Clinical NER Dataset
Collection
Publically available clinical NER datasets • 4 items • Updated • 1
text stringlengths 284 2.66k | tokens listlengths 53 546 | entity stringlengths 124 3.7k | filename stringlengths 11 15 |
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Identification of APC2, a homologue of the adenomatous polyposis coli tumour suppressor.
The adenomatous polyposis coli (APC) tumour-suppressor protein controls the Wnt signalling pathway by forming a complex with glycogen synthase kinase 3beta (GSK-3beta), axin/conductin and betacatenin. Complex formation induces the ... | [
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A common MSH2 mutation in English and North American HNPCC families: origin, phenotypic expression, and sex specific differences in colorectal cancer.
The frequency, origin, and phenotypic expression of a germline MSH2 gene mutation previously identified in seven kindreds with hereditary non-polyposis cancer syndrome (... | [
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Age of onset in Huntington disease : sex specific influence of apolipoprotein E genotype and normal CAG repeat length.
Age of onset (AO) of Huntington disease (HD) is known to be correlated with the length of an expanded CAG repeat in the HD gene. Apolipoprotein E (APOE) genotype, in turn, is known to influence AO in A... | [
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"... | [{"text": "Huntington disease", "type": "SpecificDisease", "char_start": 16, "char_end": 34, "token_start": 4, "token_end": 5}, {"text": "Huntington disease", "type": "SpecificDisease", "char_start": 140, "char_end": 158, "token_start": 28, "token_end": 29}, {"text": "HD", "type": "SpecificDisease", "char_start": 160, ... | train/10051007 |
Familial deficiency of the seventh component of complement associated with recurrent bacteremic infections due to Neisseria.
The serum of a 29-year old woman with a recent episode of disseminated gonococcal infection and a history of meningococcal meningitis and arthritis as a child was found to lack serum hemolytic co... | [
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... | [{"text": "Familial deficiency of the seventh component of complement", "type": "SpecificDisease", "char_start": 0, "char_end": 58, "token_start": 0, "token_end": 7}, {"text": "bacteremic infections due to Neisseria", "type": "DiseaseClass", "char_start": 85, "char_end": 123, "token_start": 11, "token_end": 15}, {"text... | train/100562 |
Increased incidence of cancer in patients with cartilage-hair hypoplasia.
OBJECTIVE Previous reports have suggested an increased risk of cancer among patients with cartilage-hair hypoplasia (CHH). This study was carried out to further evaluate this risk among patients with CHH and their first-degree relatives. STUDY D... | [
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Genotype and phenotype in patients with dihydropyrimidine dehydrogenase deficiency.
Dihydropyrimidine dehydrogenase (DPD) deficiency is an autosomal recessive disease characterised by thymine-uraciluria in homozygous deficient patients and has been associated with a variable clinical phenotype. In order to understand t... | [
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Fibroblast growth factor homologous factor 2 (FHF2): gene structure, expression and mapping to the Borjeson-Forssman-Lehmann syndrome region in Xq26 delineated by a duplication breakpoint in a BFLS-like patient.
Borjeson-Forssman-Lehmann syndrome (BFLS) is a syndromal X-linked mental retardation, which maps by linkage ... | [
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Germline E-cadherin gene (CDH1) mutations predispose to familial gastric cancer and colorectal cancer.
Inherited mutations in the E-cadherin gene (CDH1) were described recently in three Maori kindreds with familial gastric cancer. Familial gastric cancer is genetically heterogeneous and it is not clear what proportion ... | [
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"... | [{"text": "familial gastric cancer", "type": "SpecificDisease", "char_start": 56, "char_end": 79, "token_start": 11, "token_end": 13}, {"text": "colorectal cancer", "type": "SpecificDisease", "char_start": 84, "char_end": 101, "token_start": 15, "token_end": 16}, {"text": "familial gastric cancer", "type": "SpecificDis... | train/10072428 |
A zinc finger truncation of murine WT1 results in the characteristic urogenital abnormalities of Denys-Drash syndrome .
The Wilms tumor -suppressor gene, WT1, plays a key role in urogenital development, and WT1 dysfunction is implicated in both neoplastic (Wilms tumor, mesothelioma, leukemias, and breast cancer) and no... | [
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... | [{"text": "urogenital abnormalities", "type": "DiseaseClass", "char_start": 69, "char_end": 93, "token_start": 11, "token_end": 12}, {"text": "Denys-Drash syndrome", "type": "SpecificDisease", "char_start": 97, "char_end": 117, "token_start": 14, "token_end": 17}, {"text": "Wilms tumor", "type": "Modifier", "char_start... | train/10077614 |
Mechanism of increased iron absorption in murine model of hereditary hemochromatosis : increased duodenal expression of the iron transporter DMT1.
Hereditary hemochromatosis (HH) is a common autosomal recessive disorder characterized by tissue iron deposition secondary to excessive dietary iron absorption. We recently ... | [
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Neurophysiologic follow-up of long-term dietary treatment in adult-onset adrenoleukodystrophy.
OBJECTIVE To monitor the effects of dietary treatment in adult-onset adrenoleukodystrophy (ALD) by means of somatosensory evoked potentials (SEPs) and motor evoked potentials (MEPs). BACKGROUND SEPs and MEPs have proved use... | [
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GCH1 mutation in a patient with adult-onset oromandibular dystonia.
The authors report a mutation in exon 5 of GCH1 in a patient with adult-onset oromandibular dystonia and no obvious family history of dystonia. The patient responded positively to treatment with L-dopa. These findings demonstrate that GCH1 mutations mu... | [
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Germline mutations of the APC gene in Korean familial adenomatous polyposis patients.
We extensively analyzed genomic DNA and messenger RNA (mRNA) from 62 unrelated Korean patients with familial adenomatous polyposis (FAP) for identification of germline adenomatous polyposis coli (APC) gene mutations. We adopted both s... | [
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Molecular epidemiology of C9 deficiency heterozygotes with an Arg95Stop mutation of the C9 gene in Japan.
Deficiency of the ninth component of human complement (C9) is the most common complement deficiency in Japan, with an incidence of approximately one homozygote in 1000, but is very rare in other countries. Genetic ... | [
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The hereditary hemochromatosis protein, HFE, specifically regulates transferrin-mediated iron uptake in HeLa cells.
HFE is the protein product of the gene mutated in the autosomal recessive disease hereditary hemochromatosis (Feder, J. N., Gnirke, A., Thomas, W., Tsuchihashi, Z., Ruddy, D. A., Basava, A., Dormishian, F... | [
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Mutation and haplotype studies of familial Mediterranean fever reveal new ancestral relationships and evidence for a high carrier frequency with reduced penetrance in the Ashkenazi Jewish population.
Familial Mediterranean fever (FMF) is a recessive disorder characterized by episodes of fever with serositis or synoviti... | [
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... | [{"text": "familial Mediterranean fever", "type": "SpecificDisease", "char_start": 34, "char_end": 62, "token_start": 5, "token_end": 7}, {"text": "Familial Mediterranean fever", "type": "SpecificDisease", "char_start": 200, "char_end": 228, "token_start": 29, "token_end": 31}, {"text": "FMF", "type": "SpecificDisease"... | train/10090880 |
Autoimmune lymphoproliferative syndrome with defective Fas: genotype influences penetrance.
Autoimmune lymphoproliferative syndrome (ALPS) is a disorder of lymphocyte homeostasis and immunological tolerance. Most patients have a heterozygous mutation in the APT1 gene, which encodes Fas (CD95, APO-1), mediator of an ap... | [
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Multicentric origin of hemochromatosis gene (HFE) mutations.
Genetic hemochromatosis (GH) is believed to be a disease restricted to those of European ancestry. In northwestern Europe, > 80% of GH patients are homozygous for one mutation, the substitution of tyrosine for cysteine at position 282 (C282Y) in the unprocess... | [
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A retrospective anonymous pilot study in screening newborns for HFE mutations in Scandinavian populations.
We have retrospectively analyzed 837 random anonymized dried blood spot (DBS) samples from neonatal screening programs in Scandinavia for mutations in HFE, the candidate gene for hemochromatosis. We have found C28... | [
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Identification of the mutation in the alkaptonuria mouse model.
Alkaptonuria (aku), an inborn error of metabolism caused by the loss of homogentisate 1, 2-dioxygenase (HGD), has been described in a mouse model created by ethylnitrosourea mutagenesis but the mutation in these mice has not previously been identified. We ... | [
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Non-syndromic hearing loss associated with enlarged vestibular aqueduct is caused by PDS mutations.
Enlarged vestibular aqueduct (EVA), known as the most common form of inner ear abnormality, has recently been of particular genetic interest because this anomaly is inherited in a recessive manner. The locus for non-synd... | [
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Mutational analysis and genotype-phenotype correlation of 29 unrelated Japanese patients with X-linked adrenoleukodystrophy.
BACKGROUND X-linked adrenoleukodystrophy (ALD) is an inherited disease characterized by progressive neurologic dysfunction, occasionally associated with adrenal insufficiency. The classic form o... | [
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A common human skin tumour is caused by activating mutations in beta-catenin.
WNT signalling orchestrates a number of developmental programs. In response to this stimulus, cytoplasmic beta-catenin (encoded by CTNNB1) is stabilized, enabling downstream transcriptional activation by members of the LEF/TCF family. One of ... | [
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"s... | [{"text": "skin tumour", "type": "DiseaseClass", "char_start": 15, "char_end": 26, "token_start": 3, "token_end": 4}, {"text": "cancer", "type": "DiseaseClass", "char_start": 443, "char_end": 449, "token_start": 83, "token_end": 83}, {"text": "colon cancers", "type": "DiseaseClass", "char_start": 483, "char_end": 496, ... | train/10192393 |
The Pendred syndrome gene encodes a chloride-iodide transport protein.
Pendred syndrome is the most common form of syndromic deafness and characterized by congenital sensorineural hearing loss and goitre. This disorder was mapped to chromosome 7 and the gene causing Pendred syndrome (PDS) was subsequently identified by... | [
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HFE mutations analysis in 711 hemochromatosis probands: evidence for S65C implication in mild form of hemochromatosis.
Hereditary hemochromatosis (HH) is a common autosomal recessive genetic disorder of iron metabolism. The HFE candidate gene encoding an HLA class I-like protein involved in HH was identified in 1996. T... | [
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Germline BRCA1 alterations in a population-based series of ovarian cancer cases.
The objective of this study was to provide more accurate frequency estimates of breast cancer susceptibility gene 1 (BRCA1) germline alterations in the ovarian cancer population. To achieve this, we determined the prevalence of BRCA1 alter... | [
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Adrenoleukodystrophy-related protein can compensate functionally for adrenoleukodystrophy protein deficiency (X-ALD): implications for therapy.
Inherited defects in the peroxisomal ATP-binding cassette (ABC) transporter adrenoleukodystrophy protein (ALDP) lead to the lethal peroxisomal disorder X-linked adrenoleukodyst... | [
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Centrosome amplification and a defective G2-M cell cycle checkpoint induce genetic instability in BRCA1 exon 11 isoform-deficient cells.
Germline mutations of the Brca1 tumor suppressor gene predispose women to breast and ovarian cancers. To study mechanisms underlying BRCA1-related tumorigenesis, we derived mouse embr... | [
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Defective CD95/APO-1/Fas signal complex formation in the human autoimmune lymphoproliferative syndrome, type Ia.
Heterozygous mutations in the CD95 (APO-1/Fas) receptor occur in most individuals with autoimmune lymphoproliferative syndrome (ALPS) and dominantly interfere with apoptosis by an unknown mechanism. We show ... | [
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Analysis of alkaptonuria (AKU) mutations and polymorphisms reveals that the CCC sequence motif is a mutational hot spot in the homogentisate 1,2 dioxygenase gene (HGO).
We recently showed that alkaptonuria (AKU) is caused by loss-of-function mutations in the homogentisate 1, 2 dioxygenase gene (HGO). Herein we describe... | [
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Fabry disease: identification of novel alpha-galactosidase A mutations and molecular carrier detection by use of fluorescent chemical cleavage of mismatches.
Fabry disease (FD) (angiokeratoma corporis diffusum) is an X-linked inborn error of glycosphingolipid metabolism caused by defects in the lysosomal alpha-galactos... | [
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Prenatal diagnosis by FISH in a family with Pelizaeus-Merzbacher disease caused by duplication of PLP gene.
A diagnosis of Pelizaeus-Merzbacher disease (MIM 312080) was made in a young boy. No mutation in the coding region of the proteolipid protein (PLP) gene had been found. The boys maternal aunt came for prenatal di... | [
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Dominant negative effect of the APC1309 mutation: a possible explanation for genotype-phenotype correlations in familial adenomatous polyposis.
Inactivation of the adenomatous polyposis coli (APC) gene product initiates colorectal tumorigenesis. Patients with familial APC (FAP) carry germ-line mutations in the APC gene... | [
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BRCA1 interacts with components of the histone deacetylase complex.
Germ-line mutations in the BRCA1 tumor-suppressor gene are associated with an increased susceptibility to breast and ovarian cancer. BRCA1 contains a carboxyl-terminal domain (BRCT) that is shared with several other proteins involved in maintaining gen... | [
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Combined genetic deficiency of C6 and C7 in man.
By routine screening of sera, a subject was discovered who showed a sub-total deficiency of C6 and C7. No clinical disease was associated with this deficiency which was transmitted through the subjects family as a single genetic characteristic, the C6 deficiency being as... | [
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... | [{"text": "Combined genetic deficiency of C6 and C7", "type": "CompositeMention", "char_start": 0, "char_end": 40, "token_start": 0, "token_end": 6}, {"text": "sub-total deficiency of C6 and C7", "type": "CompositeMention", "char_start": 117, "char_end": 150, "token_start": 24, "token_end": 31}, {"text": "C6 deficiency... | train/102474 |
Changes at P183 of emerin weaken its protein-protein interactions resulting in X-linked Emery-Dreifuss muscular dystrophy.
Emery-Dreifuss muscular dystrophy (EDMD) is an X-linked recessive muscular dystrophy characterized by early contractures of the elbows, Achilles tendons and spine, slowly progressive muscle wasting... | [
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... | [{"text": "X-linked Emery-Dreifuss muscular dystrophy", "type": "SpecificDisease", "char_start": 79, "char_end": 121, "token_start": 13, "token_end": 20}, {"text": "Emery-Dreifuss muscular dystrophy", "type": "SpecificDisease", "char_start": 123, "char_end": 156, "token_start": 23, "token_end": 27}, {"text": "EDMD", "t... | train/10323252 |
Microdeletions at chromosome bands 1q32-q41 as a cause of Van der Woude syndrome.
Van der Woude syndrome (VWS) is an autosomal dominant disorder comprising cleft lip and/or cleft palate and lip pits. We reported previously a family whose underlying mutation is a 500-800 kb deletion localized to chromosome bands 1q32-q4... | [
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Splicing defects in the ataxia-telangiectasia gene, ATM: underlying mutations and consequences.
Mutations resulting in defective splicing constitute a significant proportion (30/62 [48%]) of a new series of mutations in the ATM gene in patients with ataxia-telangiectasia (AT) that were detected by the protein-truncatio... | [
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Alpha-cardiac actin is a novel disease gene in familial hypertrophic cardiomyopathy.
We identified the alpha-cardiac actin gene (ACTC) as a novel disease gene in a pedigree suffering from familial hypertrophic cardiomyopathy (FHC). Linkage analyses excluded all the previously reported FHC loci as possible disease loci ... | [
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Overgrowth of oral mucosa and facial skin, a novel feature of aspartylglucosaminuria.
Aspartylglucosaminuria (AGU) is a lysosomal storage disorder caused by deficiency of aspartylglucosaminidase (AGA). The main symptom is progressive mental retardation. A spectrum of different mutations has been reported in this diseas... | [
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... | [{"text": "Overgrowth of oral mucosa and facial skin", "type": "CompositeMention", "char_start": 0, "char_end": 41, "token_start": 0, "token_end": 6}, {"text": "aspartylglucosaminuria", "type": "SpecificDisease", "char_start": 62, "char_end": 84, "token_start": 12, "token_end": 12}, {"text": "Aspartylglucosaminuria", "... | train/10353787 |
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