Key principles and clinical applications of "next-generation" DNA sequencing

Cancer Prevention Research

Volumn 5, Issue 7, 2012, Pages 887-900

  Rizzo, Jason M ^a   Buck, Michael J ^a  

^a UNIVERSITY AT BUFFALO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA FRAGMENT; TRANSCRIPTOME;

CAPILLARY ELECTROPHORESIS; CLINICAL PROTOCOL; CLINICAL RESEARCH; COST EFFECTIVENESS ANALYSIS; CYTOGENETICS; DNA SEQUENCE; DNA TEMPLATE; EXOME; GENE TECHNOLOGY; GENOME ANALYSIS; HUMAN; MEDICAL EDUCATION; NUCLEOTIDE SEQUENCE; POINT MUTATION; PRIORITY JOURNAL; REVIEW; RNA SEQUENCE; SENSITIVITY AND SPECIFICITY; SIGNAL DETECTION; SINGLE NUCLEOTIDE POLYMORPHISM;

GENOME, HUMAN; GENOMICS; HUMANS; SEQUENCE ANALYSIS, DNA; TRANSLATIONAL MEDICAL RESEARCH;

EID: 84866467254     PISSN: 19406207     EISSN: 19406215     Source Type: Journal    
DOI: 10.1158/1940-6207.CAPR-11-0432     Document Type: Review

References (98)

1. Metzker ML. Sequencing technologies-the next generation. Nat Rev Genet 2010;11:31-46.
2. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 1977;74:5463-7.
3. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, et al. Initial sequencing and analysis of the human genome. Nature 2001;409:860-921. (Pubitemid 32165345)
4. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, et al. The sequence of the human genome. Science 2001;291: 1304-51. (Pubitemid 32173090)
5. International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 2004;431:931-45.
6. Mardis ER. Anticipating the 1,000 dollar genome. Genome Biol 2006;7:112.
7. Schloss JA. How to get genomes at one ten-thousandth the cost. Nat Biotechnol 2008;26:1113-5.
8. Bennett ST, Barnes C, Cox A, Davies L, Brown C. Toward the 1,000 dollars human genome. Pharmacogenomics 2005;6:373-82. (Pubitemid 40916360)
9. Prober JM, Trainor GL, Dam RJ, Hobbs FW, Robertson CW, Zagursky RJ, et al. A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides. Science 1987;238:336-41. (Pubitemid 17151722)
10. Hutchison CA III. DNA sequencing: bench to bedside and beyond. Nucleic Acids Res 2007;35:6227-37.
11. Metzker ML. Emerging technologies in DNA sequencing. Genome Res 2005;15:1767-76. (Pubitemid 41780407)
12. Kingsmore SF, Saunders CJ. Deep sequencing of patient genomes for disease diagnosis: when will it become routine? Sci Transl Med 2011;3:87ps23.
13. Hert DG, Fredlake CP, Barron AE. Advantages and limitations of next-generation sequencing technologies: a comparison of electrophoresis and non-electrophoresis methods. Electrophoresis 2008;29:4618-26.
14. Mardis ER. A decade's perspective on DNA sequencing technology. Nature 2011;470:198-203.
15. Linnarsson S. Recent advances in DNA sequencing methods-general principles of sample preparation. Exp Cell Res 2010;316:1339-43.
16. Natrajan R, Reis-Filho JS. Next-generation sequencing applied to molecular diagnostics. Expert Rev Mol Diagn 2011;11:425-44.
17. Hart C, Lipson D, Ozsolak F, Raz T, Steinmann K, Thompson J, et al. Single-molecule sequencing: sequence methods to enable accurate quantitation. Methods Enzymol 2010;472:407-30.
18. Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N, et al. mRNASeq whole-transcriptome analysis of a single cell. Nat Methods 2009;6:377-82.
19. Navin N, Hicks J. Future medical applications of single-cell sequencing in cancer. Genome Med 2011;3:31.
20. Fuller CW, Middendorf LR, Benner SA, Church GM, Harris T, Huang X, et al. The challenges of sequencing by synthesis. Nat Biotechnol 2009;27:1013-23.
21. Lander ES. Initial impact of the sequencing of the human genome. Nature 2011;470:187-97.
22. Thompson JF, Milos PM. The properties and applications of single-molecule DNA sequencing. Genome Biol 2011;12:217.
23. Nagarajan N, Pop M. Sequencing and genome assembly using next-generation technologies. Methods Mol Biol 2010;673:1-17.
24. Nielsen R, Paul JS, Albrechtsen A, Song YS. Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet 2011;12:443-51.
25. Pop M, Salzberg SL. Bioinformatics challenges of new sequencing technology. Trends Genet 2008;24:142-9.
26. McPherson JD. Next-generation gap. Nat Methods 2009;6:S2-5.
27. Flicek P, Birney E. Sense from sequence reads: methods for alignment and assembly. Nat Methods 2009;6:S6-12.
28. Martin JA, Wang Z. Next-generation transcriptome assembly. Nat Rev Genet 2011;12:671-82.
29. Park PJ. ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 2009;10:669-80.
30. Bamshad MJ, Ng SB, Bigham AW, Tabor HK, Emond MJ, Nickerson DA, et al. Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet 2011;12:745-55.
31. Medvedev P, Stanciu M, Brudno M. Computational methods for discovering structural variation with next-generation sequencing. Nat Methods 2009;6:S13-20.
32. Wooley JC, Godzik A, Friedberg I. A primer on metagenomics. PLoS Comput Biol 2010;6:e1000667.
33. Dohm JC, Lottaz C, Borodina T, Himmelbauer H. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 2008;36:e105.
34. Wood HM, Belvedere O, Conway C, Daly C, Chalkley R, Bickerdike M, et al. Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens. Nucleic Acids Res 2010;38:e151.
35. Schweiger MR, Kerick M, Timmermann B, Albrecht MW, Borodina T, Parkhomchuk D, et al. Genome-wide massively parallel sequencing of formaldehyde fixed-paraffi n embedded (FFPE) tumor tissues for copy-number-and mutation-analysis. PLoS One 2009;4:e5548.
36. Ajay SS, Parker SC, Ozel Abaan H, Fuentes Fajardo KV, Margulies EH. Accurate and comprehensive sequencing of personal genomes. Genome Res 2011;29:1498-505.
37. Taub MA, Corrada Bravo H, Irizarry RA. Overcoming bias and systematic errors in next generation sequencing data. Genome Med 2010;2:87.
38. Lee W, Jiang Z, Liu J, Haverty PM, Guan Y, Stinson J, et al. The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature 2010;465:473-7.
39. Li J, Jiang H, Wong WH. Modeling non-uniformity in short-read rates in RNA-Seq data. Genome Biol 2010;11:R50.
40. Kim JI, Ju YS, Park H, Kim S, Lee S, Yi JH, et al. A highly annotated whole-genome sequence of a Korean individual. Nature 2009;460:1011-5.
41. 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 2010;467:1061-73.
42. Shen P, Wang W, Krishnakumar S, Palm C, Chi AK, Enns GM, et al. High-quality DNA sequence capture of 524 disease candidate genes. Proc Natl Acad Sci U S A 2011;108:6549-54.
43. Tewhey R, Warner JB, Nakano M, Libby B, Medkova M, David PH, et al. Microdroplet-based PCR enrichment for large-scale targeted sequencing. Nat Biotechnol 2009;27:1025-31.
44. Albert TJ, Molla MN, Muzny DM, Nazareth L, Wheeler D, Song X, et al. Direct selection of human genomic loci by microarray hybridization. Nat Methods 2007;4:903-5. (Pubitemid 350042375)
45. Mamanova L, Coffey AJ, Scott CE, Kozarewa I, Turner EH, Kumar A, et al. Target-enrichment strategies for next-generation sequencing. Nat Methods 2010;7:111-8.
46. Choi M, Scholl UI, Ji W, Liu T, Tikhonova IR, Zumbo P, et al. Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc Natl Acad Sci U S A 2009;106:19096-101.
47. Bolze A, Byun M, McDonald D, Morgan NV, Abhyankar A, Premkumar L, et al. Whole-exome-sequencing-based discovery of human FADD deficiency. Am J Hum Genet 2010;87:873-81.
48. Worthey EA, Mayer AN, Syverson GD, Helbling D, Bonacci BB, Decker B, et al. Making a definitive diagnosis: successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease. Genet Med 2011;13:255-62.
49. Bell CJ, Dinwiddie DL, Miller NA, Hateley SL, Ganusova EE, Mudge J, et al. Carrier testing for severe childhood recessive diseases by next-generation sequencing. Sci Transl Med 2011;3:65ra4.
50. Holbrook JD, Parker JS, Gallagher KT, Halsey WS, Hughes AM, Weigman VJ, et al. Deep sequencing of gastric carcinoma reveals somatic mutations relevant to personalized medicine. J Transl Med 2011;9:119.
51. Heger M. Wash U Med School Offers 28-Gene Cancer Dx Panel on HiSeq through CLIA Lab. Clinical Sequencing News 2011 [cited 2011 Nov 30]. Available from: http://www.genomeweb.com/sequencing/wash-u-med-school-offers-28-gene- cancer-dx-panel-hiseq-through-clia-lab.
52. Karow J. Baylor's Cancer Genetics Lab to Offer Ion AmpliSeq Cancer Panel on PGM. Clinical Sequencing News 2011 [cited 2011 Nov 30]. Available from: http://www.genomeweb.com/sequencing/baylors-cancer-genetics-lab-offer-ion- ampliseq-cancer-panel-pgm
53. Jiao Y, Shi C, Edil BH, de Wilde RF, Klimstra DS, Maitra A, et al. DAXX/ATRX, MEN1, and mTOR pathway genes are frequently altered in pancreatic neuroendocrine tumors. Science 2011;331:1199-203.
54. Green ED, Guyer MS. Charting a course for genomic medicine from base pairs to bedside. Nature 2011;470:204-13.
55. Welch JS, Westervelt P, Ding L, Larson DE, Klco JM, Kulkarni S, et al. Use of whole-genome sequencing to diagnose a cryptic fusion oncogene. JAMA 2011;305:1577-84.
56. Roychowdhury S, Iyer MK, Robinson DR, Lonigro RJ, Wu YM, Cao X, et al. Personalized oncology through integrative high-throughput sequencing: a pilot study. Sci Transl Med 2011;3:111ra21.
57. Pleasance ED, Cheetham RK, Stephens PJ, McBride DJ, Humphray SJ, Greenman CD, et al. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 2010;463:191-6.
58. Ding L, Ellis MJ, Li S, Larson DE, Chen K, Wallis JW, et al. Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature 2010;464:999-1005.
59. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, et al. Finding the missing heritability of complex diseases. Nature 2009;461:747-53.
60. Manolio TA. Genomewide association studies and assessment of the risk of disease. N Engl J Med 2010;363:166-76.
61. Alexander RP, Fang G, Rozowsky J, Snyder M, Gerstein MB. Annotating non-coding regions of thegenome. Nat Rev Genet 2010;11:559-71.
62. Snyder TM, Khush KK, Valantine HA, Quake SR. Universal noninvasive detection of solid organ transplant rejection. Proc Natl Acad Sci U S A 2011;108:6229-34.
63. Palomaki GE, Kloza EM, Lambert-Messerlian GM, Haddow JE, Neveux LM, Ehrich M, et al. DNA sequencing of maternal plasma to detect Down syndrome: an international clinical validation study. Genet Med 2011;13:913-20.
64. Palomaki GE, Deciu C, Kloza EM, Lambert-Messerlian GM, Haddow JE, Neveux LM, et al. DNA sequencing of maternal plasma reliably identifies trisomy 18 and trisomy 13 as well as Down syndrome: an international collaborative study. Genet Med 2012;14:296-305.
65. Shah SP, Kobel M, Senz J, Morin RD, Clarke BA, Wiegand KC, et al. Mutation of FOXL2 in granulosa-cell tumors of the ovary. N Engl J Med 2009;360:2719-29.
66. Wiegand KC, Shah SP, Al-Agha OM, Zhao Y, Tse K, Zeng T, et al. ARID1A mutations in endometriosis-associated ovarian carcinomas. N Engl J Med 2010;363:1532-43.
67. Heravi-Moussavi A, Anglesio MS, Cheng SW, Senz J, Yang W, Prentice L, et al. Recurrent somatic DICER1 mutations in nonepithelial ovarian cancers. N Engl J Med 2012;366:234-42.
68. Maher CA, Palanisamy N, Brenner JC, Cao X, Kalyana-Sundaram S, Luo S, et al. Chimeric transcript discovery by paired-end transcriptome sequencing. Proc Natl Acad Sci U S A 2009;106:12353-8.
69. Pflueger D, Terry S, Sboner A, Habegger L, Esgueva R, Lin PC, et al. Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing. Genome Res 2011;21:56-67.
70. Prensner JR, Iyer MK, Balbin OA, Dhanasekaran SM, Cao Q, Brenner JC, et al. Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat Biotechnol 2011;29:742-9.
71. Hajkova P, el-Maarri O, Engemann S, Oswald J, Olek A, Walter J. DNA-methylation analysis by the bisulfite-assisted genomic sequencing method. Methods Mol Biol 2002;200:143-54.
72. Tost J, Gut IG. DNA methylation analysis by pyrosequencing. Nat Protoc 2007;2:2265-75. (Pubitemid 351575045)
73. Zhang J, Benavente CA, McEvoy J, Flores-Otero J, Ding L, Chen X, et al. A novel retinoblastoma therapy from genomic and epigenetic analyses. Nature 2012;481:329-34.
74. Giresi PG, Kim J, McDaniell RM, Iyer VR, Lieb JD. FAIRE (Formalde-hyde- Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res 2007;17:877-85. (Pubitemid 46919722)
75. Song L, Zhang Z, Grasfeder LL, Boyle AP, Giresi PG, Lee BK, et al. Open chromatin defined by DNaseI and FAIRE identifi es regulatory elements that shape cell-type identity. GenomeRes 2011;21:1757-67.
76. Song L, Crawford GE. DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells. Cold Spring Harb Protoc 2010;2010:pdb.prot5384.
77. Jiang C, Pugh BF. Nucleosome positioning and gene regulation: advances through genomics. Nat Rev Genet 2009;10:161-72.
78. Zhang Z, Pugh BF. High-resolution genome-wide mapping of the primary structure of chromatin. Cell 2011;144:175-86.
79. Riesenfeld CS, Schloss PD, Handelsman J. Metagenomics: genomic analysis of microbial communities. Annu Rev Genet 2004;38:525-52. (Pubitemid 40013737)
80. Tringe SG, Rubin EM. Metagenomics: DNA sequencing of environmental samples. Nat Rev Genet 2005;6:805-14.
81. Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature 2011;474:609-15.
82. Myers RM, Stamatoyannopoulos J, Snyder M, DunhamI, Hardison RC, Bernstein BE, et al. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 2011;9:e1001046.
83. Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, et al. The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol 2010;28:1045-8.
84. Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, et al. Real-time DNA sequencing from single polymerase molecules. Science 2009; 323:133-8.
85. Fernald GH, Capriotti E, Daneshjou R, Karczewski KJ, Altman RB. Bioinformatics challenges for personalized medicine. Bioinformatics 2011;27:1741-8.
86. This time it's personal. Nature 2008;453:697.
87. Hudson KL. Genomics, health care, and society. N Engl J Med 2011;365:1033-41.
88. Cook-Deegan R, Heaney C. Patents in genomics and human genetics. Annu Rev Genomics Hum Genet 2010;11:383-425.
89. Fujiwara Y. Genomics, health care, and society. N Engl J Med 2011;365:2339.
90. Branton D, Deamer DW, Marziali A, Bayley H, Benner SA, Butler T, et al. The potential and challenges of nanopore sequencing. Nat Biotechnol 2008;26:1146-53.
91. Zhao J, Ohsumi TK, Kung JT, Ogawa Y, Grau DJ, Sarma K, et al. Genome-wide identification of polycomb-associated RNAs by RIPseq. Mol Cell 2010;40:939-53.
92. Rizzo JM, Mieczkowski PA, Buck MJ. Tup1 stabilizes promoter nucleosome positioning and occupancy at transcriptionally plastic genes. Nucleic Acids Res 2011;39:8803-19.
93. Dostie J, Dekker J. Mapping networks of physical interactions between genomic elements using 5C technology. Nat Protoc 2007;2:988-1002. (Pubitemid 46745595)
94. van Steensel B, Dekker J. Genomics tools for unraveling chromosome architecture. Nat Biotechnol 2010;28:1089-95.
95. Alkan C, Sajjadian S, Eichler EE. Limitations of next-generation genome sequence assembly. Nat Methods 2011;8:61-5.
96. Scheibye-Alsing K, Hoffmann S, Frankel A, Jensen P, Stadler PF, Mang Y, et al. Sequence assembly. Comput Biol Chem 2009;33:121-36.
97. Chaisson MJ, Pevzner PA. Short read fragment assembly of bacterial genomes. Genome Res 2008;18:324-30. (Pubitemid 351240742)
98. Simon MP, Pedeutour F, Sirvent N, Grosgeorge J, Minoletti F, Coindre JM, et al. Deregulation of the platelet-derived growth factor B-chain gene via fusion with collagen gene COL1A1 in dermatofibrosarcoma protuberans and giant-cell fibroblastoma. Nat Genet 1997;15:95-8. (Pubitemid 27014958)