GWATCH: a web platform for automated gene association discovery analysis.
BACKGROUND
As genome-wide sequence analyses for complex human disease determinants are expanding, it is increasingly necessary to develop strategies to promote discovery and validation of potential disease-gene associations.


RESULTS
Here we present a dynamic web-based platform - GWATCH - that automates and facilitates four steps in genetic epidemiological discovery: 1) Rapid gene association search and discovery analysis of large genome-wide datasets; 2) Expanded visual display of gene associations for genome-wide variants (SNPs, indels, CNVs), including Manhattan plots, 2D and 3D snapshots of any gene region, and a dynamic genome browser illustrating gene association chromosomal regions; 3) Real-time validation/replication of candidate or putative genes suggested from other sources, limiting Bonferroni genome-wide association study (GWAS) penalties; 4) Open data release and sharing by eliminating privacy constraints (The National Human Genome Research Institute (NHGRI) Institutional Review Board (IRB), informed consent, The Health Insurance Portability and Accountability Act (HIPAA) of 1996 etc.) on unabridged results, which allows for open access comparative and meta-analysis.


CONCLUSIONS
GWATCH is suitable for both GWAS and whole genome sequence association datasets. We illustrate the utility of GWATCH with three large genome-wide association studies for HIV-AIDS resistance genes screened in large multicenter cohorts; however, association datasets from any study can be uploaded and analyzed by GWATCH.
Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russia.
Anton
A
Svitin
Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russia ; Department of Mathematics, St. Petersburg Electrotechnical University, St. Petersburg 197376, Russia.
Sergey
S
Malov
Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russia.
Nikolay
N
Cherkasov
Scientific Data Visualization Consultant, Turner, ACT 2612, Australia.
Paul
P
Geerts
Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russia.
Mikhail
M
Rotkevich
Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russia.
Pavel
P
Dobrynin
Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russia.
Andrey
A
Shevchenko
Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russia.
Li
L
Guan
Genetics and Genomics Group, Advanced Technology Program, SAIC-Frederick, National Cancer Institute, Frederick, MD 21702, USA.
Jennifer
J
Troyer
Department of Biology, Shepherd University, Shepherdstown, WV 25443, USA.
Sher
S
Hendrickson
Vanderbilt Technologies for Advanced Genomics, Office of Research, Vanderbilt University Medical Center, Nashville, TN 37204, USA.
Holli Hutcheson
HH
Dilks
Biology Department, University of Puerto Rico, Mayaguez, PR 00680, USA.
Taras K
TK
Oleksyk
Department of Biostatistics, Rho, Inc., Chapel Hill, NC 27517, USA.
Sharyne
S
Donfield
Division of Hematology-Oncology, Children's Hospital of Los Angeles, Los Angeles, CA 90027, USA.
Edward
E
Gomperts
Departments of Ophthalmology and Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Douglas A
DA
Jabs
Department of Epidemiology, The Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA.
Efe
E
Sezgin
Department of Epidemiology, The Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA.
Mark
M
Van Natta
British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada ; Division of AIDS, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
P Richard
PR
Harrigan
Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
Zabrina L
ZL
Brumme
Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russia ; Oceanographic Center, Nova Southeastern University, Ft. Lauderdale, FL 33004, USA.
Stephen J
SJ
O'Brien
AIDS; Complex diseases; Genome-wide association studies (GWAS); HIV; Whole genome sequencing (WGS)