GROM-RD: Resolving genomic biases to improve read depth detection of copy number variants

PeerJ

Volumn 2015, Issue 3, 2015, Pages

  Smith, Sean D ^a   Kawash, Joseph K ^a   Grigoriev, Andrey ^a  

^a RUTGERS UNIVERSITY   (United States)

Author keywords

Copy number variant; Genomic bias; Next gen sequencing

Indexed keywords

ALGORITHM; ARTICLE; CENTROMERE; CHROMOSOME 19; CHROMOSOME DELETION; CHROMOSOME DUPLICATION; COPY NUMBER VARIATION; DINUCLEOTIDE REPEAT; GENETIC PROCEDURES; GENOME; GOLD STANDARD; HUMAN; PREDICTION; READ DEPTH ANALYSIS; SIMULATION;

EID: 84926430385     PISSN: None     EISSN: 21678359     Source Type: Journal    
DOI: 10.7717/peerj.836     Document Type: Article

References (41)

1. Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. 2012. An integrated map of genetic variation from 1,092 human genomes. Nature 491:56-65 DOI 10.1038/nature11632.
2. Abyzov A, Urban AE, Snyder M, Gerstein M. 2011. CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Research 21:974-984 DOI 10.1101/gr.114876.110.
3. Aird D, Ross MG, ChenWS, Danielsson M, Fennell T, Russ C, Jaffe DB, Nusbaum C, Gnirke A. 2011. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biology 12:R18 DOI 10.1186/gb-2011-12-2-r18.
4. Baker M. 2012. Structural variation: the genome's hidden architecture. Nature Methods 9:133-137 DOI 10.1038/nmeth.1858.
5. Bartenhagen C, Dugas M. 2013. RSVSim: an R/Bioconductor package for the simulation of structural variations. Bioinformatics 29:1679-1681 DOI 10.1093/bioinformatics/btt198.
6. Benjamini Y, Speed TP. 2012. Summarizing and correcting the GC content bias in high-throughput sequencing. Nucleic Acids Research 40:e72 DOI 10.1093/nar/gks001.
7. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, Rasolonjatovo IM, Reed MT, Rigatti R, Rodighiero C, Ross MT, Sabot A, Sankar SV, Scally A, Schroth GP, Smith ME, Smith VP, Spiridou A, Torrance PE, Tzonev SS, Vermaas EH, Walter K, Wu X, Zhang L, Alam MD, Anastasi C, Aniebo IC, Bailey DM, Bancarz IR, Banerjee S, Barbour SG, Baybayan PA, Benoit VA, Benson KF, Bevis C, Black PJ, Boodhun A, Brennan JS, Bridgham JA, Brown RC, Brown AA, Buermann DH, Bundu AA, Burrows JC, Carter NP, Castillo N, Chiara ECM, Chang S, Neil Cooley R, Crake NR, Dada OO, Diakoumakos KD, Dominguez-Fernandez B, Earnshaw DJ, Egbujor UC, Elmore DW, Etchin SS, Ewan MR, Fedurco M, Fraser LJ, Fuentes Fajardo KV, Scott Furey W, George D, Gietzen KJ, Goddard CP, Golda GS, Granieri PA, Green DE, Gustafson DL, Hansen NF, Harnish K, Haudenschild CD, Heyer NI, Hims MM, Ho JT, Horgan AM, Hoschler K, Hurwitz S, Ivanov DV, Johnson MQ, James T, Huw Jones TA, Kang GD, Kerelska TH, Kersey AD, Khrebtukova I, Kindwall AP, Kingsbury Z, Kokko-Gonzales PI, Kumar A, Laurent MA, Lawley CT, Lee SE, Lee X, Liao AK, Loch JA, Lok M, Luo S, Mammen RM, Martin JW, McCauley PG, McNitt P, Mehta P, Moon KW, Mullens JW, Newington T, Ning Z, Ling Ng B, Novo SM, O'Neill MJ, Osborne MA, Osnowski A, Ostadan O, Paraschos LL, Pickering L, Pike AC, Pike AC, Chris Pinkard D, Pliskin DP, Podhasky J, Quijano VJ, Raczy C, Rae VH, Rawlings SR, Chiva Rodriguez A, Roe PM, Rogers J, Rogert Bacigalupo MC, Romanov N, Romieu A, Roth RK, Rourke NJ, Ruediger ST, Rusman E, Sanches-Kuiper RM, Schenker MR, Seoane JM, Shaw RJ, Shiver MK, Short SW, Sizto NL, Sluis JP, Smith MA, Ernest Sohna Sohna J, Spence EJ, Stevens K, Sutton N, Szajkowski L, Tregidgo CL, Turcatti G, Vandevondele S, Verhovsky Y, Virk SM, Wakelin S, Walcott GC, Wang J, Worsley GJ, Yan J, Yau L, Zuerlein M, Rogers J, Mullikin JC, Hurles ME, McCooke NJ, West JS, Oaks FL, Lundberg PL, Klenerman D, Durbin R, Smith AJ. 2008. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53-59 DOI 10.1038/nature07517.
8. Berger MF, Lawrence MS, Demichelis F, Drier Y, Cibulskis K, Sivachenko AY, Sboner A, Esgueva R, Pflueger D, Sougnez C, Onofrio R, Carter SL, Park K, Habegger L, Ambrogio L, Fennell T, Parkin M, Saksena G, Voet D, Ramos AH, Pugh TJ, Wilkinson J, Fisher S, Winckler W, Mahan S, Ardlie K, Baldwin J, Simons JW, Kitabayashi N, MacDonald TY, Kantoff PW, Chin L, Gabriel SB, Gerstein MB, Golub TR, Meyerson M, Tewari A, Lander ES, Getz G, Rubin MA, Garraway LA. 2011. The genomic complexity of primary human prostate cancer. Nature 470:214-220 DOI 10.1038/nature09744.
9. Boeva V, Zinovyev A, Bleakley K, Vert JP, Janoueix-Lerosey I, Delattre O, Barillot E. 2011. Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. Bioinformatics 27:268-269 DOI 10.1093/bioinformatics/btq635.
10. Campbell PJ, Yachida S, Mudie LJ, Stephens PJ, Pleasance ED, Stebbings LA, Morsberger LA, Latimer C, McLaren S, Lin ML, McBride DJ, Varela I, Nik-Zainal SA, Leroy C, Jia M, Menzies A, Butler AP, Teague JW, Griffin CA, Burton J, Swerdlow H, Quail MA, Stratton MR, Iacobuzio-Donahue C, Futreal PA. 2010. The patterns and dynamics of genomic instability in metastatic pancreatic cancer. Nature 467:1109-1113 DOI 10.1038/nature09460.
11. Chen W, Kalscheuer V, Tzschach A, Menzel C, Ullmann R, Schulz MH, Erdogan F, Li N, Kijas Z, Arkesteijn G, Pajares IL, Goetz-Sothmann M, Heinrich U, Rost I, Dufke A, Grasshoff U, Glaeser B, Vingron M, Ropers HH. 2008. Mapping translocation breakpoints by next-generation sequencing. Genome Research 18:1143-1149 DOI 10.1101/gr.076166.108.
12. Chiang DY, Getz G, Jaffe DB, O'Kelly MJ, Zhao X, Carter SL, Russ C, Nusbaum C, Meyerson M, Lander ES. 2009. High-resolution mapping of copy-number alterations with massively parallel sequencing. Nature Methods 6:99-103 DOI 10.1038/nmeth.1276.
13. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. 2011. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genetics 43:491-498 DOI 10.1038/ng.806.
14. Fromer M, Moran JL, Chambert K, Banks E, Bergen SE, Ruderfer DM, Handsaker RE, McCarroll SA, O'Donovan MC, Owen MJ, Kirov G, Sullivan PF, Hultman CM, Sklar P, Purcell SM. 2012. Discovery and statistical genotyping of copy-number variation from whole-exome sequencing depth. American Journal of Human Genetics 91:597-607 DOI 10.1016/j.ajhg.2012.08.005.
15. Gusnanto A, Wood HM, Pawitan Y, Rabbitts P, Berri S. 2012. Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data. Bioinformatics 28:40-47 DOI 10.1093/bioinformatics/btr593.
16. Hu X, Yuan J, Shi Y, Lu J, Liu B, Li Z, Chen Y, Mu D, Zhang H, Li N, Yue Z, Bai F, Li H, Fan W. 2012. pIRS: profile-based Illumina pair-end reads simulator. Bioinformatics 28:1533-1535 DOI 10.1093/bioinformatics/bts187.
17. Ivakhno S, Royce T, Cox AJ, Evers DJ, Cheetham RK, Tavare S. 2010. CNAseg-a novel framework for identification of copy number changes in cancer from second-generation sequencing data. Bioinformatics 26:3051-3058 DOI 10.1093/bioinformatics/btq587.
18. Kim TM, Luquette LJ, Xi R, Park PJ. 2010. rSW-seq: algorithm for detection of copy number alterations in deep sequencing data. BMC Bioinformatics 11:432 DOI 10.1186/1471-2105-11-432.
19. Klambauer G, Schwarzbauer K, Mayr A, Clevert DA, Mitterecker A, Bodenhofer U, Hochreiter S. 2012. cn. MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate. Nucleic Acids Research 40:e69 DOI 10.1093/nar/gks003.
20. Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, Kim PM, Palejev D, Carriero NJ, Du L, Taillon BE, Chen Z, Tanzer A, Saunders AC, Chi J, Yang F, Carter NP, Hurles ME, Weissman SM, Harkins TT, Gerstein MB, Egholm M, Snyder M. 2007. Paired-end mapping reveals extensive structural variation in the human genome. Science 318:420-426 DOI 10.1126/science.1149504.
21. Krumm N, Sudmant PH, Ko A, O'Roak BJ, Malig M, Coe BP, Quinlan AR, Nickerson DA, Eichler EE. 2012. Copy number variation detection and genotyping from exome sequence data. Genome Research 22:1525-1532 DOI 10.1101/gr.138115.112.
22. Lam HY, Mu XJ, Stutz AM, Tanzer A, Cayting PD, Snyder M, Kim PM, Korbel JO, Gerstein MB. 2010. Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. Nature Biotechnology 28:47-55 DOI 10.1038/nbt.1600.
23. Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760 DOI 10.1093/bioinformatics/btp324.
24. Li J, Lupat R, Amarasinghe KC, Thompson ER, Doyle MA, Ryland GL, Tothill RW, Halgamuge SK, Campbell IG, Gorringe KL. 2012. CONTRA: copy number analysis for targeted resequencing. Bioinformatics 28:1307-1313 DOI 10.1093/bioinformatics/bts146.
25. Lin CH, Lee GB, Fu LM, Chen SH. 2004. Integrated optical-fiber capillary electrophoresis microchips with novel spin-on-glass surface modification. Biosensors and Bioelectronics 20:83-90 DOI 10.1016/j.bios.2003.09.011.
26. Magi A, Benelli M, Yoon S, Roviello F, Torricelli F. 2011. Detecting common copy number variants in high-throughput sequencing data by using JointSLM algorithm. Nucleic Acids Research 39:e65 DOI 10.1093/nar/gkr068.
27. Magi A, Tattini L, Cifola I, D'Aurizio R, Benelli M, Mangano E, Battaglia C, Bonora E, Kurg A, Seri M, Magini P, Giusti B, Romeo G, Pippucci T, De Bellis G, Abbate R, Gensini GF. 2013. EXCAVATOR: detecting copy number variants from whole-exome sequencing data. Genome Biology 14:R120 DOI 10.1186/gb-2013-14-10-r120.
28. Marshall CR, Noor A, Vincent JB, Lionel AC, Feuk L, Skaug J, Shago M, Moessner R, Pinto D, Ren Y, Thiruvahindrapduram B, Fiebig A, Schreiber S, Friedman J, Ketelaars CE, Vos YJ, Ficicioglu C, Kirkpatrick S, Nicolson R, Sloman L, Summers A, Gibbons CA, Teebi A, Chitayat D, Weksberg R, Thompson A, Vardy C, Crosbie V, Luscombe S, Baatjes R, Zwaigenbaum L, Roberts W, Fernandez B, Szatmari P, Scherer SW. 2008. Structural variation of chromosomes in autism spectrum disorder. American Journal of Human Genetics 82:477-488 DOI 10.1016/j.ajhg.2007.12.009.
29. Miller CA, Hampton O, Coarfa C, Milosavljevic A. 2011. ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads. PLoS ONE 6:e16327 DOI 10.1371/journal.pone.0016327.
30. Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stutz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO, 1000 Genomes Project. 2011. Mapping copy number variation by population-scale genome sequencing. Nature 470:59-65 DOI 10.1038/nature09708.
31. Ou Z, Stankiewicz P, Xia Z, Breman AM, Dawson B, Wiszniewska J, Szafranski P, Cooper ML, Rao M, Shao L, South ST, Coleman K, Fernhoff PM, Deray MJ, Rosengren S, Roeder ER, Enciso VB, Chinault AC, Patel A, Kang SH, Shaw CA, Lupski JR, Cheung SW. 2011. Observation and prediction of recurrent human translocations mediated by NAHR between nonhomologous chromosomes. Genome Research 21:33-46 DOI 10.1101/gr.111609.110.
32. Pang AW, Migita O, Macdonald JR, Feuk L, Scherer SW. 2013. Mechanisms of formation of structural variation in a fully sequenced human genome. Human Mutation 34:345-354 DOI 10.1002/humu.22240.
33. Rausch T, Zichner T, Schlattl A, Stutz AM, Benes V, Korbel JO. 2012. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 28:i333-i339 DOI 10.1093/bioinformatics/bts378.
34. Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. 2011. Integrative genomics viewer. Nature Biotechnology 29:24-26 DOI 10.1038/nbt.1754.
35. Ross MG, Russ C, Costello M, Hollinger A, Lennon NJ, Hegarty R, Nusbaum C, Jaffe DB. 2013. Characterizing and measuring bias in sequence data. Genome Biology 14:R51 DOI 10.1186/gb-2013-14-5-r51.
36. Sathirapongsasuti JF, Lee H, Horst BA, Brunner G, Cochran AJ, Binder S, Quackenbush J, Nelson SF. 2011. Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV. Bioinformatics 27:2648-2654 DOI 10.1093/bioinformatics/btr462.
37. Sims D, Sudbery I, Ilott NE, Heger A, Ponting CP. 2014. Sequencing depth and coverage: key considerations in genomic analyses. Nature Reviews: Genetics 15:121-132 DOI 10.1038/nrg3642.
38. Stefansson H, Ophoff RA, Steinberg S, Andreassen OA, Cichon S, Rujescu D, Werge T, Pietilainen OP, Mors O, Mortensen PB, Sigurdsson E, Gustafsson O, Nyegaard M, Tuulio-Henriksson A, Ingason A, Hansen T, Suvisaari J, Lonnqvist J, Paunio T, Borglum AD, Hartmann A, Fink-Jensen A, Nordentoft M, Hougaard D, Norgaard-Pedersen B, Bottcher Y, Olesen J, Breuer R, Moller HJ, Giegling I, Rasmussen HB, Timm S, Mattheisen M, Bitter I, Rethelyi JM, Magnusdottir BB, Sigmundsson T, Olason P, Masson G, Gulcher JR, Haraldsson M, Fossdal R, Thorgeirsson TE, Thorsteinsdottir U, Ruggeri M, Tosato S, Franke B, Strengman E, Kiemeney LA, Genetic Risk and Outcome in Psychosis (GROUP), Melle I, Djurovic S, Abramova L, Kaleda V, Sanjuan J, de Frutos R, Bramon E, Vassos E, Fraser G, Ettinger U, Picchioni M, Walker N, Toulopoulou T, Need AC, Ge D, Yoon JL, Shianna KV, Freimer NB, Cantor RM, Murray R, Kong A, Golimbet V, Carracedo A, Arango C, Costas J, Jonsson EG, Terenius L, Agartz I, Petursson H, Nothen MM, Rietschel M, Matthews PM, Muglia P, Peltonen L, St Clair D, Goldstein DB, Stefansson K, Collier DA. 2009. Common variants conferring risk of schizophrenia. Nature 460:744-747 DOI 10.1038/nature08186.
39. Stephens PJ, McBride DJ, Lin ML, Varela I, Pleasance ED, Simpson JT, Stebbings LA, Leroy C, Edkins S, Mudie LJ, Greenman CD, Jia M, Latimer C, Teague JW, Lau KW, Burton J, Quail MA, Swerdlow H, Churcher C, Natrajan R, Sieuwerts AM, Martens JW, Silver DP, Langerod A, Russnes HE, Foekens JA, Reis-Filho JS, Van 't Veer L, Richardson AL, Borresen-Dale AL, Campbell PJ, Futreal PA, Stratton MR. 2009. Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature 462:1005-1010 DOI 10.1038/nature08645.
40. Xie C, Tammi MT. 2009. CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics 10:80 DOI 10.1186/1471-2105-10-80. Yoon S, Xuan Z, Makarov V, Ye K, Sebat J. 2009. Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Research 19:1586-1592 DOI 10.1101/gr.092981.109.
41. Yoon S, Xuan Z, Makarov V, Ye K, Sebat J. 2009. Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Research 19:1586-1592 DOI 10.1101/gr.092981.109.