title: TMC-SNPdb: an Indian germline variant database derived from whole exome sequences.
abstract: Cancer is predominantly a somatic disease. A mutant allele present in a cancer cell genome is considered somatic when it's absent in the paired normal genome along with public SNP databases. The current build of dbSNP, the most comprehensive public SNP database, however inadequately represents several non-European Caucasian populations, posing a limitation in cancer genomic analyses of data from these populations. We present the T: ata M: emorial C: entre-SNP D: ata B: ase (TMC-SNPdb), as the first open source, flexible, upgradable, and freely available SNP database (accessible through dbSNP build 149 and ANNOVAR)-representing 114 309 unique germline variants-generated from whole exome data of 62 normal samples derived from cancer patients of Indian origin. The TMC-SNPdb is presented with a companion subtraction tool that can be executed with command line option or using an easy-to-use graphical user interface with the ability to deplete additional Indian population specific SNPs over and above dbSNP and 1000 Genomes databases. Using an institutional generated whole exome data set of 132 samples of Indian origin, we demonstrate that TMC-SNPdb could deplete 42, 33 and 28% false positive somatic events post dbSNP depletion in Indian origin tongue, gallbladder, and cervical cancer samples, respectively. Beyond cancer somatic analyses, we anticipate utility of the TMC-SNPdb in several Mendelian germline diseases. In addition to dbSNP build 149 and ANNOVAR, the TMC-SNPdb along with the subtraction tool is available for download in the public domain at the following:Database URL: http://www.actrec.gov.in/pi-webpages/AmitDutt/TMCSNP/TMCSNPdp.html.
authors.affiliation: Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC).
authors.forename: Pawan
authors.initials: P
authors.lastname: Upadhyay
authors.affiliation: Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC).
authors.forename: Nilesh
authors.initials: N
authors.lastname: Gardi
authors.affiliation: Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC).
authors.forename: Sanket
authors.initials: S
authors.lastname: Desai
authors.affiliation: Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC).
authors.forename: Bikram
authors.initials: B
authors.lastname: Sahoo
authors.affiliation: Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC).
authors.forename: Ankita
authors.initials: A
authors.lastname: Singh
authors.affiliation: Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC).
authors.forename: Trupti
authors.initials: T
authors.lastname: Togar
authors.affiliation: Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC).
authors.forename: Prajish
authors.initials: P
authors.lastname: Iyer
authors.affiliation: Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC).
authors.forename: Ratnam
authors.initials: R
authors.lastname: Prasad
authors.affiliation: Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC).
authors.forename: Pratik
authors.initials: P
authors.lastname: Chandrani
authors.affiliation: Department of Medical Oncology, Tata Memorial Centre, Mumbai, Maharashtra 410012, India.
authors.forename: Sudeep
authors.initials: S
authors.lastname: Gupta
authors.affiliation: Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC) adutt@actrec.gov.in.
authors.forename: Amit
authors.initials: A
authors.lastname: Dutt
mesh_terms: D044466:Asian People / Q000235:genetics*; D030561:Databases, Nucleic Acid; D005260:Female; D015894:Genome, Human; D018095:Germ-Line Mutation; D006801:Humans; D007194:India; D008297:Male; D009369:Neoplasms / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide