Consensus rules in variant detection from next-generation sequencing data

PLoS ONE

Volumn 7, Issue 6, 2012, Pages

  Jia, Peilin ^a   Li, Fei ^b   Xia, Jufeng ^b   Chen, Haiquan ^c,d   Ji, Hongbin ^b   Pao, William ^a,e   Zhao, Zhongming ^a,e  

^a VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b INSTITUTE OF BIOCHEMISTRY AND CELL BIOLOGY   (China)

^c FUDAN UNIVERSITY SHANGHAI CANCER CENTER   (China)

^d FUDAN UNIVERSITY   (China)

^e VANDERBILT INGRAM CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; CALCULATION; CALIBRATION; CDC27 GENE; CONTROLLED STUDY; CTBP2 GENE; DATA MINING; EXON; GENE; GENE MUTATION; INFORMATION PROCESSING; INFORMATION RETRIEVAL; NEXT GENERATION SEQUENCING DATA; OR4C3 GENE; SCORING SYSTEM; SEQUENCE ANALYSIS; SEQUENCE DATABASE; VALIDITY; DEVICES; DNA SEQUENCE; HIGH THROUGHPUT SEQUENCING; PROCEDURES;

HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; SEQUENCE ANALYSIS, DNA;

EID: 84862002889     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0038470     Document Type: Article

References (29)

1. Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, (2010) Exome sequencing identifies the cause of a mendelian disorder. Nat Genet 42: 30 35.
2. Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, (2009) Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461: 272 276.
3. Xia J, Wang Q, Jia P, Wang B, Pao W, (2012) NGS Catalog: A database of next generation sequencing studies in humans. Hum Mutat 33: E2341 2355.
4. Varela I, Tarpey P, Raine K, Huang D, Ong CK, (2011) Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma. Nature 469: 539 542.
5. Wei X, Walia V, Lin JC, Teer JK, Prickett TD, (2011) Exome sequencing identifies GRIN2A as frequently mutated in melanoma. Nat Genet 43: 442 446.
6. Totoki Y, Tatsuno K, Yamamoto S, Arai Y, Hosoda F, (2011) High-resolution characterization of a hepatocellular carcinoma genome. Nat Genet 43: 464 469.
7. Yan XJ, Xu J, Gu ZH, Pan CM, Lu G, (2011) Exome sequencing identifies somatic mutations of DNA methyltransferase gene DNMT3A in acute monocytic leukemia. Nat Genet 43: 309 315.
8. Agrawal N, Frederick MJ, Pickering CR, Bettegowda C, Chang K, (2011) Exome sequencing of head and neck squamous cell carcinoma reveals inactivating mutations in NOTCH1. Science 333: 1154 1157.
9. Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061 1073.
10. Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, (2008) The complete genome of an individual by massively parallel DNA sequencing. Nature 452: 872 876.
11. Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, (2007) The diploid genome sequence of an individual human. PLoS Biol 5: e254.
12. Wang J, Wang W, Li R, Li Y, Tian G, (2008) The diploid genome sequence of an Asian individual. Nature 456: 60 65.
13. Koboldt DC, Ding L, Mardis ER, Wilson RK, (2010) Challenges of sequencing human genomes. Brief Bioinform 11: 484 498.
14. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43: 491 498.
15. Ley TJ, Mardis ER, Ding L, Fulton B, McLellan MD, (2008) DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 456: 66 72.
16. Li H, Ruan J, Durbin R, (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18: 1851 1858.
17. Teer JK, Bonnycastle LL, Chines PS, Hansen NF, Aoyama N, (2010) Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing. Genome Res 20: 1420 1431.
18. Ng SB, Nickerson DA, Bamshad MJ, Shendure J, (2010) Massively parallel sequencing and rare disease. Hum Mol Genet 19: R119 124.
19. Li H, (2011) Improving SNP discovery by base alignment quality. Bioinformatics 27: 1157 1158.
20. Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754 1760.
21. Langmead B, Trapnell C, Pop M, Salzberg SL, (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
22. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078 2079.
23. SAMtools website. Available:http://sourceforge.net/apps/mediawiki/samtools/index.php?title=SAM_FAQ. Accessed 2011 Dec 1.
24. Xu B, Roos JL, Dexheimer P, Boone B, Plummer B, (2011) Exome sequencing supports a de novo mutational paradigm for schizophrenia. Nat Genet 43: 864 868.
25. The VCF format. Available:http://vcftools.sourceforge.net/specs.html. Accessed 2011 Dec 1.
26. Johnson JO, Gibbs JR, Van Maldergem L, Houlden H, Singleton AB, (2010) Exome sequencing in Brown-Vialetto-van Laere syndrome. Am J Hum Genet 87: 567-569; author reply 569-570.
27. Hoischen A, van Bon BW, Gilissen C, Arts P, van Lier B, (2010) De novo mutations of SETBP1 cause Schinzel-Giedion syndrome. Nat Genet 42: 483 485.
28. Ju YS, Kim JI, Kim S, Hong D, Park H, (2011) Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of eighteen Korean individuals. Nat Genet 43: 745 752.
29. Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, (2011) Integrative genomics viewer. Nat Biotechnol 29: 24 26.