Category: 2013

Exome sequencing identifies frequent inactivating mutations in BAP1, ARID1A and PBRM1 in intrahepatic cholangiocarcinomas E

Jiao Y, Pawlik TM, Anders RA, Selaru FM, Streppel MM, Lucas DJ, Niknafs N, Guthrie VB, Maitra A, Argani P, Offerhaus GJ, Roa JC, Roberts LR, Gores GJ, Popescu I, Alexandrescu ST, Dima S, Fassan M, Simbolo M, Mafficini A, Capelli P, Lawlor RT, Ruzzenente A, Guglielmi A, Tortora G, de Braud F, Scarpa A, …

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Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene D

Sosnay PR, Siklosi KR, Van Goor F, Kaniecki K, Yu H, Sharma N, Ramalho AS, Amaral MD, Dorfman R, Zielenski J, Masica DL, Karchin R, Millen L, Thomas PJ, Patrinos GP, Corey M, Lewis MH, Rommens JM, Castellani C, Penland CM, Cutting GR (2013) Defining the disease-liability of mutations in the cystic fibrosis transmembrane conductance regulator …

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Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma W

Gartner JJ, Parker SCJ, Prickett TD, Dutton-Reester K, Lin JC, Simhadri VL, Jha S, Katagiri N, Gotea V, Teer JK, Wei X, Bhanot UK, NISC Comparative Sequencing Program, Willard MD, Chen G, Elnitski L, Davies MA, Gershenwald JE, Carter H, Karchin R, Barber TD, Robinson W, Robinson S, Rosenberg SA, Komar AA, Kimchi-Sarfaty C, Hayward …

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Mutational signature of aristolochic acid exposure as revealed by whole-exome sequencing M

Hoang ML, Chen CH, Sidorenko VS, He J, Dickman KG, Yun BH, Moriya M, Niknafs N, Douville C, Karchin R, Turesky RJ, Pu YS, Vogelstein B, Papadopoulos N, Grollman AP, Kinzler KW, Rosenquist T (2013) A. Mutational Signature of Aristolochic Acid Exposure as Revealed by Whole Exome Sequencing. Science Translational Medicine. 5(197):197ra102

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Computational approaches to identify functional genetic variants in cancer genomes C

International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working Group, Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, Bader GD, Boutros PC, Muthuswamy L, Ouellette BF, Reimand J, Linding R, Shibata T, Valencia A, Butler A, Dronov S, …

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Identifying Mendelian disease genes with the variant effect scoring tool I

Carter H, Douville C, Yeo G, Stenson PD, Cooper DN, Karchin R (2013) Identifying Mendelian disease genes with the Variant Effect Scoring Tool. BMC Genomics. 14(3) 1-16.

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Collections of simultaneously altered genes as biomarkers of cancer cell drug response C

Masica DL and Karchin R (2013) Collections of simultaneously altered genes as biomarkers of cancer cell drug response. Cancer Research. 73(6):1699-708

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CRAVAT: cancer-related analysis of variants toolkit C

Douville C, Carter H, Kim R, Niknafs N, Diekhans M, Stenson PD, Cooper DN, Ryan M, Karchin R (2013) CRAVAT: Cancer-Related Analysis of VAriants Toolkit. Bioinformatics. 29(5):647-8

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A hybrid likelihood model for sequence-based disease association studies A

Chen YC, Carter H, Parla J, Kramer M, Goes FS, Pirooznia M, Zandi PP, McCombie WR, Potash JB, Karchin R (2013) A hybrid likelihood model for sequence-based disease association studies. PLoS Genetics. 9(1): e1003224

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