isalgo/airr_hip

HIP — TCRβ repertoires with CMV serostatus and HLA typing

Bulk TCRβ immunosequencing of 786 subjects with known cytomegalovirus (CMV) serostatus and HLA-A/HLA-B typing — the cohort of Emerson et al. 2017 (666 discovery + 120 validation subjects). Provided as a benchmark for reproducing HLA- and CMV/HLA-associated TCR biomarker discovery: learning public TCRβ sequences that predict CMV exposure and infer HLA alleles.

According to PubMed, the source study is Emerson RO, DeWitt WS, Vignali M, Gravley J, Hu JK, Osborne EJ, Desmarais C, Klinger M, Carlson CS, Hansen JA, Rieder M, Robins HS. "Immunosequencing identifies signatures of cytomegalovirus exposure history and HLA-mediated effects on the T cell repertoire." Nature Genetics 2017;49(5):659–665. DOI: 10.1038/ng.3822 · PMID 28369038

The benchmark task

The paper's central results, to reproduce here:

1. CMV status classification — from a subject's catalog of TCRβ sequences, diagnose CMV serostatus (a set of public CMV-associated TCRβ sequences, Fisher's-exact-selected, scored per subject). High sensitivity/specificity in both the discovery cohort and a held-out validation cohort.
2. HLA allele inference — predict a subject's HLA-A and HLA-B alleles from HLA-associated public TCRβ sequences.
3. CMV × HLA — CMV-associated TCRs are HLA-restricted, so the two signals interact.

cmv and hla in the metadata are the labels; the per-subject repertoires are the input.

Layout

corr/<sample_id>.txt.gz     786 per-subject TCRβ clonotype tables (gzipped, tab-separated)
metadata.txt                all 786 subjects — sample_id, age, race, sex, cmv, hla
metadata.cmv.txt            subset with known CMV serostatus (the CMV-classification cohort)
metadata_A02.txt            subset typed HLA-A*02 (an HLA-association working set)
pool.aa.summary.txt         clonotype-incidence histogram (how many clonotypes are shared by N subjects)

Repertoire file columns (corr/*.txt.gz, VDJtools style)

column	meaning
count	reads supporting the clonotype
freq	clonotype frequency in the sample
cdr3nt	CDR3 nucleotide sequence
cdr3aa	CDR3 amino-acid sequence
v / d / j	IMGT gene calls (TRBV, TRBD, TRBJ)
VEnd / DStart / DEnd / JStart	germline segment boundaries in the CDR3

Metadata columns

column	meaning
file_name	path to the subject's repertoire (corr/<sample_id>.txt.gz)
sample_id	subject id (HIP…)
age	age in years, or NA
race	self-reported race/ethnicity, or NA
sex	male / female
cmv	CMV serostatus: + (seropositive), - (seronegative), or NA — a task label
hla	typed HLA-A/HLA-B alleles (2-digit), comma-separated — a task label
..filter..	preprocessing tag (corr:2:0.05:all — error-corrected, singleton-filtered)

Origin & attribution

The subject-level TCRβ repertoires and metadata originate from the Emerson et al. 2017 cohort, released via Adaptive Biotechnologies' immuneACCESS. Repertoires here are the error-corrected (corr) clonotype tables. If you use this dataset, cite the paper above and acknowledge the immuneACCESS source; observe the immuneACCESS data-use terms. Redistributed for benchmark reproduction, not as an original data source.

Notes

• A 12.8 GB pooled amino-acid clonotype catalogue (pool.aa.table.txt, one row per unique CDR3aa clonotype with an incidence = number of subjects it occurs in) exists upstream but is not included here — it is a derived aggregate rebuildable from the per-subject files. The incidence histogram it summarises (pool.aa.summary.txt) is included.