Quantifying single nucleotide variant detection sensitivity in exome sequencing

BMC Bioinformatics

Volumn 14, Issue 1, 2013, Pages

  Meynert, Alison M ^a   Bicknell, Louise S ^a   Hurles, Matthew E ^b   Jackson, Andrew P ^a   Taylor, Martin S ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CALIBRATED MODEL; DETECTION SENSITIVITY; POLYMORPHIC SITES; QUANTITATIVE TRAITS; SENSITIVITY MEASURES; SINGLE NUCLEOTIDES; SOMATIC MUTATION; TARGET SEQUENCES;

DISEASES; ESTIMATION; GENES; GENETIC ENGINEERING;

NUCLEOTIDES;

ALLELE; ARTICLE; EXOME; EXON; GENETIC VARIABILITY; GENOMICS; GENOTYPE; GENOTYPING TECHNIQUE; HETEROZYGOTE; HIGH THROUGHPUT SEQUENCING; HOMOZYGOTE; HUMAN; HUMAN GENOME; METHODOLOGY; PROCEDURES;

ALLELES; EXOME; EXONS; GENETIC VARIATION; GENOME, HUMAN; GENOMICS; GENOTYPE; GENOTYPING TECHNIQUES; HETEROZYGOTE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HOMOZYGOTE; HUMANS;

EID: 84879043343     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-195     Document Type: Article

References (30)

1. Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, Lee C, Shaffer T, Wong M, Bhattacharjee A, Eichler EE, Bamshad M, Nickerson DA, Shendure J. Targeted capture and massively parallel sequencing of 12 human exomes. Nature 2009, 461(7261):272-276. [http://www.hubmed.org/fulltext.cgi?uids=19684571].
2. Cooper DN, Krawczak M, Antonarakis S. The nature and mechanisms of human gene mutation. The metabolic and molecular bases of inherited disease. 7th edition 1995, 259-291. New York: McGraw-Hill, Sriver CR, Beaudet AL, Sly WS, Valle D, ISBN 0-07-909826-6.
3. Choi M, Scholl UI, Ji W, Liu T, Tikhonova IR, Zumbo P, Nayir A, Bakkaloǧlu A, Ozen S, Sanjad S, Nelson-Williams C, Farhi A, Mane S, Lifton RP. Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc Natl Acad Sci U S A 2009, 106(45):19096-19101. [http://www.hubmed.org/fulltext.cgi?uids=19861545].
4. Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, Dent KM, Huff CD, Shannon PT, Jabs EW, Nickerson DA, Shendure J, Bamshad MJ. Exome sequencing identifies the cause of a mendelian disorder. Nat Genet 2010, 42:30-35. [http://www.hubmed.org/fulltext.cgi?uids=19915526].
5. Ng SB, Bigham AW, Buckingham KJ, Hannibal MC, McMillin MJ, Gildersleeve HI, Beck AE, Tabor HK, Cooper GM, Mefford HC, Lee C, Turner EH, Smith JD, Rieder MJ, Yoshiura K, Matsumoto N, Ohta T, Niikawa N, Nickerson DA, Bamshad MJ, Shendure J. Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat Genet 2010, 42(9):790-793. [http://www.hubmed.org/fulltext.cgi?uids=20711175].
6. Timmermann B, Kerick M, Roehr C, Fischer A, Isau M, Boerno ST, Wunderlich A, Barmeyer C, Seemann P, Koenig J, Lappe M, Kuss AW, Garshasbi M, Bertram L, Trappe K, Werber M, Herrmann BG, Zatloukal K, Lehrach H, Schweiger MR. Somatic mutation profiles of MSI and MSS colorectal cancer identified by whole exome next generation sequencing and bioinformatics analysis. PLoS One 2010, 5(12). [http://www.hubmed.org/fulltext.cgi?uids=21203531].
7. Fransen K, Mitrovic M, van Diemen CC, Weersma RK. The quest for genetic risk factors for Crohn's disease in the post-GWAS era. Genome Med 2011, 3(2):13-13. [http://www.hubmed.org/display.cgi?uids=21392414].
8. Mantripragada KK, Carroll LS, Williams NM. Experimental approaches for identifying schizophrenia risk genes. Curr Top Behav Neurosci 2010, 4:587-610. [http://www.hubmed.org/display.cgi?uids=21312414].
9. Lehne B, Lewis CM, Schlitt T. Exome localization of complex disease association signals. BMC Genomics 2011, 12:92-92. [http://www.hubmed.org/fulltext.cgi?uids=21284873].
10. Li Y, Vinckenbosch N, Tian G, Huerta-Sanchez E, Jiang T, Jiang H, Albrechtsen A, Andersen G, Cao H, Korneliussen T, Grarup N, Guo Y, Hellman I, Jin X, Li Q, Liu J, Liu X, Sparso T, Tang M, Wu H, Wu R, Yu C, Zheng H, Astrup A, Bolund L, Holmkvist J, Jorgensen T, Kristiansen K, Schmitz O, Schwartz TW, Zhang X, Li R, Yang H, Wang J, Hansen T, Pedersen O, Nielsen R, Wang J. Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nat Genet 2010, [http://www.hubmed.org/fulltext.cgi?uids=20890277].
11. Depristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, Del Angel G, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 2011, [http://www.hubmed.org/fulltext.cgi?uids=21478889].
12. Clark MJ, Chen R, Lam HYK, Karczewski KJ, Chen R, Euskirchen G, Butte AJ, Snyder M. Performance comparison of exome DNA sequencing technologies. Nat Biotech 2011, 29(10):908-914. [http://dx.doi.org/10.1038/nbt.1975].
13. Degner JF, Marioni JC, Pai AA, Pickrell JK, Nkadori E, Gilad Y, Pritchard JK. Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics 2009, 25(24):3207-3212. [http://www.hubmed.org/fulltext.cgi?uids=19808877].
14. Ajay SS, Parker SC, Ozel Abaan H, Fuentes Fajardo KV, Margulies EH. Accurate and comprehensive sequencing of personal genomes. Genome Res 2011, [http://www.hubmed.org/fulltext.cgi?uids=21771779].
15. The International HapMap 3 Consortium Integrating common and rare genetic variation in diverse human populations. Nature 2010, 467(7311):52-58. [http://www.hubmed.org/fulltext.cgi?uids=20811451], The International HapMap 3 Consortium.
16. Hahn MW. Detecting natural selection on cis-regulatory DNA. Genetica 2007, 129:7-18. [http://www.hubmed.org/fulltext.cgi?uids=16955334].
17. Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee BK, Lee K, London D, Lotakis D, Neph S, et al. The accessible chromatin landscape of the human genome. Nature 2012, 489(7414):75-82. [http://www.hubmed.org/fulltext.cgi?uids=22955617].
18. Xu Y, Jiang H, Tyler-Smith C, Xue Y, Jiang T, Wang J, Wu M, Liu X, Tian G, Wang J, Wang J, Yang H, Zhang X, Asan Comprehensive comparison of three commercial human whole-exome capture platforms. Genome Biol 2011, 12(9):R95. [http://genomebiology.com/2011/12/9/R95], Asan.
19. Parla J, Iossifov I, Grabill I, Spector M, Kramer M, McCombie WR. A comparative analysis of exome capture. Genome Biol 2011, 12(9):R97. [http://genomebiology.com/content/12/9/R97].
20. Sulonen AM, Ellonen P, Almusa H, Lepisto M, Eldfors S, Hannula S, Miettinen T, Tyynismaa H, Salo P, Heckman C, Joensuu H, Raivio T, Suomalainen A, Saarela J. Comparison of solution-based exome capture methods for next generation sequencing. Genome Biol 2011, 12(9):R94. [http://genomebiology.com/2011/12/9/R94].
21. Harte RA, Farrell CM, Loveland JE, Suner MM, Wilming L, Aken B, Barrell D, Frankish A, Wallin C, Searle S, Diekhans M, Harrow J, Pruitt KD. Tracking and coordinating an international curation effort for the CCDS Project. Database (Oxford) 2012, 2012. [http://www.hubmed.org/fulltext.cgi?uids=22434842].
22. Teer JK, Bonnycastle LL, Chines PS, Hansen NF, Aoyama N, Swift AJ, Abaan HO, Albert TJ, Margulies EH, Green ED, Collins FS, Mullikin JC, Biesecker LG, NISC Comparative Sequencing Program Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing. Genome Res 2010, 20(10):1420-1431. [http://www.hubmed.org/fulltext.cgi?uids=20810667], NISC Comparative Sequencing Program.
23. Bainbridge MN, Wang M, Burgess DL, Kovar C, Rodesch MJ, D'Ascenzo M, Kitzman J, Wu YQ, Newsham I, Richmond TA, Jeddeloh JA, Muzny D, Albert TJ, Gibbs RA. Whole exome capture in solution with 3 Gbp of data. Genome Biol 2010, 11(6). [http://www.hubmed.org/fulltext.cgi?uids=20565776].
24. Kalay E, Yigit G, Aslan Y, Brown KE, Pohl E, Bicknell LS, Kayserili H, Li Y, Tüysüz B, Nürnberg G, Kiess W, Koegl M, Baessmann I, Buruk K, Toraman B, Kayipmaz S, Kul S, Ikbal M, Turner DJ, Taylor MS, Aerts J, Scott C, Milstein K, Dollfus H, Wieczorek D, Brunner HG, Hurles M, Jackson AP, Rauch A, Nürnberg P, Karagüzel A, Wollnik B. CEP152 is a genome maintenance protein disrupted in Seckel syndrome. Nat Genet 2011, 43:23-26. [http://www.hubmed.org/fulltext.cgi?uids=21131973].
25. Coffey AJ, Kokocinski F, Calafato MS, Scott CE, Palta P, Drury E, Joyce CJ, Leproust EM, Harrow J, Hunt S, Lehesjoki AE, Turner DJ, Hubbard TJ, Palotie A. The GENCODE exome: sequencing the complete human exome. Eur J Hum Genet 2011, [http://www.hubmed.org/fulltext.cgi?uids=21364695].
26. Leinonen R, Sugawara H, Shumway M The sequence read archive. Nucleic Acids Res 2011, 39(Database issue):19-21. [http://www.hubmed.org/fulltext.cgi?uids=21062823], Shumway M.
27. Mailman MD, Feolo M, Jin Y, Kimura M, Tryka K, Bagoutdinov R, Hao L, Kiang A, Paschall J, Phan L, Popova N, Pretel S, Ziyabari L, Lee M, Shao Y, Wang ZY, Sirotkin K, Ward M, Kholodov M, Zbicz K, Beck J, Kimelman M, Shevelev S, Preuss D, Yaschenko E, Graeff A, Ostell J, Sherry ST. The NCBI dbGaP database of genotypes and phenotypes. Nat Genet 2007, 39(10):1181-1186. [http://www.hubmed.org/fulltext.cgi?uids=17898773].
28. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25(14):1754-1760. [http://www.hubmed.org/fulltext.cgi?uids=19451168].
29. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010, 20(9):1297-1303. [http://www.hubmed.org/fulltext.cgi?uids=20644199].
30. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 25(16):2078-2079. [http://www.hubmed.org/fulltext.cgi?uids=19505943], 1000 Genome Project Data Processing Subgroup.