2025
Knockoff procedure improves susceptibility gene identifications in conditional transcriptome-wide association studies
Zhang X, Wang L, Zhao J, Zhao H. Knockoff procedure improves susceptibility gene identifications in conditional transcriptome-wide association studies. American Journal Of Human Genetics 2025 PMID: 40902598, PMCID: PMC12412983, DOI: 10.1016/j.ajhg.2025.08.007.Peer-Reviewed Original ResearchTranscriptome-wide association studyExpression quantitative trait lociGenome-wide association studiesGene-trait pairsFalse discovery rateAssociation studiesTranscriptome-wide association study approachTranscriptome-wide association study methodExpression quantitative trait loci dataGenes associated with complex traitsGenetic variantsGenome-wide association study summary statisticsSusceptibility genesGene-trait associationsSusceptibility gene identificationQuantitative trait lociParametric bootstrap samplingGene expression levelsGenomic regionsGenetic elementsComplex traitsGene identificationTrait lociFalse discovery rate levelKnockoff procedure
2024
Fine-mapping analysis including over 254,000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes
Chen Z, Guo X, Tao R, Huyghe J, Law P, Fernandez-Rozadilla C, Ping J, Jia G, Long J, Li C, Shen Q, Xie Y, Timofeeva M, Thomas M, Schmit S, DĂez-Obrero V, Devall M, Moratalla-Navarro F, Fernandez-Tajes J, Palles C, Sherwood K, Briggs S, Svinti V, Donnelly K, Farrington S, Blackmur J, Vaughan-Shaw P, Shu X, Lu Y, Broderick P, Studd J, Harrison T, Conti D, Schumacher F, Melas M, Rennert G, ObĂłn-Santacana M, MartĂn-Sánchez V, Oh J, Kim J, Jee S, Jung K, Kweon S, Shin M, Shin A, Ahn Y, Kim D, Oze I, Wen W, Matsuo K, Matsuda K, Tanikawa C, Ren Z, Gao Y, Jia W, Hopper J, Jenkins M, Win A, Pai R, Figueiredo J, Haile R, Gallinger S, Woods M, Newcomb P, Duggan D, Cheadle J, Kaplan R, Kerr R, Kerr D, Kirac I, Böhm J, Mecklin J, Jousilahti P, Knekt P, Aaltonen L, Rissanen H, Pukkala E, Eriksson J, Cajuso T, Hänninen U, Kondelin J, Palin K, Tanskanen T, Renkonen-Sinisalo L, Männistö S, Albanes D, Weinstein S, Ruiz-Narvaez E, Palmer J, Buchanan D, Platz E, Visvanathan K, Ulrich C, Siegel E, Brezina S, Gsur A, Campbell P, Chang-Claude J, Hoffmeister M, Brenner H, Slattery M, Potter J, Tsilidis K, Schulze M, Gunter M, Murphy N, Castells A, CastellvĂ-Bel S, Moreira L, Arndt V, Shcherbina A, Bishop D, Giles G, Southey M, Idos G, McDonnell K, Abu-Ful Z, Greenson J, Shulman K, Lejbkowicz F, Offit K, Su Y, Steinfelder R, Keku T, van Guelpen B, Hudson T, Hampel H, Pearlman R, Berndt S, Hayes R, Martinez M, Thomas S, Pharoah P, Larsson S, Yen Y, Lenz H, White E, Li L, Doheny K, Pugh E, Shelford T, Chan A, Cruz-Correa M, Lindblom A, Hunter D, Joshi A, Schafmayer C, Scacheri P, Kundaje A, Schoen R, Hampe J, Stadler Z, Vodicka P, Vodickova L, Vymetalkova V, Edlund C, Gauderman W, Shibata D, Toland A, Markowitz S, Kim A, Chanock S, van Duijnhoven F, Feskens E, Sakoda L, Gago-Dominguez M, Wolk A, Pardini B, FitzGerald L, Lee S, Ogino S, Bien S, Kooperberg C, Li C, Lin Y, Prentice R, Qu C, BĂ©zieau S, Yamaji T, Sawada N, Iwasaki M, Le Marchand L, Wu A, Qu C, McNeil C, Coetzee G, Hayward C, Deary I, Harris S, Theodoratou E, Reid S, Walker M, Ooi L, Lau K, Zhao H, Hsu L, Cai Q, Dunlop M, Gruber S, Houlston R, Moreno V, Casey G, Peters U, Tomlinson I, Zheng W. Fine-mapping analysis including over 254,000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes. Nature Communications 2024, 15: 3557. PMID: 38670944, PMCID: PMC11053150, DOI: 10.1038/s41467-024-47399-x.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesCredible causal variantsColorectal cancer susceptibility genesSusceptibility genesAssociation signalsAnalysis of single-cell RNA-seq dataAnalysis of whole-exome sequencing dataGenome-wide association study dataColorectal cancer risk lociSingle-cell RNA-seq dataTarget genesWhole-exome sequencing dataFunctional genomic investigationsFine-mapping analysisRNA-seq dataExome sequencing dataTissue-specific transcriptomesColorectal cancerCancer susceptibility genesCausal variantsFine-mappingRisk lociMethylome dataSequence dataGenomic investigations
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