VAAST 2 (the Variant Annotation, Analysis & Search Tool) is a probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences. VAAST 2 builds upon existing phylogenetic conservation, amino acid substitution (AAS) and aggregative approaches to variant prioritization, combining elements of all into a single unified likelihood-framework that allows users to identify damaged genes and deleterious variants with greater accuracy, and in an easy-to-use fashion. VAAST 2 can score both coding (SNV, indel and splice site) and non-coding variants (SNV), evaluating the cumulative impact of both types of variants simultaneously. VAAST 2 can identify rare variants causing rare genetic diseases, and it can also use both rare and common variants to identify genes responsible for common diseases. VAAST 2 thus has a much greater scope of use than any existing methodology.
Hu H Roach JC Coon H Guthery SL Voelkerding KV Margraf RL Durtschi JD Tavtigian SV Shankaracharya Wu W Scheet P Wang S Xing J Glusman G Hubley R Li H Garg V Moore B Hood L Galas DJ Srivastava D Reese MG Jorde LB Yandell M Huff CD
Nature Biotech.
Using VAAST to Identify Disease-Associated Variants in Next-Generation Sequencing Data.
Kennedy B Kronenberg Z Hu H Moore B Flygare S Reese MG Jorde LB Yandell M Huff C
Current Protocols in Human Genetics. 2014 Apr 24;81:6.14.1-6.14.25
Pharmacogenomics of 17-alpha hydroxyprogesterone caproate for recurrent preterm birth prevention.
Manuck TA Watkins WS Moore B Esplin MS Varner MW Jackson GM Yandell M Jorde L
Am J Obstet Gynecol. 2014 Apr;210(4)
Hu H Huff CD Moore B Flygare S Reese MG Yandell M
Genet Epidemiol. 2013 37(6):622-34.
Sturge-Weber syndrome and port-wine stains caused by somatic mutation in GNAQ
Shirley MD Tang H Gallione CJ Baugher JD Frelin LP Cohen B North PE Marchuk DA Comi AM Pevsner
N Engl J Med. 2013 May 23;368(21):1971-9.
A probabilistic disease-gene finder for personal genomes
Yandell M Huff CD Hu H Singleton M Moore B Xing J Jorde L Reese MG.
Genome Res. 2011 Jul
Rope AF Wang K Evjenth R Xing J Johnston JJ Swensen JJ Johnson WJ Moore B Huff CD Bird LM Carey JC Opitz JM Stevens CA Jiang T Schank C Fain HD Robison R Dalley B Chin S South ST Pysher TJ Jorde LB Hakonarson H Lillehaug JR Biesecker LG Yandell M Arnesen T Lyon GJ
Am J Hum Genet. 2011 Jul 15;89(1):28-43