TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data

Summary: TREAT (Targeted RE-sequencing Annotation Tool) is a tool for facile navigation and mining of the variants from both targeted resequencing and whole exome sequencing. It provides a rich integration of publicly available as well as in-house developed annotations and visualizations for variants, variant-hosting genes and host-gene pathways. Availability and implementation: TREAT is freely available to non-commercial users as either a stand-alone annotation and visualization tool, or as a comprehensive workflow integrating sequencing alignment and variant calling. The executables, instructions and the Amazon Cloud Images of TREAT can be downloaded at the website: http://ndc.mayo.edu/mayo/research/biostat/stand-alone-packages.cfm Contact: Hossain.Asif@mayo.edu; Kocher.JeanPierre@mayo.edu Supplementary information: Supplementary data are provided at Bioinformatics online.

[1]  P. Shannon,et al.  Exome sequencing identifies the cause of a Mendelian disorder , 2009, Nature Genetics.

[2]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[3]  R. Scharfmann,et al.  Molecular Diagnosis of Neonatal Diabetes Mellitus Using Next-Generation Sequencing of the Whole Exome , 2010, PloS one.

[4]  David J. Cutler,et al.  SeqAnt: A web service to rapidly identify and annotate DNA sequence variations , 2010, BMC Bioinformatics.

[5]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[6]  A. Bowcock,et al.  Frequent Mutation of BAP1 in Metastasizing Uveal Melanomas , 2010, Science.

[7]  David A. Nix,et al.  Next generation tools for genomic data generation, distribution, and visualization , 2010, BMC Bioinformatics.

[8]  H. Hakonarson,et al.  ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data , 2010, Nucleic acids research.

[9]  W. Ansorge.  Next-generation DNA sequencing techniques. , 2009, New biotechnology.

[10]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[11]  M. Metzker.  Sequencing technologies — the next generation , 2010, Nature Reviews Genetics.

[12]  S. Schuster.  Next-generation sequencing transforms today's biology , 2008, Nature Methods.

[13]  Kevin P. Murphy,et al.  SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors , 2010, Bioinform..

[14]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer , 2011, Nature Biotechnology.

[15]  Emily H Turner,et al.  Targeted Capture and Massively Parallel Sequencing of Twelve Human Exomes , 2009, Nature.

[16]  S. Henikoff,et al.  Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm , 2009, Nature Protocols.

[17]  Christian Gilissen,et al.  Exome sequencing identifies WDR35 variants involved in Sensenbrenner syndrome. , 2010, American journal of human genetics.

[18]  P. Stankiewicz,et al.  Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. , 2010, The New England journal of medicine.

[19]  Stefano Volinia,et al.  GAMES identifies and annotates mutations in next-generation sequencing projects , 2011, Bioinform..