A unified approach for allele frequency estimation, SNP detection and association studies based on pooled sequencing data using EM algorithms

BMC Genomics

Volumn 14, Issue , 2013, Pages

  Chen, Quan ^a   Sun, Fengzhu ^a,b  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b TSINGHUA UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; EXPECTATION MAXIMIZATION ALGORITHM; GENE FREQUENCY; GENETIC ASSOCIATION; INSULIN DEPENDENT DIABETES MELLITUS; MEASUREMENT ACCURACY; NEXT GENERATION SEQUENCING; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS; COMPUTER PROGRAM; GENETIC DATABASE; GENETICS; GENOTYPE; HIGH THROUGHPUT SEQUENCING; HUMAN; INTERNET;

ALGORITHMS; DATABASES, GENETIC; DIABETES MELLITUS, TYPE 1; GENE FREQUENCY; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INTERNET; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE;

MLCS; MLOWN;

EID: 84881265576     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-S1-S1     Document Type: Article

References (29)

1. Yang J, Benyamin B, McEvoy BP, Gordon S, Henders AK, Nyholt DR, Madden PA, Heath AC, Martin NG, Montgomery GW, Goddard ME, Visscher PM: Common SNPs explain a large proportion of the heritability for human height. Nature Genetics 2010, 42:565-569.
2. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A, Cho JH, Guttmacher AE, Kong A, Kruglyak L, Mardis E, Rotimi CN, Slatkin M, Valle D, Whittemore AS, Boehnke M, Clark AG, Eichler EE, Gibson G, Haines JL, Mackay TFC, McCarroll SA, Visscher PM: Finding the missing heritability of complex diseases. Nature 2009, 461:747-753.
3. Nelson MR, Wegmann D, Ehm MG, Kessner D, Jean PS, Verzilli C, Shen J, Tang Z, Bacanu SA, Fraser D, Warren L, Aponte J, Zawistowski M, Liu X, Zhang H, Zhang Y, Li J, Li Y, Li L, Woollard P, Topp S, Hall MD, Nangle K, Wang J, Abecasis G, Cardon LR, Zöllner S, Whittaker JC, Chissoe SL, Novembre J, Mooser V: An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science 2012, 337:100-104.
4. Tennessen JA, Bigham AW, O'Connor TD, Fu W, Kenny EE, Gravel S, McGee S, Do R, Liu X, Jun G, Kang HM, Jordan D, Leal SM, Gabriel S, Rieder MJ, Abecasis G, Altshuler D, Nickerson DA, Boerwinkle E, Sunyaev S, Bustamante CD, Bamshad MJ, Akey JM: Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 2012, 337:64-69.
5. Benaglio P, McGee TL, Capelli LP, Harper S, Berson EL, Rivolta C: Next generation sequencing of pooled samples reveals new SNRNP200 mutations associated with retinitis pigmentosa. Human Mutation 2011, 32:E2246-2258.
6. Rivas MA, Beaudoin M, Gardet A, Stevens C, Sharma Y, Zhang CK, Boucher G, Ripke S, Ellinghaus D, Burtt N, Fennell T, Kirby A, Latiano A, Goyette P, Green T, Halfvarson J, Haritunians T, Korn JM, Kuruvilla F, Lagacé C, Neale B, Lo KS, Schumm P, Törkvist L, Dubinsky MC, Brant SR, Silverberg MS, Duerr RH, Altshuler D, Gabriel S, Lettre G, Franke A, D'Amato M, McGovern DPB, Cho JH, Rioux JD, Xavier RJ, Daly MJ: Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease. Nature Genetics 2011, 43:1066-1073.
7. Out AA, van Minderhout IJHM, Goeman JJ, Ariyurek Y, Ossowski S, Schneeberger K, Weigel D, van Galen M, Taschner PEM, Tops CMJ, Breuning MH, van Ommen GJB, den Dunnen JT, Devilee P, Hes FJ: Deep sequencing to reveal new variants in pooled DNA samples. Human Mutation 2009, 30:1703-1712.
8. Nejentsev S, Walker N, Riches D, Egholm M, Todd JA: Rare variants of IFIH1, a gene implicated in antiviral responses, protect against type 1 diabetes. Science 2009, 324:387-389.
9. Druley TE, Vallania FLM, Wegner DJ, Varley KE, Knowles OL, Bonds JA, Robison SW, Doniger SW, Hamvas A, Cole FS, Fay JC, Mitra RD: Quantification of rare allelic variants from pooled genomic DNA. Nature Methods 2009, 6:263-265.
10. Bansal V: A statistical method for the detection of variants from nextgeneration resequencing of DNA pools. Bioinformatics 2010, 26:i318-i324.
11. Wei Z, Wang W, Hu P, Lyon GJ, Hakonarson H: SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data. Nucleic Acids Research 2011, 39:e132.
12. Li H, Durbin R: Fast and accurate long-read alignment with Burrows- Wheeler transform. Bioinformatics 2010, 26:589-595.
13. Altmann A, Weber P, Quast C, Rex-Haffner M, Binder EB, Müller-Myhsok B: vipR: variant identification in pooled DNA using R. Bioinformatics 2011, 27:i77-i84.
14. Kim SY, Li Y, Guo Y, Li R, Holmkvist J, Hansen T, Pedersen O, Wang J, Nielsen R: Design of association studies with pooled or un-pooled nextgeneration sequencing data. Genetic Epidemiology 2010, 34:479-491.
15. Wang T, Lin CY, Rohan TE, Ye K: Resequencing of pooled DNA for detecting disease associations with rare variants. Genetic Epidemiology 2010, 34:492-501.
16. Lee JS, Choi M, Yan X, Lifton RP, Zhao H: On optimal pooling designs to identify rare variants through massive resequencing. Genetic Epidemiology 2011, 35:139-147.
17. Chen X, Listman JB, Slack FJ, Gelernter J, Zhao H: Biases and errors on allele frequency estimation and disease association tests of next generation sequencing of pooled samples. Genetic Epidemiology 2012, (Epub ahead of print).
18. Self SG, Liang KY: Asymptotic properties of maximum likelihood estimators and likelihood ratio tests under nonstandard conditions. Journal of the American Statistical Association 1987, 82:605-610.
19. Quinlan AR, Stewart DA, Strömberg MP, Marth GT: Pyrobayes: an improved base caller for SNP discovery in pyrosequences. Nature Methods 2008, 5:179-181.
20. Flicek P, Birney E: Sense from sequence reads: methods for alignment and assembly. Nature Methods 2009, 6:S6-S12.
21. Hillier LW, Marth GT, Quinlan AR, Dooling D, Fewell G, Barnett D, Fox P, Glasscock JI, Hickenbotham M, Huang W, Magrini VJ, Richt RJ, Sander SN, Stewart DA, Stromberg M, Tsung EF, Wylie T, Schedl T, Wilson RK, Mardis ER: Whole-genome sequencing and variant discovery in C. elegans. Nature Methods 2008, 5:183-188.
22. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R: The sequence alignment/map format and SAMtools. Bioinformatics 2009, 25:2078-2079.
23. Wang K, Li M, Hakonarson H: ANNOVAR: functional annotation of genetic variants from highthroughput sequencing data. Nucleic Acids Research 2010, 38:e164-e164.
24. Sherry ST, Ward M, Sirotkin K: dbSNP-Database for single nucleotide polymorphisms and other classes of minor genetic variation. Genome Research 1999, 9:677-679.
25. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, Angel Gd, Rivas MA, 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 nextgeneration DNA sequencing data. Nature Genetics 2011, 43:491-498.
26. Cooper JD, Smyth DJ, Smiles AM, Plagnol V, Walker NM, Allen JE, Downes K, Barrett JC, Healy BC, Mychaleckyj JC, Warram JH, Todd JA: Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci. Nature Genetics 2008, 40:1399-1401.
27. Barrett JC, Clayton DG, Concannon P, Akolkar B, Cooper JD, Erlich HA, Julier C, Morahan G, Nerup J, Nierras C, Plagnol V, Pociot F, Schuilenburg H, Smyth DJ, Stevens H, Todd JA, Walker NM, Rich SS: Genomewide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes. Nature Genetics 2009, 41:703-707.
28. Huang J, Ellinghaus D, Franke A, Howie B, Li Y: 1000 Genomes-based imputation identifies novel and refined associations for the Wellcome Trust Case Control Consortium phase 1 Data. European Journal of Human Genetics 2012, 20:801-805.
29. Plagnol V, Howson JMM, Smyth DJ, Walker N, Hafler JP, Wallace C, Stevens H, Jackson L, Simmonds MJ, Bingley PJ, Gough SC, Todd JA, Consortium TDG: Genome-wide association analysis of autoantibody positivity in type 1 diabetes cases. PLoS Genetics 2011, 7:e1002216.