Sequencing genomes: From individuals to populations

Briefings in Functional Genomics and Proteomics

Volumn 8, Issue 5, 2009, Pages 367-378

  Mir, Kalim U ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DNA SEQUENCE; GENETIC ASSOCIATION; GENETIC EPIGENESIS; GENETIC RISK; GENETIC SELECTION; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE PHENOTYPE CORRELATION; HAPLOTYPE MAP; HEALTH CARE COST; HUMAN GENOME; HUMAN GENOME PROJECT; POLYMERASE CHAIN REACTION; POPULATION GENETICS; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM;

GENETICS, POPULATION; GENOME, HUMAN; GENOMICS; HAPLOTYPES; HUMANS; SEQUENCE ANALYSIS, DNA;

EID: 70350010196     PISSN: 14739550     EISSN: 14774062     Source Type: Journal    
DOI: 10.1093/bfgp/elp040     Document Type: Article

References (130)

1. Wheeler DA, Srinivasan M, Egholm M, et al. The complete genome of an individual by massively parallel DNA sequencing. Nature 2008; 452:872-6.
2. Levy S, Sutton G, Ng PC, et al. The diploid genome sequence of an individual human. PLoS Biol 2007;5:e254.
3. Ahn SM, Kim TH, Lee S, et al. The first Korean genome sequence and analysis: Full genome sequencing for a socio-ethnic group. Genome Res 2009;9:1622-9.
4. Bentley DR, Balasubramanian S, Swerdlow HP, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008;456:53-9.
5. Kim JI, Ju YS, Park H, et al. A highly annotated whole-genome sequence of a Korean individual. Nature 2009;460: 1011-5.
6. Ley TJ, Mardis ER, Ding L, et al. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 2008;456:66-72.
7. Mardis ER, Ding L, Dooling DJ, et al. Recurring mutations found by sequencing an acute myeloid leukemia genome. N Engl J Med 2009; 361:1058-66.
8. McKernan KJ, Peckham HE, Costa G, et al. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two base encoding. Genome Res 2009;19 1527-41.
9. Pushkarev D, Neff NF, Quake SR. Single-molecule sequencing of an individual human genome. Nat Biotechnol 2009;27:847-52.
10. Wang J, Wang W, Li R, et al. The diploid genome sequence of an Asian individual. Nature 2008;456:60-5.
11. Lander ES, Linton LM, Birren B, et al. Initial sequencing and analysis of the human genome. Nature 2001;409: 860-921.
12. Venter JC, Adams MD, Myers EW, et al. The sequence of the human genome. Science 2001;291:1304-51.
13. Hood L. A doctor's vision of the future of medicine. Newsweek 2009, (last accessed 15 September 2009).
14. Downing JR. Cancer genomes - continuing progress. N Engl J Med 2009;361:1111-2.
15. Frazer KA, Murray SS, Schork NJ, et al. Human genetic variation and its contribution to complex traits. Nat Rev Genet 2009;10 241-51.
16. Frazer KA, Ballinger DG, Cox DR, et al. A second generation human haplotype map of over 3.1 million SNPs. Nature 2007;449 851-61.
17. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared control. Nature 2007; 447:661-78.
18. Donnelly P. Progress and challenges in genome-wide association studies in humans. Nature 2008;456:728-31.
19. Panoutsopoulou K, Zeggini E. Finding common susceptibility variants for complex disease: Past, present and future. Brief Funct Genomic Proteomic 2009, [Epub ahead of print].
20. Reich DE, Lander ES. On the allelic spectrum of human disease. Trends Genet 2001;17:502-10.
21. Loos RJ, Beunen G, Fagard R, et al. Twin studies and estimates of heritability. Lancet 2001;357:1445.
22. McCarthy MI. Exploring the unknown: Assumptions about allelic architecture and strategies for susceptibility variant discovery. Genome Med 2009;1:66.
23. Pritchard JK. Are rare variants responsible for susceptibility to complex diseases? Am J Hum Genet 2001;69:124-37.
24. Schork NJ, Murray SS, Frazer KA, et al. Common vs. rare allele hypotheses for complex diseases. Curr Opin Genet Dev 2009;19 212-9.
25. Bodmer W, Bonilla C. Common and rare variants in multi-factorial susceptibility to common diseases. Nat Genet 2008; 40 695-701.
26. Wright A, Charlesworth B, Rudan I, et al. A polygenic basis for late-onset disease. Trends Genet 2003;19:97-106.
27. Ng PC, Levy S, Huang J, et al. Genetic variation in an individual human exome. PLoS Genet 2008;4:e1000160.
28. Mir KU, Southern EM. Sequence variation in genes and genomic DNA: methods for large-scale analysis. Annu Rev Genomics Hum Genet 2000;1:329-60.
29. Iafrate AJ, Feuk L, Rivera MN, et al. Detection of large-scale variation in the human genome. Nat Genet 2004;36: 949-51.
30. Sebat J, Lakshmi B, Troge J, et al. Large-scale copy number polymorphism in the human genome. Science 2004;305: 525-8.
31. Redon R, Ishikawa S, Fitch KR, et al. Global variation in copy number in the human genome. Nature 2006;444: 444-54.
32. McCarroll SA, Kuruvilla FG, Korn JM, et al. Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet 2008;40:1166-74.
33. Lupski JR. Structural variation in the human genome. N Engl J Med 2007;356:1169-71.
34. Walsh T, McClellan JM, McCarthy SE, et al. Rare structural variants disrupt multiple genes in neuro-developmental pathways in schizophrenia. Science 2008; 320:539-43.
35. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 1977; 74:5463-67.
36. Metzker ML. Emerging technologies in DNA sequencing. Genome Res 2005;15:1761-67.
37. Margulies M, Egholm M, Altman WE, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005; 437:376-80.
38. Shendure J, Porreca GJ, Reppas NB, et al. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 2005; 309:1728-32.
39. Harris TD, Buzby PR, Babcock H, et al. Single-molecule DNA sequencing of a viral genome. Science 2008;320: 106-9.
40. Quail MA, Kozarewa I, Smith F, et al. A large genome center's improvements to the Illumina sequencing system. Nat Methods 2008;5:1005-10.
41. Druley TE, Vallania FL, Wegner DJ, et al. Quantification of rare allelic variants from pooled genomic DNA. Nat Methods 2009;6 263-5.
42. Dohm JC, Lottaz C, Borodina T, et al. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 2008;36:e105.
43. Church GM. Genomes for all. Sci Am 2006;294:46-54.
44. Church GM. The personal genome project. Mol Syst Biol 2005;1 2005-0030.
45. Harismendy O, Ng PC, Strausberg RL, et al. Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol 2009;10:R32.
46. Green ED. Strategies for the systematic sequencing of complex genomes. Nat Rev Genet 2001;2:573-83.
47. Staden R. A strategy of DNA sequencing employing computer programs. Nucleic Acids Res 1979;6:2601-10.
48. Lander ES, Waterman MS. Genomic mapping by finger-printing random clones: A mathematical analysis. Genomics 1988;2:231-9.
49. Wendl MC, Wilson RK. Aspects of coverage in medical DNA sequencing. BMC Bioinformatics 2008;9:239.
50. Weinstein JA, Jiang N, White RA, 3rd, et al. High-throughput sequencing of the zebrafish antibody repertoire. Science 2009; 324:807-10.
51. Yoon S, Xuan Z, Makarov V, et al. Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res 2009.
52. Voelkerding KV, Dames SA, Durtschi JD. Next-generation sequencing: From basic research to diagnostics. Clin Chem 2009;55:641-58.
53. ten Bosch JR, Grody WW. Keeping up with the next generation: Massively parallel sequencing in clinical diagnostics. J Mol Diagn 2008; 10:484-92.
54. Fan HC, Blumenfeld YJ, Chitkara U, et al. Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood. Proc Natl Acad Sci USA 2008;105: 16266-71.
55. Chiu RW, Chan KC, Gao Y, et al. Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma. Proc Natl Acad Sci USA 2008;105 20458-63.
56. Altshuler D, Daly MJ, Lander ES. Genetic mapping in human disease. Science 2008;322:881-8.
57. McCarthy MI, Hirschhorn JN. Genome-wide association studies: Potential next steps on a genetic journey. Hum Mol Genet 2008;17 R156-65.
58. Nejentsev S, Walker N, Riches D, et al. Rare variants of IFIH1, a gene implicated in antiviral responses, protect against type 1 diabetes. Science 2009;324:387-9.
59. King MC, Wilson AC. Evolution at two levels in humans and chimpanzees. Science 1975;188:107-16.
60. Loos RJ, Lindgren CM, Li S, et al. Common variants near MC4R are associated with fat mass, weight and risk of obesity. Nat Genet 2008;40:768-75.
61. Heintzman ND, Hon GC, Hawkins RD, et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 2009;459: 108-12.
62. Birney E, Stamatoyannopoulos JA, Dutta A, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007;447:799-816.
63. Varley KE, Mitra RD. Nested Patch PCR enables highly multiplexed mutation discovery in candidate genes. Genome Res 2008;18 1844-50.
64. Akhras MS, Unemo M, Thiyagarajan S, et al. Connector inversion probe technology: A powerful one-primer multiplex DNA amplification system for numerous scientific applications. PLoS ONE 2007;2 e915.
65. Hardenbol P, Yu F, Belmont J, et al. Highly multiplexed molecular inversion probe genotyping: Over 10,000 targeted SNPs genotyped in a single tube assay. Genome Res 2005;15: 269-75.
66. Dahl F, Gullberg M, Stenberg J, et al. Multiplex amplification enabled by selective circularization of large sets of genomic DNA fragments. Nucleic Acids Res 2005;33:e71.
67. Turner EH, Lee C, Ng SB, et al. Massively parallel exon capture and library-free resequencing across 16 genomes. Nat Methods 2009;6:315-16.
68. Guo Z, Hood L, Malkki M, et al. Long-range multilocus haplotype phasing of the MHC. Proc Natl Acad Sci USA 2006;103:6964-9.
69. Dapprich J, Ferriola D, Magira EE, et al. SNP-specific extraction of haplotype-resolved targeted genomic regions. Nucleic Acids Res 2008;36:e94.
70. Albert TJ, Molla MN, Muzny DM, et al. Direct selection of human genomic loci by microarray hybridization. Nat Methods 2007;4 903-5.
71. Hodges E, Xuan Z, Bali ja V, et al. Genome-wide in situ exon capture for selective resequencing. Nat Genet 2007;39: 1522-7.
72. Zheng J, Moorhead M, Weng L, et al. High-throughput, high-accuracy array-based resequencing. Proc Natl Acad Sci USA 2009;106 6712-17.
73. Patil N, Berno AJ, Hinds DA, et al. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 2001; 294:1719-23.
74. Mir KU, Qi H, Salata O, et al. Sequencing by Cyclic Ligation and Cleavage (CycLiC) directly on a microarray captured template. Nucleic Acids Res 2009;37:e5.
75. Meyer M, Stenzel U, Myles S, et al. Targeted high-throughput sequencing of tagged nucleic acid samples. Nucleic Acids Res 2007;35:e97.
76. Erlich Y, Chang K, Gordon A, et al. DNA Sudoku-harnessing high-throughput sequencing for multiplexed specimen analysis. Genome Res 2009;19:1243-53.
77. Prabhu S, Pe'er I. Overlapping pools for high-throughput targeted resequencing. Genome Res 2009;19:1254-61.
78. Bovee D, Zhou Y, Haugen E, et al. Closing gaps in the human genome with fosmid resources generated from multiple individuals. Nat Genet 2008;40:96-101.
79. Consortium IGS. Finishing the euchromatic sequence of the human genome. Nature 2004;431:931-45.
80. Khoury MJ, Millikan R, Little J, et al. The emergence of epidemiology in the genomics age. Int J Epidemiol 2004;33: 936-44.
81. Mir KU. Ultrasensitive RNA profiling: Counting single molecules on microarrays. Genome Res 2006;16: 1195-7.
82. Rich A. The rise of single-molecule DNA biochemistry. Proc Natl Acad Sci USA 1998;95:13999-14000.
83. Erlich Y, Mitra PP, delaBastide M, et al. Alta-Cyclic: A self-optimizing base caller for next-generation sequencing. Nat Methods 2008;5:679-82.
84. Gupta PK. Single-molecule DNA sequencing technologies for future genomics research. Trends Biotechnol 2008;26: 602-11.
85. Branton D, Deamer DW, Marziali A, et al. The potential and challenges of nanopore sequencing. Nat Biotechnol 2008; 26 1146-53.
86. Bayley H. Sequencing single molecules of DNA. Curr Opin Chem Biol 2006;10:628-37.
87. Tanaka H, Kawai T. Visualization of detailed structures within DNA. Surface Science 2003;539:L531-6.
88. Tanaka H, Kawai T. Partial sequencing of a single DNA molecule with a scanning tunnelling microscope. Nat Nanotechnol 2009;4 518-22.
89. Pihlak A, Bauren G, Hersoug E, et al. Rapid genome sequencing with short universal tiling probes. Nat Biotechnol 2008;26:676-84.
90. Eid J, Fehr A, Gray J, et al. Real-time DNA sequencing from single polymerase molecules. Science 2009;323:133-8.
91. Trapnell C, Salzberg SL. How to map billions of short reads onto genomes. Nat Biotechnol 2009;27:455-7.
92. Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol 2008;26:1135-45.
93. Altschul SF, Gish W, Miller W, et al. Basic local alignment search tool. J Mol Biol 1990;215:403-10.
94. Lander ES, Linton LM, Birren B, et al. Initial sequencing and analysis of the human genome. Nature 2001;409:860-921.
95. Pevzner PA, Tang H, Waterman MS. An Eulerian path approach to DNA fragment assembly. Proc Natl Acad Sci USA 2001;98:9748-53.
96. Zerbino DR, Birney E. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008;18:821-9.
97. Ahn SM, Kim TH, Lee S, et al. The first Korean genome sequence and analysis: Full genome sequencing for a socio-ethnic group. Genome Res 2009.
98. Crawford DC, Akey DT, Nickerson DA. The patterns of natural variation in human genes. Annu Rev Genomics Hum Genet 2005;6:287-312.
99. Bansal V, Halpern AL, Axelrod N, et al. An MCMC algorithm for haplotype assembly from whole-genome sequence data. Genome Res 2008;18:1336-46.
100. Pop M. Genome assembly reborn: Recent computational challenges. Brief Bioinform 2009;10:354-66.
101. Korbel JO, Urban AE, Affourtit JP, et al. Paired-end mapping reveals extensive structural variation in the human genome. Science 2007;318:420-6.
102. Campbell PJ, Stephens PJ, Pleasance ED, et al. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet 2008;40 722-9.
103. Tuzun E, Sharp AJ, Bailey JA, et al. Fine-scale structural variation of the human genome. Nat Genet 2005;37:727-32.
104. Du J, Bjornson RD, Zhang ZD, et al. Integrating sequencing technologies in personal genomics: Optimal low cost reconstruction of structural variants. PLoS Comput Biol 2009; 5:e1000432.
105. Fullwood MJ, Wei CL, Liu ET, et al. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res 2009;19:521-32.
106. Dear PH, Cook PR. Happy mapping: A proposal for linkage mapping the human genome. Nucleic Acids Res 1989;17: 6795-807.
107. Jiang Z, Rokhsar DS, Harland RM. Old can be new again: HAPPY whole genome sequencing, mapping and assembly. Int J Biol Sci 2009;5 298-303.
108. Anantharaman TS, Mysore V, Mishra B. Fast and cheap genome wide haplotype construction via optical mapping. Pac Symp Biocomput 2005;385-96.
109. Anantharaman TS, Mishra B, Schwartz DC. Genomics via optical mapping. II: Ordered restriction maps. J Comput Biol 1997;4:91-118.
110. Aston C, Mishra B, Schwartz DC. Optical mapping and its potential for large-scale sequencing projects. Trends Biotechnol 1999;17 297-302.
111. Samad A, Huff EF, Cai W, et al. Optical mapping: A novel, single-molecule approach to genomic analysis. Genome Res 1995;5 1-4.
112. Valouev A, Schwartz DC, Zhou S, et al. An algorithm for assembly of ordered restriction maps from single DNA molecules. Proc Natl Acad Sci USA 2006;103:15770-5.
113. Buchanan JA, Carson AR, Chitayat D, et al. The cycle of genome-directed medicine. Genome Med 2009;1:16.
114. Henderson M. 'Genetic mapping of babies by 2019 will transform preventive medicine'. Times Online 2009, http://www.timesonline.co.uk/tol/news/science/article5689052.ece (last accessed 15 September 2009).
115. Kraft P, Hunter DJ. Genetic risk prediction-are we there yet? N Engl J Med 2009;360:1701-3.
116. Bogardus C. Missing heritability and GWAS utility. Obesity (Silver Spring) 2009;17:209-10.
117. Goldstein DB. Common genetic variation and human traits. N Engl J Med 2009;360:1696-8.
118. Janssens AC, van Duijn CM. Genome-based prediction of common diseases: advances and prospects. Hum Mol Genet 2008;17:R166-73.
119. Strohman R. Epigenesis: The missing beat in biotechnology? Biotechnology (NY) 1994;12:156-64.
120. Cordell HJ. Genome-wide association studies: Detecting gene-gene interactions that underlie human diseases. Nat Rev Genet 2009.
121. Marchini J, Donnelly P, Cardon LR. Genome-wide strategies for detecting multiple loci that influence complex diseases. Nat Genet 2005; 37:413-7.
122. Elbers CC, van Eijk KR, Franke L, et al. Using genome-wide pathway analysis to unravel the etiology of complex diseases. Genet Epidemiol 2009.
123. Gill SR, Pop M, Deboy RT, et al. Metagenomic analysis of the human distal gut microbiome. Science 2006;312: 1355-9.
124. Imhof A. Epigenetic regulators and histone modification. Brief Funct Genomic Proteomic 2006;5:222-7.
125. Jaenisch R, Bird A. Epigenetic regulation of gene expression: How the genome integrates intrinsic and environmental signals. Nat Genet 2003;33(Suppl):245-54.
126. Clarke J, Wu HC, Jayasinghe L, et al. Continuous base identification for single-molecule nanopore DNA sequencing. Nat Nanotechnol 2009;4:265-70.
127. Kaprio J. Science, medicine, and the future. Genetic Epidemiol, BMJ 2000;320:1257-9.
128. Peltonen L, McKusick VA. Genomics and medicine. Dissecting human disease in the postgenomic era. Science 2001;291:1224-9.
129. Hirschhorn JN. Genomewide association studies - illuminating biologic pathways. N Engl J Med 2009;360: 1699-701.
130. Blencowe BJ, Ahmad S, Lee LJ. Current-generation high-throughput sequencing: Deepening insights into mammalian transcriptomes. Genes Dev 2009;23:1379-86.