The diploid genome sequence of an individual human

PLoS Biology

Volumn 5, Issue 10, 2007, Pages 2113-2144

  Levy, Samuel ^a   Sutton, Granger ^a   Ng, Pauline C ^a   Feuk, Lars ^b,c   Halpern, Aaron L ^a   Walenz, Brian P ^a   Axelrod, Nelson ^a   Huang, Jiaqi ^a   Kirkness, Ewen F ^a   Denisov, Gennady ^a   Lin, Yuan ^a   MacDonald, Jeffrey R ^b,c   Pang, Andy Wing Chun ^b,c   Shago, Mary ^b,c   Stockwell, Timothy B ^a   Tsiamouri, Alexia ^a   Bafna, Vineet ^d   Bansal, Vikas ^d   Kravitz, Saul A ^a   Busam, Dana A ^a   Beeson, Karen Y ^a   McIntosh, Tina C ^a   Remington, Karin A ^a   Abril, Josep F ^e   Gill, John ^a   Borman, Jon ^a   Rogers, Yu Hui ^a   Frazier, Marvin E ^a   Scherer, Stephen W ^b,c   Strausberg, Robert L ^a   Venter, J Craig ^a   more..

^a J CRAIG VENTER INSTITUTE   (United States)

^b HOSPITAL FOR SICK CHILDREN   (Canada)

^c UNIVERSITY OF TORONTO   (Canada)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e UNIVERSITY OF BARCELONA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ALLELE; ARTICLE; CHROMOSOME ANALYSIS; COMPARATIVE GENOMIC HYBRIDIZATION; DIPLOIDY; DNA DETERMINATION; DNA SEQUENCE; GENE DELETION; GENE DUPLICATION; GENE INSERTION SEQUENCE; GENETIC VARIABILITY; GENOME ANALYSIS; HAPLOTYPE; HETEROZYGOSITY; HOMOZYGOSITY; HUMAN GENOME; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; CHROMOSOME MAP; FLUORESCENCE IN SITU HYBRIDIZATION; GENE DOSAGE; GENETICS; GENOME; GENOTYPE; HUMAN; HUMAN CHROMOSOME; HUMAN GENOME PROJECT; INSERTION DELETION MUTATION; INSTRUMENTATION; MALE; METHODOLOGY; MICROARRAY ANALYSIS; MIDDLE AGED; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PEDIGREE; PHENOTYPE; REPRODUCIBILITY; Y CHROMOSOME;

BASE SEQUENCE; CHROMOSOME MAPPING; CHROMOSOMES, HUMAN; CHROMOSOMES, HUMAN, Y; DIPLOIDY; GENE DOSAGE; GENOME, HUMAN; GENOTYPE; HAPLOTYPES; HUMAN GENOME PROJECT; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; INDEL MUTATION; MALE; MICROARRAY ANALYSIS; MIDDLE AGED; MOLECULAR SEQUENCE DATA; PEDIGREE; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA;

EID: 35648976118     PISSN: 15449173     EISSN: 15457885     Source Type: Journal    
DOI: 10.1371/journal.pbio.0050254     Document Type: Article

References (106)

1. Painter TS (1924) The sex chromosomes of man. Am Nat 58: 506-524.
2. Tjio TH, Levan A (1956) The chromosome number of man. Hereditas 42: 1.
3. Lejeune J, Turpin R (1961) Chromosomal aberrations in man. Am J Hum Genet 13: 175-184.
4. Caspersson T, Zech L, Johansson C, Modest EJ (1970) Identification of human chromosomes by DNA-binding fluorescent agents. Chromosoma 30: 215-227.
5. Fodor SP, Read JL, Pirrung MC, Stryer L, Lu AT, et al. (1991) Light-directed, spatially addressable parallel chemical synthesis. Science 251: 767-773.
6. 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.
7. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, et al. (2001) The sequence of the human genome. Science 291: 1304-1351.
8. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921.
9. International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature 431: 931-945.
10. She X, Jiang Z, Clark RA, Liu G, Cheng Z, et al. (2004) Shotgun sequence assembly and recent segmental duplications within the human genome. Nature 431: 927-930.
11. Feuk L, Carson AR, Scherer SW (2006) Structural variation in the human genome. Nat Rev Genet 7: 85-97.
12. Carson AR, Feuk L, Mohammed M, Scherer SW (2006) Strategies for the detection of copy number and other structural variants in the human genome. Hum Genomics 2: 403-414.
13. Freeman JL, Perry GH, Feuk L, Redon R, McCarroll SA, et al. (2006) Copy number variation: New insights in genome diversity. Genome Res 16: 949-961.
14. Feuk L, Marshall CR, Wintle RF, Scherer SW (2006) Structural variants: Changing the landscape of chromosomes and design of disease studies. Hum Mol Genet 15 Spec No 1: R57-R66.
15. Sharp AJ, Cheng Z, Eichler EE (2006) Structural variation of the human genome. Annu Rev Genomics Hum Genet 7: 407-442.
16. Chuzhanova NA, Anassis EJ, Ball EV, Krawczak M, Cooper DN (2003) Meta-analysis of indels causing human genetic disease: Mechanisms of mutagenesis and the role of local DNA sequence complexity. Hum Mutat 21: 28-44.
17. Ball EV, Stenson PD, Abeysinghe SS, Krawczak M, Cooper DN, et al. (2005) Microdeletions and microinsertions causing human genetic disease: Common mechanisms of mutagenesis and the role of local DNA sequence complexity. Hum Mutat 26: 205-213.
18. Stenson PD, Ball EV, Mort M, Phillips AD, Shiel JA, et al. (2003) Human Gene Mutation Database (HGMD): 2003 update. Hum Mutat 21: 577-581.
19. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, et al. (2005) The transcriptional landscape of the mammalian genome. Science 309: 1559-1563.
20. Carninci P (2006) Tagging mammalian transcription complexity. Trends Genet 22: 501-510.
21. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
22. Chimpanzee Sequencing and Analysis Consortium (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69-87.
23. Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, et al. (2007) Evolutionary and biomedical insights from the rhesus macaque genome. Science 316: 222-234.
24. Pennacchio LA, Rubin EM (2001) Genomic strategies to identify mammalian regulatory sequences. Nat Rev Genet 2: 100-109.
25. Loots GG, Ovcharenko I, Pachter L, Dubchak I, Rubin EM (2002) rVista for comparative sequence-based discovery of functional transcription factor binding sites. Genome Res 12: 832-839. [doi].
26. Rubin GM, Yandell MD, Wortman JR, Miklos GLG, Nelson CR, et al. (2000) Comparative genomics of the eukaryotes. Science 287: 2204-2215.
27. Couronne O, Poliakov A, Bray N, Ishkhanov T, Ryaboy D, et al. (2003) Strategies and tools for whole-genome alignments. Genome Res 13: 73-80.
28. Frazer KA, Elnitski L, Church DM, Dubchak I, Hardison RC (2003) Cross-species sequence comparisons: A review of methods and available resources. Genome Res 13: 1-12.
29. Dermitzakis ET, Clark AG (2002) Evolution of transcription factor binding sites in Mammalian gene regulatory regions: conservation and turnover. Mol Biol Evol 19: 1114-1121.
30. Rivas E, Eddy SR (2001) Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics 2: 8.
31. Griffiths-Jones S (2004) The microRNA registry. Nucleic Acids Res 32: D109-111.
32. Griffiths-Jones S (2006) miRBase: The microRNA sequence database. Methods Mol Biol 342: 129-138.
33. Megraw M, Sethupathy P, Corda B, Hatzigeorgiou AG (2007) miRGen: A database for the study of animal microRNA genomic organization and function. Nucleic Acids Res 35: D149-155.
34. Coutinho LL, Matukumalli LK, Sonstegard TS, Van Tassell CP, Gasbarre LC, et al. (2007) Discovery and profiling of bovine microRNAs from immune-related and embryonic tissues. Physiol Genomics 29: 35-43.
35. The International HapMap Consortium (2005) A haplotype map of the human genome. Nature 437: 1299-1320.
36. Laitinen T, Polvi A, Rydman P, Vendelin J, Pulkkinen V, et al. (2004) Characterization of a common susceptibility locus for asthma-related traits. Science 304: 300-304.
37. Klein RJ, Zeiss C, Chew EY, Tsai JY, Sackler RS, et al. (2005) Complement factor H polymorphism in age-related macular degeneration. Science 308: 385-389.
38. Sladek R, Rocheleau G, Rung J, Dina C, Shen L, et al. (2007) A genome-wide association study identifies novel risk loci for type 2 diabetes. Nature 445: 881-885.
39. Hirschhorn JN, Daly MJ (2005) Genome-wide association studies for common diseases and complex traits. Nat Rev Genet 6: 95-108.
40. Istrail S, Sutton GG, Florea L, Halpern AL, Mobarry CM, et al. (2004) Whole-genome shotgun assembly and comparison of human genome assemblies. Proc Natl Acad Sci U S A 101: 1916-1921.
41. Zhao S, Malek J, Mahairas G, Fu L, Nierman W, et al. (2000) Human BAC ends quality assessment and sequence analyses. Genomics 63: 321-332.
42. Dew IM, Walenz B, Sutton G (2005) A tool for analyzing mate pairs in assemblies (TAMPA). J Comput Biol 12: 497-513.
43. Watterson GA, Guess HA (1977) Is the most frequent allele the oldest? Theor Popul Biol 11: 141-160.
44. Bhangale TR, Rieder MJ, Livingston RJ, Nickerson DA (2005) Comprehensive identification and characterization of diallelic insertion-deletion polymorphisms in 330 human candidate genes. Hum Mol Genet 14: 59-69.
45. Livingston RJ, von Niederhausern A, Jegga AG, Crawford DC, Carlson CS, et al. (2004) Pattern of sequence variation across 213 environmental response genes. Genome Res 14: 1821-1831.
46. Halushka MK, Fan JB, Bentley K, Hsie L, Shen N, et al. (1999) Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nat Genet 22: 239-247.
47. Cargill M, Altshuler D, Ireland J, Sklar P, Ardlie K, et al. (1999) Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat Genet 22: 231-238.
48. Benson G (1999) Tandem repeats finder: A program to analyze DNA sequences. Nucleic Acids Res 27: 573-580.
49. Encode Project Consortium (2004) The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306: 636-640.
50. Weber JL, David D, Heil J, Fan Y, Zhao C, et al. (2002) Human diallelic insertion/deletion polymorphisms. Am J Hum Genet 71: 854-862.
51. Bhangale TR, Stephens M, Nickerson DA (2006) Automating resequencing-based detection of insertion-deletion polymorphisms. Nat Genet 38: 1457-1462.
52. Batzer MA, Deininger PL (2002) Alu repeats and human genomic diversity. Nat Rev Genet 3: 370-379.
53. Wang J, Song L, Gonder MK, Azrak S, Ray DA, et al. (2006) Whole genome computational comparative genomics: A fruitful approach for ascertaining Alu insertion polymorphisms. Gene 365: 11-20.
54. Wang J, Song L, Grover D, Azrak S, Batzer MA, et al. (2006) dbRIP: A highly integrated database of retrotransposon insertion polymorphisms in humans. Hum Mutat 27: 323-329.
55. Mills RE, Luttig CT, Larkins CE, Beauchamp A, Tsui C, et al. (2006) An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res 16: 1182-1190.
56. Conrad DF, Andrews TD, Carter NP, Hurles ME, Pritchard JK (2006) A high-resolution survey of deletion polymorphism in the human genome. Nat Genet 38: 75-81.
57. McCarroll SA, Hadnott TN, Perry GH, Sabeti PC, Zody MC, et al. (2006) Common deletion polymorphisms in the human genome. Nat Genet 38: 86-92.
58. Hinds DA, Kloek AP, Jen M, Chen X, Frazer KA (2006) Common deletions and SNPs are in linkage disequilibrium in the human genome. Nat Genet 38: 82-85.
59. Khaja R, Zhang J, Macdonald JR, He Y, Joseph-George AM, et al. (2006) Genome assembly comparison identifies structural variants in the human genome. Nat Genet 38: 1413-1418.
60. Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, et al. (2002) Recent segmental duplications in the human genome. Science 297: 1003-1007.
61. Cheung J, Estivill X, Khaja R, MacDonald JR, Lau K, et al. (2003) Genomewide detection of segmental duplications and potential assembly errors in the human genome sequence. Genome Biol 4: R25.
62. 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.
63. Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, et al. (2004) Detection of large-scale variation in the human genome. Nat Genet 36: 949-951.
64. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, et al. (2004) Large-scale copy number polymorphism in the human genome. Science 305: 525-528.
65. Wang X, Ria M, Kelmenson PM, Eriksson P, Higgins DC, et al. (2005) Positional identification of TNFSF4, encoding OX40 ligand, as a gene that influences atherosclerosis susceptibility. Nat Genet 37: 365-372.
66. Daly MJ, Rioux JD, Schaffner SF, Hudson TJ, Lander ES (2001) High-resolution haplotype structure in the human genome. Nat Genet 29: 229-232.
67. Stephens JC, Schneider JA, Tanguay DA, Choi J, Acharya T, et al. (2001) Haplotype variation and linkage disequilibrium in 313 human genes. Science 293: 489-493.
68. Kruglyak L (1999) Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat Genet 22: 139-144.
69. Carlson CS, Eberle MA, Rieder MJ, Yi Q, Kruglyak L, et al. (2004) Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am J Hum Genet 74: 106-120.
70. Lippert R, Schwartz R, Lancia G, Istrail S (2002) Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem. Brief Bioinform 3: 23-31.
71. Bafna V, Istrail S, Lancia G, Rizzi R (2005) Polynomial and APX-hard cases of individual haplotyping problems. Theor Comp Sci 335: 109-125.
72. Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, et al. (2002) The structure of haplotype blocks in the human genome. Science 296: 2225-2229.
73. McKusick VA (2007) Mendelian Inheritance in Man and its online version, OMIM. Am J Hum Genet 80: 588-604.
74. Brinkman RR, Mezei MM, Theilmann J, Almqvist E, Hayden MR (1997) The likelihood of being affected with Huntington disease by a particular age, for a specific CAG size. Am J Hum Genet 60: 1202-1210.
75. Arking DE, Atzmon G, Arking A, Barzilai N, Dietz HC (2005) Association between a functional variant of the KLOTHO gene and high-density lipoprotein cholesterol, blood pressure, stroke, and longevity. Circ Res 96: 412-418.
76. Medley TL, Kingwell BA, Gatzka CD, Pillay P, Cole TJ (2003) Matrix metalloproteinase-3 genotype contributes to age-related aortic stiffening through modulation of gene and protein expression. Circ Res 92: 1254-1261.
77. Strange RC, Matharoo B, Faulder GC, Jones P, Cotton W, et al. (1991) The human glutathione S-transferases: A case-control study of the incidence of the GST1 0 phenotype in patients with adenocarcinoma. Carcinogenesis 12: 25-28.
78. van Poppel G, de Vogel N, van Balderen PJ, Kok FJ (1992) Increased cytogenetic damage in smokers deficient in glutathione S-transferase isozyme mu. Carcinogenesis 13: 303-305.
79. Gilliland FD, Li YF, Saxon A, Diaz-Sanchez D (2004) Effect of glutathione-S-transferase M1 and P1 genotypes on xenobiotic enhancement of allergic responses: Randomised, placebo-controlled crossover study. Lancet 363: 119-125.
80. Baumgart E, Vanhooren JC, Fransen M, Marynen P, Puype M, et al. (1996) Molecular characterization of the human peroxisomal branched-chain acyl-CoA oxidase: cDNA cloning, chromosomal assignment, tissue distribution, and evidence for the absence of the protein in Zellweger syndrome. Proc Natl Acad Sci U S A 93: 13748-13753.
81. Enattah NS, Sahi T, Savilahti E, Terwilliger JD, Peltonen L, et al. (2002) Identification of a variant associated with adult-type hypolactasia. Nat Genet 30: 233-237.
82. Church GM (2006) Genomes for all. Sci Am 294: 46-54.
83. Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, et al. (2007) The Sorcerer II global ocean sampling expedition: Northwest Atlantic through Eastern tropical Pacific. PLoS Biol 5: e77. doi:10.1371/journal.pbio. 0050077.
84. 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.
85. Metzker ML (2005) Emerging technologies in DNA sequencing. Genome Res 15: 1767-1776.
86. Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, et al. (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309: 1728-1732.
87. Rudd MK, Willard HF (2004) Analysis of the centromeric regions of the human genome assembly. Trends Genet 20: 529-533.
88. Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces usingphred. I. Accuracy assessment. Genome Res 8: 175-185.
89. Sambrook J, Fritsch E, Maniatis T (1989) Molecular cloning. A laboratory manual. Cold Spring Harbor (New York): Cold Spring Laboratory Press. 999 p.
90. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74: 5463-5467.
91. Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP, et al. (2000) A whole-genome assembly of Drosophila. Science 287: 2196-2204.
92. Jaffe DB, Butler J, Gnerre S, Mauceli E, Lindblad-Toh K, et al. (2003) Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res 13: 91-96.
93. Shatkay H, Miller J, Mobarry C, Flanigan M, Yooseph S, et al. (2004) ThurGood: Evaluating assembly-to-assembly mapping. J Comput Biol 11: 800-811.
94. Lippert RA, Zhao X, Florea L, Mobarry C, Istrail S (2005) Finding anchors for genomic sequence comparison. J Comput Biol 12: 762-776.
95. Crawford DC, Carlson CS, Rieder MJ, Carrington DP, Yi Q, et al. (2004) Haplotype diversity across 100 candidate genes for inflammation, lipid metabolism, and blood pressure regulation in two populations. Am J Hum Genet 74: 610-622.
96. Kennedy GC, Matsuzaki H, Dong S, Liu WM, Huang J, et al. (2003) Large-scale genotyping of complex DNA. Nat Biotechnol 21: 1233-1237.
97. Li C, Wong WH (2003) DNA-Chip Analyzer (dChip). In: Parmigiani G, Garrett ES, Irizarry R, Zeger SL, editors. The analysis of gene expression data: methods and software. New York: Springer. 504 p.
98. Nannya Y, Sanada M, Nakazaki K, Hosoya N, Wang L, et al. (2005) A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays. Cancer Res 65: 6071-6079.
99. Komura D, Shen F, Ishikawa S, Fitch KR, Chen W, et al. (2006) Genomewide detection of human copy number variations using high-density DNA oligonucleotide arrays. Genome Res 16: 1575-1584.
100. Zhao X, Weir BA, LaFramboise T, Lin M, Beroukhim R, et al. (2005) Homozygous deletions and chromosome amplifications in human lung carcinomas revealed by single nucleotide polymorphism array analysis. Cancer Res 65: 5561-5570.
101. Colella S, Yau C, Taylor JM, Mirza G, Butler H, et al. (2007) QuantiSNP: An Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data. Nucleic Acids Res 35: 2013-2025.
102. 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.
103. Fiegler H, Redon R, Andrews D, Scott C, Andrews R, et al. (2006) Accurate and reliable high-throughput detection of copy number variation in the human genome. Genome Res 16: 1566-1574.
104. Scherer SW, Cheung J, MacDonald JR, Osborne LR, Nakabayashi K, et al. (2003) Human chromosome 7: DNA sequence and biology. Science 300: 767-772.
105. Mural RJ, Adams MD, Myers EW, Smith HO, Miklos GL, et al. (2002) A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science 296: 1661-1671.
106. Kim JH, Waterman MS, Li LM (2007) Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyi. Genome Res 17: 1101-1110.