Home LiteratureArticle Details
PMID: 22155872 Published · ppublish English Journal Article Research Support, N.I.H., Extramural

SomaticSniper: identification of somatic point mutations in whole genome sequencing data.

Bioinformatics (Oxford, England) ·Vol. 28 ·No. 3 ·2012-02-01 ·Pages 311-7

Larson DE, Harris CC, Chen K, Koboldt DC, Abbott TE, Dooling DJ, Ley TJ, Mardis ER, Wilson RK, Ding L

Abstract

The sequencing of tumors and their matched normals is frequently used to study the genetic composition of cancer. Despite this fact, there remains a dearth of available software tools designed to compare sequences in pairs of samples and identify sites that are likely to be unique to one sample. In this article, we describe the mathematical basis of our SomaticSniper software for comparing tumor and normal pairs. We estimate its sensitivity and precision, and present several common sources of error resulting in miscalls. Binaries are freely available for download at http://gmt.genome.wustl.edu/somatic-sniper/current/, implemented in C and supported on Linux and Mac OS X. [email protected]; [email protected] Supplementary data are available at Bioinformatics online.

MeSH Terms
Genome, Human Humans Neoplasms/genetics Point Mutation Polymorphism, Single Nucleotide Software
Authors & Affiliations
10 authors, click to expand affiliations / ORCID
Larson David E
The Genome Institute, Washington University, St Louis, MO 63108, USA. [email protected]
Harris Christopher C
Chen Ken
Koboldt Daniel C
Abbott Travis E
Dooling David J
Ley Timothy J
Mardis Elaine R
Wilson Richard K
Ding Li
References (20)
20 references, click to expand
  1. Aspects of coverage in medical DNA sequencing.
    BMC Bioinformatics. 2008 May 16;9:239 PMID: 18485222
  2. dbSNP: the NCBI database of genetic variation.
    Nucleic Acids Res. 2001 Jan 1;29(1):308-11 PMID: 11125122
  3. Genome remodelling in a basal-like breast cancer metastasis and xenograft.
    Nature. 2010 Apr 15;464(7291):999-1005 PMID: 20393555
  4. Quantifying uncertainty in genotype calls.
    Bioinformatics. 2010 Jan 15;26(2):242-9 PMID: 19906825
  5. COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer.
    Nucleic Acids Res. 2011 Jan;39(Database issue):D945-50 PMID: 20952405
  6. Frequent mutations of chromatin remodeling gene ARID1A in ovarian clear cell carcinoma.
    Science. 2010 Oct 8;330(6001):228-31 PMID: 20826764
  7. VarScan: variant detection in massively parallel sequencing of individual and pooled samples.
    Bioinformatics. 2009 Sep 1;25(17):2283-5 PMID: 19542151
  8. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.
    Nature. 2008 Nov 6;456(7218):66-72 PMID: 18987736
  9. The Sequence Alignment/Map format and SAMtools.
    Bioinformatics. 2009 Aug 15;25(16):2078-9 PMID: 19505943
  10. Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution.
    Nature. 2009 Oct 8;461(7265):809-13 PMID: 19812674
  11. ARID1A mutations in endometriosis-associated ovarian carcinomas.
    N Engl J Med. 2010 Oct 14;363(16):1532-43 PMID: 20942669
  12. Patterns of somatic mutation in human cancer genomes.
    Nature. 2007 Mar 8;446(7132):153-8 PMID: 17344846
  13. DNMT3A mutations in acute myeloid leukemia.
    N Engl J Med. 2010 Dec 16;363(25):2424-33 PMID: 21067377
  14. A comprehensive catalogue of somatic mutations from a human cancer genome.
    Nature. 2010 Jan 14;463(7278):191-6 PMID: 20016485
  15. SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors.
    Bioinformatics. 2010 Mar 15;26(6):730-6 PMID: 20130035
  16. A small-cell lung cancer genome with complex signatures of tobacco exposure.
    Nature. 2010 Jan 14;463(7278):184-90 PMID: 20016488
  17. Mapping short DNA sequencing reads and calling variants using mapping quality scores.
    Genome Res. 2008 Nov;18(11):1851-8 PMID: 18714091
  18. Recurring mutations found by sequencing an acute myeloid leukemia genome.
    N Engl J Med. 2009 Sep 10;361(11):1058-66 PMID: 19657110
  19. SNP detection for massively parallel whole-genome resequencing.
    Genome Res. 2009 Jun;19(6):1124-32 PMID: 19420381
  20. Mutation of FOXL2 in granulosa-cell tumors of the ovary.
    N Engl J Med. 2009 Jun 25;360(26):2719-29 PMID: 19516027
Article Info
Journal
Bioinformatics (Oxford, England)
Abbr.
Bioinformatics
ISSN
1367-4811
DOI
10.1093/bioinformatics/btr665
Email
[email protected]
Published
2012-02-01
Epub
2011-00-06
Pages
311-7
Language
English
Region
England
NLM ID
9808944
PMCID
PMC3268238
Subset
IM
Grants
NCI NIH HHS · P01 CA101937 · United States
NHGRI NIH HHS · U54 HG003079 · United States
NHGRI NIH HHS · HG003079 · United States
External Links
PubMed source DOI: 10.1093/bioinformatics/btr665 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2