pVAAST publicly available

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We are pleased to announce that the paper describing pVAAST (the pedigree Variant Annotation, Analysis, and Search Tool has just been published in Nature Biotechnology.

Hao Hu, Jared C Roach, Hilary Coon, Stephen L Guthery, Karl V Voelkerding, Rebecca L Margraf, Jacob D Durtschi, Sean V Tavtigian, Shankaracharya, Wilfred Wu, Paul Scheet, Shuoguo Wang, Jinchuan Xing, Gustavo Glusman, Robert Hubley, Hong Li, Vidu Garg, Barry Moore, Leroy Hood, David J Galas, Deepak Srivastava, Martin G Reese, Lynn B Jorde, Mark Yandell, Chad D Huff: A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data. In: Nature Biotechnology, 2014.

pVAAST is a software tool that searches whole-exome and whole-genome sequence data in families to identify genetic variants that directly influence disease risk. pVAAST analyzes the DNA sequences of patients, their relatives, and healthy people in a highly automated fashion to provide probabilistic predictions of the specific genetic variants and genes that are increasing the risk of developing disease. pVAAST combines the existing variant prioritization and case-control association features in VAAST with a new linkage analysis method specifically designed for sequence data. This model is broadly similar to traditional linkage analysis but is capable of modeling de novo mutations and is more sensitive in scenarios with incomplete penetrance or locus heterogeneity. pVAAST supports dominant, recessive, and de novo inheritance models, and maintains high power across a wide variety of study designs, from monogenic, Mendelian diseases in a single family to highly polygenic, common diseases involving hundreds of families.

In a separate paper published two weeks ago in Cancer Discovery and led by our collaborators at the University of Utah and the University of Melbourne, we used pVAAST to aid in the discovery that rare variants in the gene RINT1 increase the risk of developing breast cancer and Lynch-Syndrome spectrum cancers.

Daniel J Park, Kayoko Tao, Florence Le Calvez-Kelm, Tu Nguyen-Dumont, Nivonirina Robinot, Fleur Hammet, Fabrice Odefrey, Helen Tsimiklis, Zhi L Teo, Louise B Thingholm, others: Rare mutations in RINT1 predispose carriers to breast and Lynch Syndrome-spectrum cancers. In: Cancer Discovery, pp. CD–14, 2014.

Learn more about pVAAST or click here to register to download pVAAST as part of the VAAST software package.