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Database Commons - TMC-SNPdb

TMC-SNPdb

Citations: 1

z-index 0.50

Short name TMC-SNPdb
Full name Tata Memorial Centre-SNP data base
Description an Indian germline variant database derived from whole exome sequences
URL http://www.actrec.gov.in/pi-webpages/AmitDutt/TMCSNP/TMCSNPdp.html
Year founded
Last update & version 2016-07-09    
Availability Free to all users
University/Institution hosted Advanced Centre for Treatment Research Education in Cancer (ACTREC)
Address Integrated Genomics Laboratory
City Navi Mumbai
Province/State
Country/Region India
Contact name Amit Dutt
Contact email adutt@actrec.gov.in
Data type(s)
Major organism(s)
Keyword(s)
  • Indian germline variant
  • SNP
Publication(s)
  • TMC-SNPdb: an Indian germline variant database derived from whole exome sequences. [PMID: 27402678]

    Pawan Upadhyay, Nilesh Gardi, Sanket Desai, Bikram Sahoo, Ankita Singh, Trupti Togar, Prajish Iyer, Ratnam Prasad, Pratik Chandrani, Sudeep Gupta, Amit Dutt
    Database : the journal of biological databases and curation 2016:2016
    1 Citations (Google Scholar as of 2017-03-28)

    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. © The Author(s) 2016. Published by Oxford University Press.

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Accessibility

Rate of accessibility:
HTTP status codeDate requested
200 OK2018-11-13
200 OK2018-11-09
200 OK2018-11-06
200 OK2018-11-02
200 OK2018-10-30
200 OK2018-10-26
200 OK2018-10-23
200 OK2018-10-19
200 OK2018-10-16
200 OK2018-10-12
200 OK2018-10-09
200 OK2018-10-05
200 OK2018-10-02
200 OK2018-09-28
200 OK2018-09-25
200 OK2018-09-21
200 OK2018-09-18
200 OK2018-09-14
200 OK2018-09-11
200 OK2018-09-07
200 OK2018-09-04
200 OK2018-08-31
200 OK2018-08-28
200 OK2018-08-24
200 OK2018-08-21
200 OK2018-08-17
200 OK2018-08-14
200 OK2018-08-10
200 OK2018-08-07
200 OK2018-08-03
200 OK2018-07-31
200 OK2018-07-27
200 OK2018-07-24
200 OK2018-07-20
200 OK2018-07-17
200 OK2018-07-13
200 OK2018-07-10
200 OK2018-07-06
200 OK2018-07-03
200 OK2018-06-29
200 OK2018-06-26
200 OK2018-06-22
200 OK2018-06-19
200 OK2018-06-15
200 OK2018-06-12
200 OK2018-06-08
200 OK2018-06-05
200 OK2018-06-01
200 OK2018-05-29
200 OK2018-05-25
200 OK2018-05-22
200 OK2018-05-18
200 OK2018-05-15
200 OK2018-05-11
200 OK2018-05-08
200 OK2018-05-04
200 OK2018-05-01
200 OK2018-04-27
200 OK2018-04-24
200 OK2018-04-20
200 OK2018-04-17
200 OK2018-04-13
200 OK2018-04-10
200 OK2018-04-06
200 OK2018-04-03
200 OK2018-02-27
200 OK2018-02-23
200 OK2018-02-20
200 OK2018-02-16
200 OK2018-02-13
200 OK2018-02-09
200 OK2018-02-06
200 OK2018-02-02
200 OK2018-01-30
200 OK2018-01-26
200 OK2018-01-23
200 OK2018-01-19
200 OK2018-01-16
200 OK2018-01-12
200 OK2018-01-09
200 OK2018-01-05
200 OK2018-01-02
200 OK2017-12-29
200 OK2017-12-26
200 OK2017-12-22
200 OK2017-12-19
200 OK2017-12-15
200 OK2017-12-12
200 OK2017-12-08
200 OK2017-12-05
200 OK2017-12-01
200 OK2017-11-28
200 OK2017-11-24
200 OK2017-11-21
200 OK2017-11-17
200 OK2017-11-14
200 OK2017-11-10
200 OK2017-11-07
200 OK2017-11-03
200 OK2017-10-31
200 OK2017-10-27
200 OK2017-10-24
200 OK2017-10-20
200 OK2017-10-17
200 OK2017-10-13
200 OK2017-10-10
200 OK2017-10-06
200 OK2017-10-03
200 OK2017-09-29
200 OK2017-09-26
200 OK2017-09-22
200 OK2017-09-19
200 OK2017-09-15
200 OK2017-09-12
200 OK2017-09-08
200 OK2017-09-05
200 OK2017-09-01
200 OK2017-08-29
200 OK2017-08-25
200 OK2017-08-22
200 OK2017-08-18
200 OK2017-08-15
200 OK2017-08-11
200 OK2017-08-08
200 OK2017-08-04
200 OK2017-08-01
200 OK2017-07-28
200 OK2017-07-25
200 OK2017-07-21
200 OK2017-07-18
200 OK2017-07-14
200 OK2017-07-04
200 OK2017-06-30
200 OK2017-06-27
200 OK2017-06-23
200 OK2017-06-20
200 OK2017-06-16
200 OK2017-06-13
200 OK2017-06-09
200 OK2017-06-06
200 OK2017-06-02
200 OK2017-05-30
200 OK2017-05-26
200 OK2017-05-23
200 OK2017-05-19
200 OK2017-05-16
200 OK2017-05-12
200 OK2017-05-09
200 OK2017-05-05
200 OK2017-05-02
200 OK2017-04-28
200 OK2017-04-25
200 OK2017-04-21
200 OK2017-04-18
200 OK2017-04-14
200 OK2017-04-11
200 OK2017-04-07
200 OK2017-04-04
200 OK2017-03-31
200 OK2017-03-28

Tags

Phenotype
Homo sapiens
Indian germline variant SNP

Record metadata

  • Created on: 2017-03-28
  • Curated by:
    • Lina Ma [2017-06-01]
    • Shixiang Sun [2017-03-28]
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