Nidhi Bindal

Publications (3)18.12 Total impact

• Source

  Available from: PubMed Central

  Article: Data mining using the Catalogue of Somatic Mutations in Cancer BioMart.

  Rebecca Shepherd, Simon A Forbes, David Beare, S Bamford, Charlotte G Cole, Sari Ward, Nidhi Bindal, Prasad Gunasekaran, Mingming Jia, Chai Yin Kok, Kenric Leung, Andrew Menzies, Adam P Butler, Jon W Teague, Peter J Campbell, Michael R Stratton, P Andrew Futreal
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  ABSTRACT: Catalogue of Somatic Mutations in Cancer (COSMIC) (http://www.sanger.ac.uk/cosmic) is a publicly available resource providing information on somatic mutations implicated in human cancer. Release v51 (January 2011) includes data from just over 19,000 genes, 161,787 coding mutations and 5573 gene fusions, described in more than 577,000 tumour samples. COSMICMart (COSMIC BioMart) provides a flexible way to mine these data and combine somatic mutations with other biological relevant data sets. This article describes the data available in COSMIC along with examples of how to successfully mine and integrate data sets using COSMICMart. DATABASE URL: http://www.sanger.ac.uk/genetics/CGP/cosmic/biomart/martview/.
  Database The Journal of Biological Databases and Curation 01/2011; 2011:bar018. · 2.07 Impact Factor
• Source

  Available from: PubMed Central

  Article: COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer.

  Simon A Forbes, Nidhi Bindal, Sally Bamford, Charlotte Cole, Chai Yin Kok, David Beare, Mingming Jia, Rebecca Shepherd, Kenric Leung, Andrew Menzies, Jon W Teague, Peter J Campbell, Michael R Stratton, P Andrew Futreal
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  ABSTRACT: COSMIC (http://www.sanger.ac.uk/cosmic) curates comprehensive information on somatic mutations in human cancer. Release v48 (July 2010) describes over 136,000 coding mutations in almost 542,000 tumour samples; of the 18,490 genes documented, 4803 (26%) have one or more mutations. Full scientific literature curations are available on 83 major cancer genes and 49 fusion gene pairs (19 new cancer genes and 30 new fusion pairs this year) and this number is continually increasing. Key amongst these is TP53, now available through a collaboration with the IARC p53 database. In addition to data from the Cancer Genome Project (CGP) at the Sanger Institute, UK, and The Cancer Genome Atlas project (TCGA), large systematic screens are also now curated. Major website upgrades now make these data much more mineable, with many new selection filters and graphics. A Biomart is now available allowing more automated data mining and integration with other biological databases. Annotation of genomic features has become a significant focus; COSMIC has begun curating full-genome resequencing experiments, developing new web pages, export formats and graphics styles. With all genomic information recently updated to GRCh37, COSMIC integrates many diverse types of mutation information and is making much closer links with Ensembl and other data resources.
  Nucleic Acids Research 10/2010; 39(Database issue):D945-50. · 8.03 Impact Factor
• Source

  Available from: PubMed Central

  Article: COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer.

  Simon A Forbes, Gurpreet Tang, Nidhi Bindal, Sally Bamford, Elisabeth Dawson, Charlotte Cole, Chai Yin Kok, Mingming Jia, Rebecca Ewing, Andrew Menzies, Jon W Teague, Michael R Stratton, P Andrew Futreal
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  ABSTRACT: The catalogue of Somatic Mutations in Cancer (COSMIC) (http://www.sanger.ac.uk/cosmic/) is the largest public resource for information on somatically acquired mutations in human cancer and is available freely without restrictions. Currently (v43, August 2009), COSMIC contains details of 1.5-million experiments performed through 13,423 genes in almost 370,000 tumours, describing over 90,000 individual mutations. Data are gathered from two sources, publications in the scientific literature, (v43 contains 7797 curated articles) and the full output of the genome-wide screens from the Cancer Genome Project (CGP) at the Sanger Institute, UK. Most of the world's literature on point mutations in human cancer has now been curated into COSMIC and while this is continually updated, a greater emphasis on curating fusion gene mutations is driving the expansion of this information; over 2700 fusion gene mutations are now described. Whole-genome sequencing screens are now identifying large numbers of genomic rearrangements in cancer and COSMIC is now displaying details of these analyses also. Examination of COSMIC's data is primarily web-driven, focused on providing mutation range and frequency statistics based upon a choice of gene and/or cancer phenotype. Graphical views provide easily interpretable summaries of large quantities of data, and export functions can provide precise details of user-selected data.
  Nucleic Acids Research 11/2009; 38(Database issue):D652-7. · 8.03 Impact Factor