← All .science files
pmid:29088836
Common, germline genetic variations in the novel tumor suppressor BAP1 and risk of developing different types of cancer.
Moubin Lin · Liren Zhang · Michelle A T Hildebrandt · Maosheng Huang · Xifeng Wu · Yuanqing Ye
Oncotarget · 2017 doi:10.18632/oncotarget.20465
Paper
complete
Experiment
partial
Data
partial
Analysis
complete
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 6 items
claims array · 3 items
[0] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
[1] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
[2] object · 6 fields
target object · 4 fields
evidence array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 1 item
data object · 3 fields
assets array · 6 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 46 items
[0] array · 4 items
[1] array · 2 items
[2] array · 4 items
[3] array · 4 items
[4] array · 4 items
[5] array · 4 items
[6] array · 4 items
[7] array · 4 items
[8] array · 4 items
[9] array · 4 items
[10] array · 2 items
[11] array · 4 items
[12] array · 4 items
[13] array · 4 items
[14] array · 4 items
[15] array · 4 items
[16] array · 4 items
[17] array · 4 items
[18] array · 4 items
[19] array · 2 items
[20] array · 4 items
[21] array · 4 items
[22] array · 4 items
[23] array · 4 items
[24] array · 4 items
[25] array · 4 items
[26] array · 4 items
[27] array · 4 items
[28] array · 2 items
[29] array · 4 items
[30] array · 4 items
[31] array · 4 items
[32] array · 4 items
[33] array · 4 items
[34] array · 4 items
[35] array · 4 items
[36] array · 4 items
[37] array · 2 items
[38] array · 4 items
[39] array · 4 items
[40] array · 4 items
[41] array · 4 items
[42] array · 4 items
[43] array · 4 items
[44] array · 4 items
[45] array · 4 items
[2] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 31 items
[0] array · 6 items
[1] array · 1 item
[2] array · 6 items
[3] array · 6 items
[4] array · 6 items
[5] array · 6 items
[6] array · 6 items
[7] array · 5 items
[8] array · 6 items
[9] array · 6 items
[10] array · 6 items
[11] array · 6 items
[12] array · 6 items
[13] array · 5 items
[14] array · 6 items
[15] array · 6 items
[16] array · 6 items
[17] array · 6 items
[18] array · 6 items
[19] array · 6 items
[20] array · 6 items
[21] array · 6 items
[22] array · 6 items
[23] array · 6 items
[24] array · 6 items
[25] array · 5 items
[26] array · 6 items
[27] array · 6 items
[28] array · 6 items
[29] array · 6 items
[30] array · 6 items
[3] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 28 items
[0] array · 7 items
[1] array · 1 item
[2] array · 6 items
[3] array · 7 items
[4] array · 7 items
[5] array · 7 items
[6] array · 7 items
[7] array · 7 items
[8] array · 7 items
[9] array · 7 items
[10] array · 1 item
[11] array · 6 items
[12] array · 7 items
[13] array · 7 items
[14] array · 7 items
[15] array · 7 items
[16] array · 7 items
[17] array · 7 items
[18] array · 7 items
[19] array · 1 item
[20] array · 6 items
[21] array · 7 items
[22] array · 7 items
[23] array · 7 items
[24] array · 7 items
[25] array · 7 items
[26] array · 7 items
[27] array · 7 items
[4] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 8 items
[0] array · 6 items
[1] array · 6 items
[2] array · 6 items
[3] array · 6 items
[4] array · 6 items
[5] array · 6 items
[6] array · 6 items
[7] array · 6 items
[5] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 7 items
[0] array · 5 items
[1] array · 5 items
[2] array · 5 items
[3] array · 5 items
[4] array · 5 items
[5] array · 5 items
[6] array · 5 items
gaps array · 0 items
analysis object · 4 fields
methods array · 2 items
[0] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[1] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
targets array · 1 item
gaps array · 0 items
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 1 item
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 0 items
resolved_accessions array · 0 items
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 1 item
assets array · 6 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 1 item
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 5 items
assays array · 2 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[1] object · 11 fields
required_operations array · 1 item
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29088836", "kind": "science-record", "revision": 6, "content_hash": "sha256:ce527a47d7a3b9367f3e279d18e21bd0159e8f057698e383a8a65305dfc1b1b5", "created_at": "2026-11-01T15:40:29Z", "updated_at": "2026-11-01T21:21:08Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Common, germline genetic variations in the novel tumor suppressor BAP1 and risk of developing different types of cancer.", "doi": "10.18632/oncotarget.20465", "pmid": "29088836", "authors": ["Moubin Lin", "Liren Zhang", "Michelle A T Hildebrandt", "Maosheng Huang", "Xifeng Wu", "Yuanqing Ye"], "journal": "Oncotarget", "year": 2017, "abstract": "BRCA1 associated protein-1 (BAP1) is a novel tumor suppressor that has recently been shown to be somatically mutated in several cancers. The BAP1 gene also carries rare germline mutations in families with a high incidence of several types of cancers, such as mesothelioma, uveal melanoma, lung adenocarcinoma, melanocytic neoplasms, and renal cell carcinoma. To test the hypothesis that common, germline genetic variants in BAP1 may also contribute to the risk of developing different types of cancer, we genotyped germline single nucleotide polymorphisms (SNPs) for BAP1 in a large population of patients with cancer, including 2,340 with colorectal cancer, 1,436 with bladder cancer, 3,313 with lung cancer, 1,325 with renal cell carcinoma, and 1,162 with esophageal cancer. We identified significant association of rs11708581 (P = 0.0034) and rs390802 (P = 0.015) with risk of renal cell carcinoma and rs12163565 (P = 0.038) with risk of lung cancer. Expression quantitative trait loci analysis in renal cell carcinoma using publicly available data from TCGA showed that the proxy SNPs for rs11708581 and rs390802 were negatively associated with the expression level of BAP1. Our study indicate that common germline genetic variants of BAP1 play a role in mediating the risk of developing renal cell carcinoma and lung cancer.", "claims": [{"id": "claim-method", "statement": "The association of each SNP with the risk of developing different types of cancer was estimated as ORs with 95% CIs using unconditional multivariate logistic regression, adjusting for age, sex, and smoking status for all five cancer types.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29088836", "locator": "sections[12] \"Statistical analysis\" paragraph 2", "quote": "The association of each SNP with the risk of developing different types of cancer was estimated as ORs with 95% CIs using unconditional multivariate logistic regression, adjusting for age, sex, and smoking status for all five cancer types."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data on renal clear cell carcinoma were downloaded from The Cancer Genome Atlas (TCGA, dbGaP Study Accession: phs000178.v9.p8, data portal: https://tcga-data.nci.nih.gov/tcga/tcgaHome2.jsp). Expression data (RNA-seq) and methylation (HumanMethylation450 chip) were measured in tumor samples, somatic copy number was inferred from the tumor samples and paired normal controls (Affymetrix SNP 6.0 platform), and genotyping data were measured from blood derived DNA samples (Affymetrix SNP 6.0 platform).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29088836", "locator": "sections[13] \"Expression quantitative trait loci (eQTL) analysis\" paragraph 2", "quote": "Data on renal clear cell carcinoma were downloaded from The Cancer Genome Atlas (TCGA, dbGaP Study Accession: phs000178.v9.p8, data portal: https://tcga-data.nci.nih.gov/tcga/tcgaHome2.jsp). Expression data (RNA-seq) and methylation (HumanMethylation450 chip) were measured in tumor samples, somatic copy number was inferred from the tumor samples and paired normal controls (Affymetrix SNP 6.0 platform), and genotyping data were measured from blood derived DNA samples (Affymetrix SNP 6.0 platform)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study found that common germline BAP1 variants were associated with renal cell carcinoma and lung cancer risk; cancer-risk associations were analyzed by unconditional multivariate logistic regression, while potential BAP1-expression mechanisms were assessed through eQTL analysis of TCGA renal clear cell carcinoma data.", "kind": "quantitative", "target": {"value": 95.0, "unit": "per cent", "tolerance": null, "source": "The association of each SNP with the risk of developing different types of cancer was estimated as ORs with 95% CIs using unconditional multivariate logistic regression, adjusting for age, sex, and smoking status for all five cancer types."}, "evidence": [{"asset": "source:pmid:29088836", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Our study indicate that common germline genetic variants of BAP1 play a role in mediating the risk of developing renal cell carcinoma and lung cancer."}, {"asset": "source:pmid:29088836", "locator": "sections[12] \"Statistical analysis\" paragraph 2", "quote": "The association of each SNP with the risk of developing different types of cancer was estimated as ORs with 95% CIs using unconditional multivariate logistic regression, adjusting for age, sex, and smoking status for all five cancer types."}, {"asset": "source:pmid:29088836", "locator": "sections[13] \"Expression quantitative trait loci (eQTL) analysis\" paragraph 2", "quote": "Data on renal clear cell carcinoma were downloaded from The Cancer Genome Atlas (TCGA, dbGaP Study Accession: phs000178.v9.p8, data portal: https://tcga-data.nci.nih.gov/tcga/tcgaHome2.jsp)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The study found that common germline BAP1 variants were associated with renal cell carcinoma and lung cancer risk; cancer-risk associations were analyzed by unconditional multivariate logistic regression, while potential BAP1-expression mechanisms were assessed through eQTL analysis of TCGA renal clear cell carcinoma data.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:29088836"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29088836", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/oncotarget.20465", "sha256": "sha256:9255f4e3a0317f1ed5234db6437f9aa93e96d2cfe533d76d2296e49e85a1dba8", "bytes": 37793, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.18632/oncotarget.20465", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5650391", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:29088836:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:45cb84534fa16c8454d7bb367e5699b9f6d7a9b376f14d7e6b4a1458931cc896", "bytes": 1698, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#T1", "version": null, "note": "Study populations", "structure": {"pmcid": "PMC5650391", "section_index": 3, "section_title": "Host characteristics", "row_count": 46, "column_count": 4}, "table": {"label": "Table 1", "caption": "Study populations", "rows": [["Variables", "Cases, N(%)", "Controls, N(%)", "P-value"], ["Bladder Cancer", ""], ["Total", "1436", "1436", ""], ["Age, mean(SD)", "65.40(11.09)", "65.40(11.07)", "1.00"], ["Sex", "", "", "1.00"], ["Male", "1147(80)", "1147(80)", ""], ["Female", "289(20)", "289(20)", ""], ["Smoking status", "", "", "<0.001"], ["Never", "340(28)", "491(34)", ""], ["Ever", "877(72)", "941(66)", ""], ["Colorectal Cancer", ""], ["Total", "2340", "2340", ""], ["Age, mean(SD)", "56.48(11.89)", "56.52(11.83)", "0.91"], ["Sex", "", "", "1.00"], ["Male", "1350(58)", "1350(58)", ""], ["Female", "990(42)", "990(42)", ""], ["Smoking status", "", "", "<0.001"], ["Never", "1270(54)", "899(39)", ""], ["Ever", "1070(46)", "1432(61)", ""], ["Esophageal Cancer", ""], ["Total", "1162", "1162", ""], ["Age, mean(SD)", "62.67(10.76)", "62.68(10.74)", "0.99"], ["Sex", "", "", "1.00"], ["Male", "1027(88)", "1027(88)", ""], ["Female", "135(12)", "135(12)", ""], ["Smoking status", "", "", "<0.001"], ["Never", "270(27)", "398(34)", ""], ["Ever", "718(73)", "760(66)", ""], ["Renal Cell Carcinoma", ""], ["Total", "1325", "1325", ""], ["Age, mean(SD)", "59.54(10.80)", "59.54(10.78)", "1.00"], ["Sex", "", "", "1.00"], ["Male", "882(66.57)", "882(67)", ""], ["Female", "443(33.43)", "443(33)", ""], ["Smoking status", "", "", "<0.001"], ["Never", "580(46)", "488(37)", ""], ["Ever", "687(54)", "834(63)", ""], ["Lung Cancer", ""], ["Total", "3313", "3313", ""], ["Age, mean(SD)", "62.40(10.81)", "62.32(10.78)", "0.78"], ["Sex", "", "", "1.00"], ["Male", "1824(55)", "1824(55)", ""], ["Female", "1489(45)", "1489(45)", ""], ["Smoking status", "", "", "1.00"], ["Never", "589(18)", "589(18)", ""], ["Ever", "2724(82)", "2724(82)", ""]], "row_count": 46, "column_count": 4, "numeric_cells": 75, "header_rows": 1, "locator": "section[3]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:29088836:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:dfbc1b4f20f108c9bdc3a55d14a9d700206568b74ceb97600eac37d7626ae9ed", "bytes": 2394, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#T2", "version": null, "note": "Effects of BAP1 genetic variation on the risk of developing different types of cancer", "structure": {"pmcid": "PMC5650391", "section_index": 4, "section_title": "BAP1 genetic variants and risk of developing different types of cancer", "row_count": 31, "column_count": 6}, "table": {"label": "Table 2", "caption": "Effects of BAP1 genetic variation on the risk of developing different types of cancer", "rows": [["SNP", "Cases, N (cc/cv/vv)", "Control, N (cc/cv/vv)", "Model", "*OR(95% CI)", "p-value"], ["Bladder Cancer"], ["rs11708581", "1066\\310\\16", "1064\\325\\23", "Dom", "0.90(0.74-1.10)", "0.30"], ["rs123598", "1260\\135\\1", "1272\\133\\2", "Dom", "1.04(0.79-1.36)", "0.79"], ["rs12163565", "893\\461\\50", "945\\422\\53", "Dom", "1.17(0.99-1.39)", "0.070"], ["rs390802", "922\\427\\40", "941\\422\\46", "Dom", "0.99(0.83-1.18)", "0.89"], ["rs13094687", "617\\632\\135", "613\\631\\163", "Dom", "1.06(0.89-1.26)", "0.51"], ["Esophageal Cancer", "", "", "", ""], ["rs11708581", "880\\247\\20", "848\\261\\20", "Dom", "0.94(0.76-1.16)", "0.54"], ["rs123598", "1033\\114\\2", "1046\\95\\2", "Dom", "1.07(0.79-1.45)", "0.67"], ["rs12163565", "755\\340\\33", "759\\345\\39", "Dom", "1.00(0.83-1.21)", "1.00"], ["rs390802", "772\\333\\37", "758\\344\\33", "Dom", "0.93(0.77-1.13)", "0.49"], ["rs13094687", "502\\488\\135", "516\\484\\142", "Dom", "1.00(0.88-1.13)", "0.96"], ["Renal Cell Carcinoma", "", "", "", ""], ["rs11708581", "1028\\251\\9", "982\\295\\18", "Dom", "0.74(0.61-0.91)", "0.0034"], ["rs123598", "1173\\127\\1", "1169\\123\\3", "Dom", "0.99(0.71-1.38)", "0.95"], ["rs12163565", "825\\420\\56", "861\\391\\55", "Dom", "1.05(0.86-1.29)", "0.62"], ["rs390802", "918\\340\\34", "861\\400\\35", "Dom", "0.80(0.67-0.96)", "0.015"], ["rs13094687", "571\\584\\139", "613\\547\\136", "Dom", "1.09(0.93-1.28)", "0.30"], ["Lung Cancer", "", "", "", "", ""], ["rs11708581", "2521\\685\\41", "2467\\721\\42", "Dom", "0.93(0.82-1.04)", "0.21"], ["rs123598", "2937\\320\\3", "2900\\330\\6", "Dom", "0.93(0.79-1.10)", "0.39"], ["rs12163565", "2060\\1073\\135", "2122\\1001\\129", "Dom", "1.11(1.01-1.24)", "0.038"], ["rs390802", "2207\\970\\76", "2163\\970\\94", "Dom", "0.96(0.86-1.06)", "0.41"], ["rs13094687", "1476\\1435\\342", "1468\\1404\\357", "Dom", "1.00(0.90-1.11)", "0.99"], ["Colorectal Cancer", "", "", "", ""], ["rs11708581", "1767\\503\\30", "1744\\514\\29", "Dom", "1.00(0.86-1.17)", "0.80"], ["rs123598", "2083\\224\\1", "2056\\234\\2", "Dom", "0.89(0.72-1.09)", "0.93"], ["rs12163565", "1506\\729\\89", "1501\\700\\95", "Dom", "1.07(0.94-1.22)", "0.30"], ["rs390802", "1553\\690\\61", "1526\\697\\64", "Dom", "0.97(0.85-1.11)", "0.73"], ["rs13094687", "1062\\1024\\230", "1054\\992\\241", "Dom", "1.00(0.88-1.13)", "0.96"]], "row_count": 31, "column_count": 6, "numeric_cells": 126, "header_rows": 1, "locator": "section[4]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:29088836:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:51101f06ccf990dd007f4d8c92baa9f586312c1e8cc6573d3711a69adf6d79c2", "bytes": 1995, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#T3", "version": null, "note": "Effect of BAP1 genetic variants by sex, smoking status, and age", "structure": {"pmcid": "PMC5650391", "section_index": 5, "section_title": "Stratified analysis for BAP1 genetic variants and risk of of developing different types of cancer", "row_count": 28, "column_count": 7}, "table": {"label": "Table 3", "caption": "Effect of BAP1 genetic variants by sex, smoking status, and age", "rows": [["SNP", "Group", "Case N(cc/cv/vv)", "Control N (cc/cv/vv)", "Model", "*OR(95% CI)", "P-value"], ["Sex"], ["Renal Cell Carcinoma", "", "", "", "", ""], ["rs11708581", "Male", "689\\165\\5", "652\\197\\16", "Dom", "0.75(0.60-0.95)", "0.017"], ["", "Female", "339\\86\\4", "330\\98\\2", "Dom", "0.88(0.63-1.23)", "0.45"], ["rs390802", "Male", "625\\217\\22", "575\\263\\26", "Dom", "0.77(0.63-0.95)", "0.014"], ["", "Female", "293\\123\\12", "286\\137\\9", "Dom", "0.93(0.69-1.25)", "0.65"], ["Lung", "", "", "", "", "", ""], ["rs12163565", "Male", "1128\\594\\73", "1203\\531\\59", "Dom", "1.19(1.04-1.37)", "0.013"], ["", "Female", "932\\479\\62", "919\\470\\70", "Dom", "0.99(0.85-1.15)", "0.90"], ["Smoking Status"], ["Renal Cell Carcinoma", "", "", "", "", ""], ["rs11708581", "Never", "447\\109\\6", "372\\103\\6", "Dom", "0.87(0.65-1.17)", "0.36"], ["", "Ever", "538\\128\\3", "607\\192\\12", "Dom", "0.73(0.57-0.94)", "0.014"], ["rs390802", "Never", "390\\159\\14", "329\\140\\11", "Dom", "0.96(0.74-1.25)", "0.78"], ["", "Ever", "485\\168\\18", "529\\260\\24", "Dom", "0.73(0.58-0.91)", "0.0051"], ["Lung", "", "", "", "", "", ""], ["rs12163565", "Never", "377\\187\\18", "375\\177\\29", "Dom", "1.00(0.78-1.27)", "0.98"], ["", "Ever", "1683\\886\\117", "1747\\824\\100", "Dom", "1.12(1.00-1.26)", "0.047"], ["Age"], ["Renal Cell Carcinoma", "", "", "", "", ""], ["rs11708581", "Subjects<65", "679\\157\\5", "639\\196\\15", "Dom", "0.72(0.57-0.91)", "0.0065"], ["", "Subjects≥65", "349\\94\\4", "343\\99\\3", "Dom", "0.92(0.66-1.27)", "0.60"], ["rs390802", "Subjects<65", "601\\226\\18", "552\\265\\32", "Dom", "0.77(0.62-0.95)", "0.014"], ["", "Subjects≥65", "317\\114\\16", "309\\135\\3", "Dom", "0.90(0.67-1.21)", "0.47"], ["Lung", "", "", "", "", "", ""], ["rs12163565", "Subjects<65", "1103\\584\\72", "1138\\554\\72", "Dom", "1.07(0.93-1.23)", "0.32"], ["", "Subjects≥65", "956\\489\\63", "984\\446\\57", "Dom", "1.13(0.97-1.31)", "0.12"]], "row_count": 28, "column_count": 7, "numeric_cells": 88, "header_rows": 1, "locator": "section[5]/table-wrap[1]#T3"}}, {"id": "asset:table:pmid:29088836:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:19671cf81cf94399b0fc4ae16ab7584b1f2186209ab5ad77e7b8ea540d536eed", "bytes": 751, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[1]#T4", "version": null, "note": "eQTL analysis on the effect of Proxy SNPs on BAP1 expression level for renal cell carcinoma using data downloaded from TCGA", "structure": {"pmcid": "PMC5650391", "section_index": 6, "section_title": "eQTL analysis", "row_count": 8, "column_count": 6}, "table": {"label": "Table 4", "caption": "eQTL analysis on the effect of Proxy SNPs on BAP1 expression level for renal cell carcinoma using data downloaded from TCGA", "rows": [["Proxy SNP", "r2", "SNP of interest", "Coefficient", "Standard error", "P-value"], ["rs1769", "0.94", "rs11708581", "-0.062", "0.042", "0.142"], ["rs6793317", "0.9", "rs11708581", "-0.079", "0.040", "0.051"], ["rs17052053", "0.9", "rs11708581", "-0.113", "0.041", "0.006"], ["rs11713914", "1.0", "rs11708581", "-0.084", "0.042", "0.050"], ["rs6763882", "0.93", "rs390802", "-0.070", "0.038", "0.067"], ["rs11714402", "0.98", "rs390802", "-0.086", "0.038", "0.023"], ["rs123602", "0.98", "rs390802", "-0.050", "0.041", "0.222"]], "row_count": 8, "column_count": 6, "numeric_cells": 42, "header_rows": 1, "locator": "section[6]/table-wrap[1]#T4"}}, {"id": "asset:table:pmid:29088836:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3c4819e47406ff792c17480b6a98387dee40f687df8f3c08cf00937aeffcbd52", "bytes": 600, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#T5", "version": null, "note": "Genotyped genetic variants for BAP1", "structure": {"pmcid": "PMC5650391", "section_index": 11, "section_title": "SNP selection and genotyping", "row_count": 7, "column_count": 5}, "table": {"label": "Table 5", "caption": "Genotyped genetic variants for BAP1", "rows": [["SNP", "Chromosome (hg36)", "Position", "Nucleotide change", "MAF*"], ["rs11708581", "chr3: 52428988", "3’ Flanking", "C>A", "0.05"], ["rs12163565", "chr3: 52430526", "3’ Flanking", "G>A", "0.17"], ["rs390802", "chr3: 52431671", "3’ Flanking", "G>A", "0.13"], ["rs123598", "chr3: 52435860", "3’ UTR", "G>A", "0.03"], ["rs56238158", "chr3: 52439302", "Glu>Lys", "C>T", "0.13"], ["rs13094687", "chr3: 52450043", "5’ Flanking", "A>G", "0.29"]], "row_count": 7, "column_count": 5, "numeric_cells": 24, "header_rows": 1, "locator": "section[11]/table-wrap[1]#T5"}}], "gaps": []}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "regression_modelling", "specific": "logistic", "label": "Regression modelling", "dsl_operations": ["glm_logit_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictors_and_outcome"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The association of each SNP with the risk of developing different types of cancer was estimated as ORs with 95% CIs using unconditional multivariate logistic regression, adjusting for age, sex, and smoking status for all five cancer types."}}, {"id": "method-2", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "χ2"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "chi_square_test", "expected_value": 95.0, "unit": "per cent", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["glm_logit_fit"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: logistic."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": ["Data on renal clear cell carcinoma were downloaded from The Cancer Genome Atlas (TCGA, dbGaP Study Accession: phs000178.v9.p8, data portal: https://tcga-data.nci.nih.gov/tcga/tcgaHome2.jsp). Expression data (RNA-seq) and methylation (HumanMethylation450 chip) were measured in tumor samples, somatic copy number was inferred from the tumor samples and paired normal controls (Affymetrix SNP 6.0 platform), and genotyping data were measured from blood derived DNA samples (Affymetrix SNP 6.0 platform)."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": ["glm_logit_fit"], "assets": ["source:pmid:29088836", "asset:table:pmid:29088836:1", "asset:table:pmid:29088836:2", "asset:table:pmid:29088836:3", "asset:table:pmid:29088836:4", "asset:table:pmid:29088836:5"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:32:37Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 88891, "completion_tokens": 3208, "cached_tokens": 1816}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:29088836", "type": "paper", "label": "pmid:29088836"}, {"id": "source:pmid:29088836", "type": "manuscript", "label": "PMID 29088836 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29088836", "type": "paper", "label": "pmid:29088836"}, {"id": "source:pmid:29088836", "type": "manuscript", "label": "PMID 29088836 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29088836", "type": "extraction", "used": ["source:pmid:29088836"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:29088836", "parent_hash": "sha256:c2618e6783b782471c9c2666e55d2939aba38c04e523986df935a37789aa147c", "fork_of": null, "generation": 5}, "gaps": ["execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "assays": [{"role": "data_generation", "definition_id": "chip_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["rk, DNAse clusters, and transcription factor ChIP-seq plots in Supplementary Figure 1 were generat"], "order_basis": "paper_text_order:2420", "id": "assay:1"}, {"role": "analysis", "definition_id": "regression_modelling", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["glm_logit_fit"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The association of each SNP with the risk of developing different types of cancer was estimated as ORs with 95% CIs using unconditional multivariate logistic regression, adjusting for age, sex, and smoking status for all five cancer types."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}