CODEX: A normalization and copy number variation detection method for whole exome sequencing

Nucleic Acids Research

Volumn 43, Issue 6, 2015, Pages e39-

  Jiang, Yuchao ^a   Oldridge, Derek A ^a,b   Diskin, Sharon J ^a,b,c   Zhang, Nancy R ^d  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b CHILDREN S HOSPITAL OF PHILADELPHIA   (United States)

^c UNIVERSITY OF PENNSYLVANIA   (United States)

^d UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ARTIFACT REDUCTION; ATRX GENE; CONTROLLED STUDY; COPY NUMBER DETECTION BY EXOME SEQUENCING; COPY NUMBER VARIATION; FEMALE; GENE; GENE DELETION; GENE SEQUENCE; HAPLOTYPE MAP; HUMAN; MALE; NEUROBLASTOMA; NOISE REDUCTION; PRIORITY JOURNAL; WHOLE EXOME SEQUENCING; ALGORITHM; CASE CONTROL STUDY; DNA BASE COMPOSITION; DNA SEQUENCE; EXOME; GENETICS; HIGH THROUGHPUT SEQUENCING; NUCLEIC ACID DATABASE; PROCEDURES; STATISTICAL BIAS; STATISTICAL MODEL; STATISTICS AND NUMERICAL DATA;

ATRX PROTEIN, HUMAN; DNA; DNA HELICASE; NUCLEAR PROTEIN;

ALGORITHMS; BASE COMPOSITION; BIAS (EPIDEMIOLOGY); CASE-CONTROL STUDIES; DATABASES, NUCLEIC ACID; DNA COPY NUMBER VARIATIONS; DNA HELICASES; DNA, NEOPLASM; EXOME; FEMALE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; LIKELIHOOD FUNCTIONS; MALE; NEUROBLASTOMA; NUCLEAR PROTEINS; SEQUENCE ANALYSIS, DNA;

EID: 84942234652     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku1363     Document Type: Article

References (46)

1. McCarroll,S.A., Hadnott,T.N., Perry,G.H., Sabeti,P.C., Zody,M.C., Barrett,J.C., Dallaire,S., Gabriel,S.B., Lee,C., Daly,M.J. et al. (2006) Common deletion polymorphisms in the human genome. Nat. Genet., 38, 86-92.
2. Conrad,D.F., Andrews,T.D., Carter,N.P., Hurles,M.E. and Pritchard,J.K. (2006) A high-resolution survey of deletion polymorphism in the human genome. Nat. Genet., 38, 75-81.
3. Redon,R., Ishikawa,S., Fitch,K.R., Feuk,L., Perry,G.H., Andrews,T.D., Fiegler,H., Shapero,M.H., Carson,A.R., Chen,W. et al. (2006) Global variation in copy number in the human genome. Nature, 444, 444-454.
4. Khaja,R., Zhang,J., MacDonald,J.R., He,Y., Joseph-George,A.M., Wei,J., Rafiq,M.A., Qian,C., Shago,M., Pantano,L. et al. (2006) Genome assembly comparison identifies structural variants in the human genome. Nat. Genet., 38, 1413-1418.
5. Diskin,S.J., Hou,C., Glessner,J.T., Attiyeh,E.F., Laudenslager,M., Bosse,K., Cole,K., Mosse,Y.P., Wood,A., Lynch,J.E. et al. (2009) Copy number variation at 1q21.1 associated with neuroblastoma. Nature, 459, 987-991.
6. Glessner,J.T., Wang,K., Cai,G., Korvatska,O., Kim,C.E., Wood,S., Zhang,H., Estes,A., Brune,C.W., Bradfield,J.P. et al. (2009) Autism genome-wide copy number variation reveals ubiquitin and neuronal genes. Nature, 459, 569-573.
7. McCarroll,S.A., Huett,A., Kuballa,P., Chilewski,S.D., Landry,A., Goyette,P., Zody,M.C., Hall,J.L., Brant,S.R., Cho,J.H. et al. (2008) Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease. Nat. Genet., 40, 1107-1112.
8. Pinkel,D., Segraves,R., Sudar,D., Clark,S., Poole,I., Kowbel,D., Collins,C., Kuo,W.L., Chen,C., Zhai,Y. et al. (1998) High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat. Genet., 20, 207-211.
9. Wang,K., Li,M., Hadley,D., Liu,R., Glessner,J., Grant,S.F., Hakonarson,H. and Bucan,M. (2007) PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res., 17, 1665-1674.
10. Carter,N.P. (2007) Methods and strategies for analyzing copy number variation using DNA microarrays. Nat. Genet., 39, S16-S21.
11. Mills,R.E., Luttig,C.T., Larkins,C.E., Beauchamp,A., Tsui,C., Pittard,W.S. and Devine,S.E. (2006) An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res., 16, 1182-1190.
12. Chiang,D.Y., Getz,G., Jaffe,D.B., O'Kelly,M.J., Zhao,X., Carter,S.L., Russ,C., Nusbaum,C., Meyerson,M. and Lander,E.S. (2009) High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat. Methods, 6, 99-103.
13. Yoon,S., Xuan,Z., Makarov,V., Ye,K. and Sebat,J. (2009) Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res., 19, 1586-1592.
14. Korbel,J.O., Abyzov,A., Mu,X.J., Carriero,N., Cayting,P., Zhang,Z., Snyder,M. and Gerstein,M.B. (2009) PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol., 10, R23.
15. Abyzov,A., Urban,A.E., Snyder,M. and Gerstein,M. (2011) CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res., 21, 974-984.
16. Ng,S.B., Buckingham,K.J., Lee,C., Bigham,A.W., Tabor,H.K., Dent,K.M., Huff,C.D., Shannon,P.T., Jabs,E.W., Nickerson,D.A. et al. (2010) Exome sequencing identifies the cause of a mendelian disorder. Nat. Genet., 42, 30-35.
17. O'Roak,B.J., Deriziotis,P., Lee,C., Vives,L., Schwartz,J.J., Girirajan,S., Karakoc,E., Mackenzie,A.P., Ng,S.B., Baker,C. et al. (2011) Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations. Nat. Genet., 43, 585-589.
18. Yan,X.J., Xu,J., Gu,Z.H., Pan,C.M., Lu,G., Shen,Y., Shi,J.Y., Zhu,Y.M., Tang,L., Zhang,X.W. et al. (2011) Exome sequencing identifies somatic mutations of DNA methyltransferase gene DNMT3A in acute monocytic leukemia. Nat. Genet., 43, 309-315.
19. Sanders,S.J., Murtha,M.T., Gupta,A.R., Murdoch,J.D., Raubeson,M.J., Willsey,A.J., Ercan-Sencicek,A.G., DiLullo,N.M., Parikshak,N.N., Stein,J.L. et al. (2012) De novo mutations revealed by whole-exome sequencing are strongly associated with autism. Nature, 485, 237-241.
20. Pugh,T.J., Morozova,O., Attiyeh,E.F., Asgharzadeh,S., Wei,J.S., Auclair,D., Carter,S.L., Cibulskis,K., Hanna,M., Kiezun,A. et al. (2013) The genetic landscape of high-risk neuroblastoma. Nat. Genet., 45, 279-284.
21. Sathirapongsasuti,J.F., Lee,H., Horst,B.A., Brunner,G., Cochran,A.J., Binder,S., Quackenbush,J. and Nelson,S.F. (2011) Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV. Bioinformatics, 27, 2648-2654.
22. Koboldt,D.C., Zhang,Q., Larson,D.E., Shen,D., McLellan,M.D., Lin,L., Miller,C.A., Mardis,E.R., Ding,L. and Wilson,R.K. (2012) VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res., 22, 568-576.
23. Amarasinghe,K.C., Li,J. and Halgamuge,S.K. (2013) CoNVEX: copy number variation estimation in exome sequencing data using HMM. BMC Bioinformatics, 14(Suppl 2), S2.
24. Plagnol,V., Curtis,J., Epstein,M., Mok,K.Y., Stebbings,E., Grigoriadou,S., Wood,N.W., Hambleton,S., Burns,S.O., Thrasher,A.J. et al. (2012) A robust model for read count data in exome sequencing experiments and implications for copy number variant calling. Bioinformatics, 28, 2747-2754.
25. Magi,A., Tattini,L., Cifola,I., D'Aurizio,R., Benelli,M., Mangano,E., Battaglia,C., Bonora,E., Kurg,A., Seri,M. et al. (2013) EXCAVATOR: detecting copy number variants from whole-exome sequencing data. Genome Biol., 14, R120.
26. Krumm,N., Sudmant,P.H., Ko,A., O'Roak,B.J., Malig,M., Coe,B.P., Project,N.E.S., Quinlan,A.R., Nickerson,D.A. and Eichler,E.E. (2012) Copy number variation detection and genotyping from exome sequence data. Genome Res., 22, 1525-1532.
27. Coin,L.J., Cao,D., Ren,J., Zuo,X., Sun,L., Yang,S., Zhang,X., Cui,Y., Li,Y., Jin,X. et al. (2012) An exome sequencing pipeline for identifying and genotyping common CNVs associated with disease with application to psoriasis. Bioinformatics, 28, i370-i374.
28. Fromer,M., Moran,J.L., Chambert,K., Banks,E., Bergen,S.E., Ruderfer,D.M., Handsaker,R.E., McCarroll,S.A., O'Donovan,M.C., Owen,M.J. et al. (2012) Discovery and statistical genotyping of copy-number variation from whole-exome sequencing depth. Am. J. Hum. Genet., 91, 597-607.
29. 1000 Genomes Project Consortium, Abecasis,G.R., Altshuler,D., Auton,A., Brooks,L.D., Durbin,R.M., Gibbs,R.A., Hurles,M.E. and McVean,G.A. (2010) A map of human genome variation from population-scale sequencing. Nature, 467, 1061-1073.
30. International HapMap 3 Consortium, Altshuler,D.M., Gibbs,R.A., Peltonen,L., Altshuler,D.M., Gibbs,R.A., Peltonen,L., Dermitzakis,E., Schaffner,S.F., Yu,F. et al. (2010) Integrating common and rare genetic variation in diverse human populations. Nature, 467, 52-58.
31. McCarroll,S.A., Kuruvilla,F.G., Korn,J.M., Cawley,S., Nemesh,J., Wysoker,A., Shapero,M.H., de Bakker,P.I., Maller,J.B., Kirby,A. et al. (2008) Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat. Genet., 40, 1166-1174.
32. Conrad,D.F., Pinto,D., Redon,R., Feuk,L., Gokcumen,O., Zhang,Y., Aerts,J., Andrews,T.D., Barnes,C., Campbell,P. et al. (2010) Origins and functional impact of copy number variation in the human genome. Nature, 464, 704-712.
33. Molenaar,J.J., Koster,J., Zwijnenburg,D.A., van Sluis,P., Valentijn,L.J., van der Ploeg,I., Hamdi,M., van Nes,J., Westerman,B.A., van Arkel,J. et al. (2012) Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes. Nature, 483, 589-593.
34. Cheung,N.K., Zhang,J., Lu,C., Parker,M., Bahrami,A., Tickoo,S.K., Heguy,A., Pappo,A.S., Federico,S., Dalton,J. et al. (2012) Association of age at diagnosis and genetic mutations in patients with neuroblastoma. J. Am. Med. Assoc., 307, 1062-1071.
35. Li,H., Handsaker,B., Wysoker,A., Fennell,T., Ruan,J., Homer,N., Marth,G., Abecasis,G., Durbin,R. and 1000 Genome Project Data Processing Subgroup. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25, 2078-2079.
36. Lee,S., Chugh,P.E., Shen,H., Eberle,R. and Dittmer,D.P. (2013) Poisson factor models with applications to non-normalized microRNA profiling. Bioinformatics, 29, 1105-1111.
37. Leek,J.T. and Storey,J.D. (2008) A general framework for multiple testing dependence. Proc. Natl. Acad. Sci. U.S.A., 105, 18718-18723.
38. Carvalho,C.M., Chang,J., Lucas,J.E., Nevins,J.R., Wang,Q. and West,M. (2008) High-dimensional sparse factor modeling: applications in gene expression genomics. J. Am. Stat. Assoc., 103, 1438-1456.
39. Friguet,C., Kloareg,M. and Causeur,D. (2009) A factor model approach to multiple testing under dependence. J. Am. Stat. Assoc., 104, 1406-1415.
40. Sun,Y.T., Zhang,N.R. and Owen,A.B. (2012) Multiple hypothesis testing adjusted for latent variables, with an application to the Agemap gene expression data. Ann. Appl. Stat., 6, 1664-1688.
41. Zhang,N.R., Siegmund,D.O., Ji,H. and Li,J.Z. (2010) Detecting simultaneous changepoints in multiple sequences. Biometrika, 97, 631-645.
42. Olshen,A.B., Venkatraman,E.S., Lucito,R. and Wigler,M. (2004) Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics, 5, 557-572.
43. Zhang,N.R. and Siegmund,D.O. (2007) A modified Bayes information criterion with applications to the analysis of comparative genomic hybridization data. Biometrics, 63, 22-32.
44. Benjamini,Y. and Speed,T.P. (2012) Summarizing and correcting the GC content bias in high-throughput sequencing. Nucleic Acids Res., 40, e72.
45. Redon,R., Ishikawa,S., Fitch,K.R., Feuk,L., Perry,G.H., Andrews,T.D., Fiegler,H., Shapero,M.H., Carson,A.R., Chen,W. et al. (2006) Global variation in copy number in the human genome. Nature, 444, 444-454.
46. Kidd,J.M., Cooper,G.M., Donahue,W.F., Hayden,H.S., Sampas,N., Graves,T., Hansen,N., Teague,B., Alkan,C., Antonacci,F. et al. (2008) Mapping and sequencing of structural variation from eight human genomes. Nature, 453, 56-64.