5 - Tumor within a blood vessel. B6 - Representative sections of multiple adjacent tumor nodules B7 - Additional tumor nodule. B8 - Uninvolved liver away. B9-Bl0 - Tumor in relationship to the green soft tissue margin, perpendicular Bll - Tumor in relationship to the bowel B12 - Tumor in relationship to lateral sidewall muscle B13 - Vascular margin with thrombus, en face B14-B15 - Multiple colonic lymph nodes Container c is additionally labeled "ileum." It holds a 6 cm in length x 2.1 cm in diameter segment of small bowel. There is a 2.5 x 1.8 cm area of hemorrhagic adhesions 0.5 cm from the closest mucosal margin. The serosal surface is pink/tan and smooth. Opening reveals pink/tan mucosa with normal folding. Beneath the hemorrhagic adhesions, the cut surface is yellow fat. Block summary: c1-c2 - unoriented mucosal margins, en face c3 - hemorrhagic adhesions, en face. 1243 113

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+Sample Number Sample Type TUMOUR Diagnosis  Renal cell carcinoma, papillary type (types 1 and 2) Year of Sample Collection Age at Sample Collection (yrs)  Days to Procedure Date  Days to Diagnosis Type of Procedure Resect  Site of Tissue/Primary (Histology)  Left kidney Tumour Size (cm) 3  Histology  Renal cell carcinoma, papillary type (types 1 and 2)  Grade/Differentiation III  Pathological T T1a  Pathological N  NX  Clinical M  MO Histology Commentse Grade/Diff: Fuhrman grade 3/4. Sample Number Sample Type  BUFFY Year of Sample Collection. Age at Sample Collection (yrs)  Days to Procedure Date. Days to Diagnosis UUID:E24C3E1C-D148-4C68-A691-CD1AF8014C4B TCGA-HE-A5NH-01A-PR Redacted IcDo-3 8QbD/3 Site  Kidnuy NbS C64.9 OpO`xnJ3 W y7j3 riteria iagnosis ual/Symhr ase is cir