Resolving complex structural genomic rearrangements using a randomized approach

Genome Biology

Volumn 17, Issue 1, 2016, Pages

  Zhao, Xuefang ^a   Emery, Sarah B ^a   Myers, Bridget ^a   Kidd, Jeffrey M ^a   Mills, Ryan E ^a  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

Complex structural rearrangements; Copy number variant (CNV); Human; Sequence analysis; Structural variation (SV)

Indexed keywords

CHROMOSOME; CONTROLLED CLINICAL TRIAL; DNA STRUCTURE; GENE AMPLIFICATION; GENE DELETION; GENE REARRANGEMENT; HUMAN; RANDOMIZED CONTROLLED TRIAL; SEQUENCE ANALYSIS; ALGORITHM; BIOLOGY; CHROMOSOME BREAKAGE; COMPUTER SIMULATION; GENE TRANSLOCATION; GENOMICS; HUMAN GENOME; PROCEDURES; REPRODUCIBILITY; SOFTWARE; WEB BROWSER;

ALGORITHMS; CHROMOSOME BREAKPOINTS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; GENE REARRANGEMENT; GENOME, HUMAN; GENOMICS; HUMANS; REPRODUCIBILITY OF RESULTS; SOFTWARE; TRANSLOCATION, GENETIC; WEB BROWSER;

EID: 84973530151     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-016-0993-1     Document Type: Article

References (32)

1. Zarrei M, Mehdi Z, MacDonald JR, Daniele M, Scherer SW. A copy number variation map of the human genome. Nat Rev Genet. 2015;16:172-83.
2. Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, et al. Mapping copy number variation by population-scale genome sequencing. Nature. 2011;470:59-65.
3. 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, et al. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012;491:56-65.
4. Brand H, Pillalamarri V, Collins RL, Eggert S, O'Dushlaine C, Braaten EB, et al. Cryptic and complex chromosomal aberrations in early-onset neuropsychiatric disorders. Am J Hum Genet. 2014;95:454-61.
5. Chiang C, Colby C, Jacobsen JC, Carl E, Carrie H, Adrian H, et al. Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration. Nat Genet. 2012;44:390-7.
6. Stankiewicz P, Paweł S, Lupski JR. Structural variation in the human genome and its role in disease. Annu Rev Med. 2010;61:437-55.
7. Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, et al. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods. 2009;6:677-81.
8. Ye K, Schulz MH, Long Q, Apweiler R, Ning Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics. 2009;25:2865-71.
9. Layer RM, Chiang C, Quinlan AR, Hall IM. LUMPY: a probabilistic framework for structural variant discovery. Genome Biol. 2014;15:R84.
10. Handsaker RE, Korn JM, Nemesh J, McCarroll SA. Discovery and genotyping of genome structural polymorphism by sequencing on a population scale. Nat Genet. 2011;43:269-76.
11. Rausch T, Zichner T, Schlattl A, Stütz AM, Benes V, Korbel JO. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics. 2012;28:i333-9.
12. Alkan C, Can A, Coe BP, Eichler EE. Genome structural variation discovery and genotyping. Nat Rev Genet. 2011;12:363-76.
13. Sindi SS, Selim Ö, Peng LC, Hsin-Ta W, Raphael BJ. An integrative probabilistic model for identification of structural variation in sequencing data. Genome Biol. 2012;13:R22.
14. Quinlan AR, Hall IM. Characterizing complex structural variation in germline and somatic genomes. Trends Genet. 2012;28:43-53.
15. Usher CL, McCarroll SA. Complex and multi-allelic copy number variation in human disease. Brief Funct Genomics. 2015;14:329-38.
16. Raphael BJ, Volik S, Collins C, Pevzner PA. Reconstructing tumor genome architectures. Bioinformatics. 2003;19(2):ii162-71.
17. Moncunill V, Gonzalez S, Beà S, Andrieux LO, Salaverria I, Royo C, et al. Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads. Nat Biotechnol. 2014;32:1106-12.
18. Greenman CD, Pleasance ED, Newman S, Yang F, Fu B, Nik-Zainal S, et al. Estimation of rearrangement phylogeny for cancer genomes. Genome Res. 2012;22:346-61.
19. Conrad DF, Bird C, Blackburne B, Lindsay S, Mamanova L, Lee C, et al. Mutation spectrum revealed by breakpoint sequencing of human germline CNVs. Nat Genet. 2010;42:385-91.
20. Lawrence CE, Altschul SF, Boguski MS, Liu JS, Neuwald AF, Wootton JC. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science. 1993;262:208-14.
21. Kim JH, Waterman MS, Li LM. Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyi. Genome Res. 2007;17:1101-10.
22. Handsaker RE, Van Doren V, Berman JR, Genovese G, Kashin S, Boettger LM, et al. Large multiallelic copy number variations in humans. Nat Genet. 2015;47:296-303.
23. Zhu M, Need AC, Han Y, Ge D, Maia JM, Zhu Q, et al. Using ERDS to infer copy-number variants in high-coverage genomes. Am J Hum Genet. 2012;91:408-21.
24. Chaisson MJP, Huddleston J, Dennis MY, Sudmant PH, Malig M, Hormozdiari F, et al. Resolving the complexity of the human genome using single-molecule sequencing. Nature. 2015;517:608-11.
25. Steinberg KM, Schneider VA, Graves-Lindsay TA, Fulton RS, Agarwala R, Huddleston J, et al. Single haplotype assembly of the human genome from a hydatidiform mole. Genome Res. 2014;24:2066-76.
26. Pendleton M, Sebra R, Pang AWC, Ummat A, Franzen O, Rausch T, et al. Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nat Methods. 2015;12:780-6.
27. Parikh H, Mohiyuddin M, Lam HYK, Iyer H, Chen D, Pratt M, et al. svclassify: a method to establish benchmark structural variant calls. BMC Genomics. 2016;17:64.
28. Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, et al. An integrated map of structural variation in 2,504 human genomes. Nature. 2015;526:75-81.
29. Chiang C, Layer RM, Faust GG, Lindberg MR, Rose DB, Garrison EP, et al. SpeedSeq: ultra-fast personal genome analysis and interpretation. Nat Methods. 2015;12:966-8.
30. Pinto D, Darvishi K, Shi X, Rajan D, Rigler D, Fitzgerald T, et al. Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants. Nat Biotechnol. 2011;29:512-20.
31. ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489:57-74.
32. Kidd JM, Graves T, Newman TL, Fulton R, Hayden HS, Malig M, et al. A human genome structural variation sequencing resource reveals insights into mutational mechanisms. Cell. 2010;143:837-47.