Wham: Identifying Structural Variants of Biological Consequence

PLoS Computational Biology

Volumn 11, Issue 12, 2015, Pages

  Kronenberg, Zev N ^a   Osborne, Edward J ^a,b   Cone, Kelsey R ^a   Kennedy, Brett J ^a,b   Domyan, Eric T ^b   Shapiro, Michael D ^b   Elde, Nels C ^a   Yandell, Mark ^a,b  

^a UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF UTAH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HTTP; VIRUSES;

ASSOCIATED SOFTWARES; COMMUNITY SUPPORT; DISEASE GENES; GENES IDENTIFICATION; GENETIC VARIATION; IDENTIFICATION TOOLS; INTEGRATED FRAMEWORKS; SHORT READS; VACCINIA VIRUS; WHOLE GENOME ALIGNMENT;

GENES;

ANIMAL GENETICS; ARTICLE; COMPUTER ANALYSIS; COMPUTER PROGRAM; CONTROLLED STUDY; DATA ANALYSIS; DATA SYNTHESIS; GENETIC VARIABILITY; GENOTYPE; HUMAN GENOME; PHENOTYPE; PIGEON; SIMULATION; STRUCTURE ANALYSIS; VACCINIA VIRUS; VALIDATION STUDY; VIRAL GENETICS; ALGORITHM; CHROMOSOMAL MAPPING; GENETIC ASSOCIATION STUDY; GENETIC VARIATION; GENETICS; HUMAN; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROCEDURES; SOFTWARE;

ALGORITHMS; BASE SEQUENCE; CHROMOSOME MAPPING; GENETIC ASSOCIATION STUDIES; GENETIC VARIATION; GENOME, HUMAN; GENOMIC STRUCTURAL VARIATION; HUMANS; MOLECULAR SEQUENCE DATA; SOFTWARE;

EID: 84953207632     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1004572     Document Type: Article

References (63)

1. Gemayel R, Vinces MD, Legendre M, Verstrepen KJ, (2010) Variable tandem repeats accelerate evolution of coding and regulatory sequences. Annu Rev Genet 44: 445–477. doi: 10.1146/annurev-genet-072610-155046 20809801
2. Chan YF, Marks ME, Jones FC, Villarreal G, Shapiro MD, et al. (2010) Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer. Science 327: 302–305. doi: 10.1126/science.1182213 20007865
3. Perry G, Yang F, Marques-Bonet T, (2008) Copy number variation and evolution in humans and chimpanzees. Genome Res 18: 1698–1710. doi: 10.1101/gr.082016.108 18775914
4. Axelsson E, Ratnakumar A, Arendt M-L, Maqbool K, Webster MT, et al. (2013) The genomic signature of dog domestication reveals adaptation to a starch-rich diet. Nature 495: 360–364. doi: 10.1038/nature11837 23354050
5. McCarroll S, Altshuler DM, (2007) Copy-number variation and association studies of human disease. Nat Genet 39: S37–S42. 17597780
6. Weischenfeldt J, Symmons O, Spitz F, Korbel JO, (2013) Phenotypic impact of genomic structural variation: insights from and for human disease. Nat Rev Genet 14: 125–138. doi: 10.1038/nrg3373 23329113
7. Stankiewicz P, Lupski JR, (2010) Structural variation in the human genome and its role in disease. Annu Rev Med 61: 437–455. doi: 10.1146/annurev-med-100708-204735 20059347
8. Onishi-Seebacher M, Korbel JO, (2011) Challenges in studying genomic structural variant formation mechanisms: the short-read dilemma and beyond. Bioessays 33: 840–850. doi: 10.1002/bies.201100075 21959584
9. Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, et al. (2008) Mapping and sequencing of structural variation from eight human genomes. Nature 453: 56–64. doi: 10.1038/nature06862 18451855
10. Sindi SS, Onal S, Peng LC, Wu H-T, Raphael BJ, (2012) An integrative probabilistic model for identification of structural variation in sequencing data. Genome Biol 13: R22. doi: 10.1186/gb-2012-13-3-r22 22452995
11. Rausch T, Zichner T, Schlattl A, Stütz AM, Benes V, et al. (2012) DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 28: i333–i339. doi: 10.1093/bioinformatics/bts378 22962449
12. Marschall T, Hajirasouliha I, Schönhuth A, (2013) MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels. Bioinformatics 29: 3143–3150. doi: 10.1093/bioinformatics/btt556 24072733
13. Marschall T, Costa IG, Canzar S, Bauer M, Klau GW, et al. (2012) CLEVER: clique-enumerating variant finder. Bioinformatics 28: 2875–2882. doi: 10.1093/bioinformatics/bts566 23060616
14. Layer RM, Chiang C, Quinlan AR, Hall IM, (2014) LUMPY: A probabilistic framework for structural variant discovery. Genome Biol 15: R84. doi: 10.1186/gb-2014-15-6-r84 24970577
15. Hart SN, Sarangi V, Moore R, Baheti S, Bhavsar JD, et al. (2013) SoftSearch: integration of multiple sequence features to identify breakpoints of structural variations. PLoS One 8: e83356. doi: 10.1371/journal.pone.0083356 24358278
16. Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, et al. (2009) BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods 6: 677–681. doi: 10.1038/nmeth.1363 19668202
17. Mimori T, Nariai N, Kojima K, Takahashi M, Ono A, et al. (2013) iSVP: an integrated structural variant calling pipeline from high-throughput sequencing data. BMC Syst Biol 7 Suppl 6: S8.
18. Wong K, Keane TM, Stalker J, Adams DJ, (2010) Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly. Genome Biol 11: R128. doi: 10.1186/gb-2010-11-12-r128 21194472
19. Chapman B. bcbio-nextgen. github. https://github.com/chapmanb/bcbio-nextgen. Accessed 27 April 2015.
20. Li Y, Zheng H, Luo R, Wu H, Zhu H, et al. (2011) Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly. Nat Biotechnol 29: 725–732.
21. Kemena C, Notredame C, (2009) Upcoming challenges for multiple sequence alignment methods in the high-throughput era. Bioinformatics 25: 2455–2465. doi: 10.1093/bioinformatics/btp452 19648142
22. Chen K, Chen L, Fan X, Wallis J, Ding L, et al. (2014) TIGRA: A targeted iterative graph routing assembler for breakpoint assembly. Genome Res 24: 310–317. doi: 10.1101/gr.162883.113 24307552
23. Quinlan A, Clark R, (2010) Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. Genome Research: 623–635. doi: 10.1101/gr.102970.109 20308636
24. Narzisi G, O’Rawe J a, Iossifov I, Fang H, Lee Y, et al. (2014) Accurate de novo and transmitted indel detection in exome-capture data using microassembly. Nat Methods 11: 1–7.
25. Sims D, Sudbery I, Ilott NE, Heger A, Ponting CP, (2014) Sequencing depth and coverage: key considerations in genomic analyses. Nat Rev Genet 15: 121–132. doi: 10.1038/nrg3642 24434847
26. Kim SY, Li Y, Guo Y, Li R, Holmkvist J, et al. (2010) Design of association studies with pooled or un-pooled next-generation sequencing data. Genet Epidemiol 34: 479–491. doi: 10.1002/gepi.20501 20552648
27. Döring A, Weese D, Rausch T, Reinert K, (2008) SeqAn an efficient, generic C++ library for sequence analysis. BMC Bioinformatics 9: 11. doi: 10.1186/1471-2105-9-11 18184432
28. Zhao M, Lee WP, Garrison EP, Marth GT, (2013) SSW library: An SIMD Smith-Waterman C/C++ library for use in genomic applications. PLoS One 8: 1–7.
29. Li H, (2011) A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27: 2987–2993. doi: 10.1093/bioinformatics/btr509 21903627
30. Nielsen R, Paul JS, Albrechtsen A, Song YS, (2011) Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet 12: 443–451. doi: 10.1038/nrg2986 21587300
31. Li H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv Prepr arXiv13033997 00: 1–3.
32. Langmead B, Salzberg SL, (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9: 357–359. doi: 10.1038/nmeth.1923 22388286
33. Pedregosa F, Varoquaux G, Gramfort A, Michel V, Thirion B, et al. (2011) Scikit-learn: Machine learning in Python. J Mach Learn Res 12: 2825–2830.
34. Michaelson J, Sebat J, (2012) forestSV: structural variant discovery through statisical learning. Nat Methods 9: 819–821. doi: 10.1038/nmeth.2085 22751202
35. Yandell M, Huff C, Hu H, Singleton M, Moore B, et al. (2011) A probabilistic disease-gene finder for personal genomes. Genome Res 21: 1529–1542. doi: 10.1101/gr.123158.111 21700766
36. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, et al. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81: 559–575. 17701901
37. Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, et al. (2007) TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23: 2633–2635. 17586829
38. Kronenberg Z. GPAT++. github. https://github.com/jewmanchue/vcflib/wiki. Accessed 27 April 2015.
39. Ye K, Schulz MH, Long Q, Apweiler R, Ning Z, (2009) Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25: 2865–2871. doi: 10.1093/bioinformatics/btp394 19561018
40. Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, et al. (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061–1073. doi: 10.1038/nature09534 20981092
41. Pang AW, MacDonald JR, Pinto D, Wei J, Rafiq M a, et al. (2010) Towards a comprehensive structural variation map of an individual human genome. Genome Biol 11: R52. doi: 10.1186/gb-2010-11-5-r52 20482838
42. Abecasis GR, Auton A, Brooks LD, DePristo M a, Durbin RM, et al. (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491: 56–65. doi: 10.1038/nature11632 23128226
43. Lappalainen I, Lopez J, Skipper L, Hefferon T, Spalding JD, et al. (2013) DbVar and DGVa: Public archives for genomic structural variation. Nucleic Acids Res 41: D936–D941. doi: 10.1093/nar/gks1213 23193291
44. Bickhart DM, Hutchison JL, Xu L, Schnabel RD, Taylor JF, et al. (2015) RAPTR-SV: a hybrid method for the detection of structural variants. Bioinformatics 31: 2084–2090. doi: 10.1093/bioinformatics/btv086 25686638
45. Chaisson MJP, Huddleston J, Dennis MY, Sudmant PH, Malig M, et al. (2014) Resolving the complexity of the human genome using single-molecule sequencing. Nature 517: 608–611. doi: 10.1038/nature13907 25383537
46. Steinberg KM, Schneider VA, Graves-lindsay TA, Fulton RS, Agarwala R, et al. (2014) Single haplotype assembly of the human genome from a hydatidiform mole: 2066–2076.
47. Mills RE, (2006) An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res 16: 1182–1190. 16902084
48. Handsaker RE, Van Doren V, Berman JR, Genovese G, Kashin S, et al. (2015) Large multiallelic copy number variations in humans. Nat Genet 47: 296–303. doi: 10.1038/ng.3200 25621458
49. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, et al. (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20: 1297–1303. doi: 10.1101/gr.107524.110 20644199
50. Illumina. Whole-genome sequencing performed on Illumina HiSeq. http://www.illumina.com/platinumgenomes/. Accessed 27 April 2015.
51. Shapiro MD, Domyan ET, (2013) Domestic pigeons. Curr Biol 23: R302–R303. doi: 10.1016/j.cub.2013.01.063 23618660
52. Domyan ET, Guernsey MW, Kronenberg Z, Krishnan S, Boissy RE, et al. (2014) Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon. Curr Biol 24: 459–464. doi: 10.1016/j.cub.2014.01.020 24508169
53. Shapiro MD, Kronenberg Z, Li C, Domyan ET, Pan H, et al. (2013) Genomic diversity and evolution of the head crest in the rock pigeon. Science 339: 1063–1067. doi: 10.1126/science.1230422 23371554
54. Slabaugh MB, Roseman NA, Mathews CK, (1989) Amplification of the ribonucleotide reductase small subunit gene: analysis of novel joints and the mechanism of gene duplication in vaccinia virus. Nucleic Acids Res 17: 7073–7088. 2674905
55. Elde NC, Child SJ, Eickbush MT, Kitzman JO, Rogers KS, et al. (2012) Poxviruses deploy genomic accordions to adapt rapidly against host antiviral defenses. Cell 150: 831–841. doi: 10.1016/j.cell.2012.05.049 22901812
56. Brennan G, Kitzman JO, Rothenburg S, Shendure J, Geballe AP, (2014) Adaptive Gene Amplification As an Intermediate Step in the Expansion of Virus Host Range. PLoS Pathog 10: e1004002. doi: 10.1371/journal.ppat.1004002 24626510
57. Erlandson KJ, Cotter CA, Charity JC, Martens C, Fischer ER, et al. (2014) Duplication of the A17L Locus of Vaccinia Virus Provides an Alternate Route to Rifampin Resistance. J Virol 88: 11576–11585. doi: 10.1128/JVI.00618-14 25078687
58. Beattie E, Denzler KL, Tartaglia J, Perkus ME, Paoletti E, et al. (1995) Reversal of the interferon-sensitive phenotype of a vaccinia virus lacking E3L by expression of the reovirus S4 gene. J Virol 69: 499–505. 7527085
59. Romero D, Palacios R, (1997) Gene amplification and genomic plasticity in prokaryotes. Annu Rev Genet 31: 91–111. 9442891
60. Andersson DI, Hughes D, (2009) Gene Amplification and Adaptive Evolution in Bacteria. Annu Rev Genet 43: 167–195. doi: 10.1146/annurev-genet-102108-134805 19686082
61. Sandegren L, Andersson DI, (2009) Bacterial gene amplification: implications for the evolution of antibiotic resistance. Nat Rev Microbiol 7: 578–588. doi: 10.1038/nrmicro2174 19609259
62. Elliott KT, Cuff LE, Neidle EL, (2013) Copy number change: evolving views on gene amplification. Future Microbiol 8: 887–899. doi: 10.2217/fmb.13.53 23841635
63. Parnell LD, Lindenbaum P, Shameer K, Dall’Olio GM, Swan DC, et al. (2011) BioStar: an online question & answer resource for the bioinformatics community. PLoS Comput Biol 7: e1002216. doi: 10.1371/journal.pcbi.1002216 22046109