Integrating sequencing technologies in personal genomics: Optimal low cost reconstruction of structural variants

PLoS Computational Biology

Volumn 5, Issue 7, 2009, Pages

  Du, Jiang ^a   Bjornson, Robert D ^a,b   Zhang, Zhengdong D ^c   Kong, Yong ^b   Snyder, Michael ^c   Gerstein, Mark B ^a,c  

^a Yale University   (United States)

^b YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL EFFICIENCY; COST EFFECTIVENESS; GENES;

AFFYMETRIX; ASSEMBLY ALGORITHM; CANONICAL PROBLEMS; DE NOVO ASSEMBLIES; GENOMICS; HUMAN GENOMES; INTEGRATING TECHNOLOGY; LOW-COSTS; REALISTIC SIMULATION; SHORT READS;

GENOME;

ACCURACY; ALGORITHM; ARTICLE; COST EFFECTIVENESS ANALYSIS; GENE CONSTRUCT; GENE DUPLICATION; GENE STRUCTURE; GENE TECHNOLOGY; GENOME ANALYSIS; HUMAN; HUMAN GENOME; INDEL MUTATION; QUANTITATIVE ANALYSIS; SEQUENCE ANALYSIS; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; STRUCTURAL GENOMICS; BIOLOGICAL MODEL; CHROMOSOME MAP; COMPUTER PROGRAM; COMPUTER SIMULATION; DNA MICROARRAY; DNA SEQUENCE; ECONOMICS; GENETIC DATABASE; GENOMICS; METHODOLOGY; STATISTICAL MODEL;

CHROMOSOME MAPPING; COMPUTER SIMULATION; DATABASES, GENETIC; GENOMICS; MODELS, GENETIC; MODELS, STATISTICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 68249117657     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000432     Document Type: Article

References (30)

1. Hehir-Kwa JY, Egmont-Petersen M, Janssen IM, Smeets D, van Kessel AG, et al. (2007) Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis. DNA Res 14: 1-11.
2. Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, et al. (2007) Pairedend mapping reveals extensive structural variation in the human genome. Science 318: 420-426. (Pubitemid 47614521)
3. Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, et al. (2007) The diploid genome sequence of an individual human. PLoS Biol 5: e254. doi:10.1371/journal.- pbio.0050254. (Pubitemid 350035416)
4. Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, et al. (2008) The complete genome of an individual by massively parallel DNA sequencing. Nature 452: 872-876. (Pubitemid 351550870)
5. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chainterminating inhibitors. Proc Natl Acad Sci U S A 74: 5463-5467.
6. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380. (Pubitemid 41613494)
7. Bentley DR (2006) Whole-genome re-sequencing. Curr Opin Genet Dev 16: 545-552.
8. Dohm JC, Lottaz C, Borodina T, Himmelbauer H (2007) SHARCGS a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Res 17: 1697-1706. (Pubitemid 350074864)
9. Warren RL, Sutton GG, Jones SJM, Holt RA (2007) Assembling millions of short DNA sequences using SSAKE. Bioinformatics 23: 500-501.
10. Butler J, Maccallum I, Kleber M, Shlyakhter IA, Belmonte MK, et al. (2008) ALLPATHS: De novo assembly of whole-genome shotgun microreads. Genome Res 18: 810-820. (Pubitemid 351645071)
11. Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821-829.
12. Pop M, Salzberg SL (2008) Bioinformatics challenges of new sequencing technology. Trends Genet 24: 142-149.
13. Pinkel D, Segraves R, Sudar D, Clark S, Poole I, et al. (1998) High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 20: 207-211. (Pubitemid 28455458)
14. Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.
15. Urban AE, Korbel JO, Selzer R, Richmond T, Hacker A, et al. (2006) Highresolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays. Proc Natl Acad Sci U S A 103: 4534-4539.
16. Perry GH, Ben-Dor A, Tsalenko A, Sampas N, Rodriguez-Revenga L, et al. (2008) The fine-scale and complex architecture of human copy-number variation. Am J Hum Genet 82: 685-695.
17. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, et al. (2006) Global variation in copy number in the human genome. Nature 444: 444-454. (Pubitemid 44809057)
18. International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature 431: 931-945. (Pubitemid 39434409)
19. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, et al. (2001) The sequence of the human genome. Science 291: 1304-1351.
20. Chaisson MJ, Pevzner PA (2008) Short read fragment assembly of bacterial genomes. Genome Res 18: 324-330.
21. Goldberg SMD, Johnson J, Busam D, Feldblyum T, Ferriera S, et al. (2006) A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes. Proc Natl Acad Sci U S A 103: 11240-11245. (Pubitemid 44156503)
22. Pop M, Phillippy A, Delcher AL, Salzberg SL (2004) Comparative genome assembly. Brief Bioinform 5: 237-248.
23. Pevzner PA, Tang H, Waterman MS (2001) An Eulerian path approach to DNA fragment assembly. Proc Natl Acad Sci U S A 98: 9748-9753. (Pubitemid 32769375)
24. Lippert R, Schwartz R, Lancia G, Istrail S (2002) Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem. Brief Bioinform 3: 23-31.
25. Bansal V, Halpern AL, Axelrod N, Bafna V (2008) An MCMC algorithm for haplotype assembly from whole-genome sequence data. Genome Res 18: 1336-1346.
26. International HapMap Consortium (2005) A haplotype map of the human genome. Nature 437: 1299-1320.
27. Korbel JO, Urban AE, Grubert F, Du J, Royce TE, et al. (2007) Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome. Proc Natl Acad Sci U S A 104: 10110-10115. (Pubitemid 47175271)
28. Schmid R, Schuster S, Steel M, Huson D (2006) ReadSim - A simulator for Sanger and 454 sequencing .
29. Rozowsky J, Euskirchen G, Auerbach R, Zhang Z, Gibson T, et al. (2008) PeakSeq: systematic scoring of ChIP-seq experiments relative to controls. Nature Biotechnol 27: 66-75.
30. Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, et al. (2002) ARACHNE: a whole-genome shotgun assembler. Genome Res 12: 177-189.