Next-generation sequencing:from basic research to diagnostics

Clinical Chemistry

Volumn 55, Issue 4, 2009, Pages 641-658

  Voelkerding, Karl V ^a,b,c   Dames, Shale A ^a   Durtschi, Jacob D ^a  

^a ARUP INSTITUTE FOR CLINICAL AND EXPERIMENTAL PATHOLOGY   (United States)

^b UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

^c ARUP LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN; TRANSCRIPTOME;

BIOINFORMATICS; CHROMATIN; CLINICAL RESEARCH; COST EFFECTIVENESS ANALYSIS; DATA ANALYSIS; DIAGNOSTIC TEST; DNA ISOLATION; DNA SEQUENCE; GENE AMPLIFICATION; GENOME ANALYSIS; HUMAN; METAGENOMICS; NANOPORE; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PROTEIN DETERMINATION; REVIEW; RNA ANALYSIS; SEQUENCE ANALYSIS; STANDARD; ANIMAL; COMPUTER PROGRAM; DIAGNOSTIC PROCEDURE; GENETICS; GENOMICS; MEDICAL RESEARCH; METHODOLOGY; PEER REVIEW;

ANIMALS; BASE SEQUENCE; BIOMEDICAL RESEARCH; GENOMICS; HUMANS; MOLECULAR DIAGNOSTIC TECHNIQUES; PEER REVIEW, RESEARCH; SOFTWARE;

EID: 64149123778     PISSN: 00099147     EISSN: 15308561     Source Type: Journal    
DOI: 10.1373/clinchem.2008.112789     Document Type: Review

References (98)

1. Maxam AM, Gilbert W. A new method for se- quencing DNA. Proc Natl Acad Sci U S A 1977; 74:560-4.
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. Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, et al. The complete genome of an individual by massively parallel DNA se- quencing. Nature 2008;452:872-6.
4. Nyren P, Pettersson B, Uhlen M. Solid phase DNA minisequencing by an enzymatic luminometric inorganic pyrophosphate detection assay. Anal Biochem 1993;208:171-5.
5. Ronaghi M, Karamohamed S, Pettersson B, Uhlen M, Nyren P. Real-time DNA sequencing using detection of pyrophosphate release. Anal Bio- chem 1996;242:84-9.
6. Ronaghi M, Uhlen M, Nyren P. A sequencing method based on real-time pyrophosphate. Sci- ence 1998;281:363-5.
7. Tawfik DS, Griffiths AD. Man-made cell-like com- partments for molecular evolution. Nat Biotech- nol 1998;16:652-6.
8. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005;437:376-80.
9. Pearson BM, Gaskin DJ, Segers RP, Wells JM, Nuijten PJ, van Vliet AH. The complete genome sequence of Campylobacter jejuni strain 81116 (NCTC11828). J Bacteriol 2007;189:8402-3.
10. Huse SM, Huber JA, Morrison HG, Sogin ML, Welch DM. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 2007; 8:R143.
11. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, et al. Accurate whole human genome sequencing using re- versible terminator chemistry. Nature 2008; 456:53-9.
12. Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, et al. Paired-end mapping reveals extensive structural variation in the hu- man genome. Science 2007;318:420-6.
13. Campbell PJ, Stephens PJ, Pleasance ED, O'Meara S, Li H, Santarius T, et al. Identification of somat- ically acquired rearrangements in cancer using genome-wide massively parallel paired-end se- quencing. Nat Genet 2008;40:722-9.
14. 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.
15. Erlich Y, Mitra PP, delaBastide M, McCombie WR, Hannon GJ. Alta-Cyclic: a self-optimizing base caller for next-generation sequencing. Nat Meth- ods 2008;5:679-82.
16. Quail MA, Kozarewa I, Smith F, Scally A, Ste- phens PJ, Durbin R, et al. A large genome center's improvements to the Illumina sequencing system. Nat Methods 2008;5:1005-10.
17. Shendure J, Porreca GJ, Reppas NB, Lin X, Mc- Cutcheon JP, Rosenbaum AM, et al. Accurate multiplex polony sequencing of an evolved bac- terial genome. Science 2005;309:1728-32.
18. Braslavsky I, Hebert B, Kartalov E, Quake SR. Sequence information can be obtained from sin- gle DNA molecules. Proc Natl Acad Sci U S A 2003;100:3960-4.
19. Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, Braslavsky I, et al. Single-molecule DNA se- quencing of a viral genome. Science 2008;320: 106-9.
20. Smith DR, Quinlan AR, Peckham HE, Makowsky K, Tao W, Woolf B, et al. Rapid whole-genome mutational profiling using next-generation se- quencing technologies. Genome Res 2008;18: 1638-42.
21. Quinn NL, Levenkova N, Chow W, Bouffard P, Boroevich KA, Knight JR, et al. Assessing the feasibility of GS FLX Pyrosequencing for sequenc- ing the Atlantic salmon genome. BMC Genomics 2008;9:404.
22. Satkoski JA, Malhi R, Kanthaswamy S, Tito R, Malladi V, Smith D. Pyrosequencing as a method for SNP identification in the rhesus macaque (Macaca mulatta). BMC Genomics 2008;9:256.
23. Borneman AR, Forgan AH, Pretorius IS, Chambers PJ. Comparative genome analysis of a Saccharo- myces cerevisiae wine strain. FEMS Yeast Res 2008;8:1185-95.
24. Wang J, Wang W, Li R, Li Y, Tian G, Goodman L, et al. The diploid genome sequence of an Asian individual. Nature 2008;456:60-5.
25. Ley TJ, Mardis ER, Ding L, Fulton B, McLellan MD, Chen K, et al. DNA sequencing of a cytogeneti- cally normal acute myeloid leukaemia genome. Nature 2008;456:66-72.
26. Kim PM, Lam HY, Urban AE, Korbel JO, Affourtit J, Grubert F, et al. Analysis of copy number variants and segmental duplications in the hu- man genome: evidence for a change in the pro- cess of formation in recent evolutionary history. Genome Res 2008;18:1865-74.
27. Chen J, Kim YC, Jung YC, Xuan Z, Dworkin G, Zhang Y, et al. Scanning the human genome at kilobase resolution. Genome Res 2008;18:751-62.
28. Yeager M, Xiao N, Hayes RB, Bouffard P, Desany B, Burdett L, et al. Comprehensive resequence analysis of a 136 kb region of human chromo- some 8q24 associated with prostate and colon cancers. Hum Genet 2008;124:161-70.
29. Ding L, Getz G, Wheeler DA, Mardis ER, McLellan MD, Cibulskis K, et al. Somatic mutations affect key pathways in lung adenocarcinoma. Nature 2008;455:1069-75.
30. 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.
31. Hodges E, Xuan Z, Balija V, Kramer M, Molla MN, Smith SW, et al. Genome-wide in situ exon cap- ture for selective resequencing. Nat Genet 2007; 39:1522-7.
32. Okou DT, Steinberg KM, Middle C, Cutler DJ, Albert TJ, Zwick ME. Microarray-based genomic selection for high-throughput resequencing. Nat Methods 2007;4:907-9.
33. Porreca GJ, Zhang K, Li JB, Xie B, Austin D, Vassallo SL, et al. Multiplex amplification of large sets of human exons. Nat Methods 2007;4: 931-6.
34. Huber JA, Mark Welch DB, Morrison HG, Huse SM, Neal PR, Butterfield DA, Sogin ML. Microbial population structures in the deep marine bio- sphere. Science 2007;318:97-100.
35. Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, Neal PR, et al. Microbial diversity in the deep sea and the underexplored "rare bio- sphere." Proc Natl Acad Sci U S A 2006;103: 12115-20.
36. Urich T, Lanzen A, Qi J, Huson DH, Schleper C, Schuster SC. Simultaneous assessment of soil mi- crobial community structure and function through analysis of the meta-transcriptome. PLoS ONE 2008;3:e2527.
37. Palacios G, Druce J, Du L, Tran T, Birch C, Briese T, et al. A new arenavirus in a cluster of fatal transplant-associated diseases. N Engl J Med 2008;358:991-8.
38. Keijser BJ, Zaura E, Huse SM, van der Vossen JM, Schuren FH, Montijn RC, et al. Pyrosequencing analysis of the oral microflora of healthy adults. J Dent Res 2008;87:1016-20.
39. Turnbaugh PJ, Hamady M, Yatsunenko T, Can- tarel BL, Duncan A, Ley RE, et al. A core gut microbiome in obese and lean twins. Nature 2008;457:480-4.
40. Wang Z, Gerstein M, Snyder M. RNA-Seq: a rev- olutionary tool for transcriptomics. Nat Rev Genet 2009;10:57-63.
41. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. The tran- scriptional landscape of the yeast genome de- fined by RNA sequencing. Science 2008;320: 1344-9.
42. Wilhelm BT, Marguerat S, Watt S, Schubert F, Wood V, Goodhead I, et al. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 2008;453: 1239-43.
43. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008; 5:621-8.
44. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR. Highly inte- grated single-base resolution maps of the epi- genome in Arabidopsis. Cell 2008;133:523-36.
45. Cloonan N, Forrest AR, Kolle G, Gardiner BB, Faulkner GJ, Brown MK, et al. Stem cell transcrip- tome profiling via massive-scale mRNA sequenc- ing. Nat Methods 2008;5:613-9.
46. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: an assessment of tech- nical reproducibility and comparison with gene expression arrays. Genome Res 2008;18:1509-17.
47. Morin R, Bainbridge M, Fejes A, Hirst M, Krzy- winski M, Pugh T, et al. Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. Bio- techniques 2008;45:81-94.
48. Morin RD, O'Connor MD, Griffith M, Kuchen- bauer F, Delaney A, Prabhu AL, et al. Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res 2008;18:610-21.
49. Emrich SJ, Barbazuk WB, Li L, Schnable PS. Gene discovery and annotation using LCM-454 tran- scriptome sequencing. Genome Res 2007;17: 69-73.
50. Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput se- quencing. Nat Genet 2008;40:1413-5.
51. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, et al. Alternative isoform reg- ulation in human tissue transcriptomes. Nature 2008;456:470-6.
52. Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I, et al. Genome-wide location and function of DNA binding proteins. Science 2000; 290:2306-9.
53. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, et al. High-resolution profiling of histone methylations in the human genome. Cell 2007; 129:823-37.
54. Schones DE, Zhao K. Genome-wide approaches to studying chromatin modifications. Nat Rev Genet 2008;9:179-91.
55. Valouev A, Ichikawa J, Tonthat T, Stuart J, Ra- nade S, Peckham H, et al. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res 2008;18:1051-63.
56. Johnson DS, Mortazavi A, Myers RM, Wold B. Genome-wide mapping of in vivo protein-DNA interactions. Science 2007;316:1497-502.
57. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, et al. Genome-wide profiles of STAT1 DNA association using chromatin immu- noprecipitation and massively parallel sequenc- ing. Nat Methods 2007;4:651-7.
58. Korshunova Y, Maloney RK, Lakey N, Citek RW, Bacher B, Budiman A, et al. Massively parallel bisulphite pyrosequencing reveals the molecu- lar complexity of breast cancer-associated cytosine-methylation patterns obtained from tissue and serum DNA. Genome Res 2008;18: 19-29.
59. Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 2008;452: 215-9.
60. Marguerat S, Wilhelm BT, Bahler J. Next- generation sequencing: applications beyond ge- nomes. Biochem Soc Trans 2008;36:1091-6.
61. Pop M, Salzberg SL. Bioinformatics challenges of new sequencing technology. Trends Genet 2008; 24:142-9.
62. Rougemont J, Amzallag A, Iseli C, Farinelli L, Xenarios I, Naef F. Probabilistic base calling of Solexa sequencing data. BMC Bioinformatics 2008;9:431.
63. Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabili- ties. Genome Res 1998;8:186-94.
64. Ewing B, Hillier L, Wendl MC, Green P. Base- calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 1998;8:175-85.
65. Brockman W, Alvarez P, Young S, Garber M, Giannoukos G, Lee WL, et al. Quality scores and SNP detection in sequencing-by-synthesis sys- tems. Genome Res 2008;18:763-70.
66. Smith AD, Xuan Z, Zhang MQ. Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinformatics 2008; 9:128.
67. Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using map- ping quality scores. Genome Res 2008;18: 1851-8.
68. Whiteford N, Haslam N, Weber G, Prugel-Bennett A, Essex JW, Roach PL, et al. An analysis of the feasibility of short read sequencing. Nucleic Acids Res 2005;33:e171.
69. Warren RL, Sutton GG, Jones SJ, Holt RA. Assem- bling millions of short DNA sequences using SSAKE. Bioinformatics 2007;23:500-1.
70. Hernandez D, Francois P, Farinelli L, Osteras M, Schrenzel J. De novo bacterial genome sequencing: millions of very short reads assem- bled on a desktop computer. Genome Res 2008;18:802-9.
71. Lin H, Zhang Z, Zhang MQ, Ma B, Li M. ZOOM Zillions Of Oligos Mapped. Bioinformatics 2008; 24:2431-7.
72. Smith DR, Quinlan AR, Peckham HE, Makowsky K, Tao W, Woolf B, et al. Rapid whole-genome mutational profiling using next-generation se- quencing technologies. Genome Res 2008;18: 1638-42.
73. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformat- ics 2008;24:713-4.
74. Chaisson MJ, Pevzner PA. Short read fragment assembly of bacterial genomes. Genome Res 2008;18:324-30.
75. Dohm JC, Lottaz C, Borodina T, Himmelbauer H. SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic se- quencing. Genome Res 2007;17:1697-706.
76. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008;18:821-9.
77. Zhu QH, Spriggs A, Matthew L, Fan L, Kennedy G, Gubler F, Helliwell C. A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains. Genome Res 2008;18:1456-65.
78. Glazov EA, Cottee PA, Barris WC, Moore RJ, Dalrymple BP, Tizard ML. A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. Genome Res 2008; 18:957-64.
79. Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, Batzoglou S, et al. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods 2008;5: 829-34.
80. Zhang Y, Liu T, Meyer CA, Eeckhoute J, John- son DS, Bernstein BE, et al. Model-based anal- ysis of ChIP-Seq (MACS). Genome Biol 2008;9: R137.
81. Binladen J, Gilbert MT, Bollback JP, Panitz F, Bendixen C, Nielsen R, Willerslev E. The use of coded PCR primers enables high-throughput se- quencing of multiple homolog amplification prod- ucts by 454 parallel sequencing. PLoS ONE 2007; 2:e197.
82. Meyer M, Stenzel U, Hofreiter M. Parallel tagged sequencing on the 454 platform. Nat Protoc 2008;3:267-78.
83. Meyer M, Stenzel U, Myles S, Prufer K, Hofreiter M. Targeted high-throughput sequencing of tagged nucleic acid samples. Nucleic Acids Res 2007;35:e97.
84. Wang C, Mitsuya Y, Gharizadeh B, Ronaghi M, Shafer RW. Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance. Genome Res 2007;17: 1195-201.
85. Fokstuen S, Lyle R, Munoz A, Gehrig C, Lerch R, Perrot A, et al. A DNA resequencing array for pathogenic mutation detection in hypertrophic cardiomyopathy. Hum Mutat 2008;29:879-85.
86. Morita H, Rehm HL, Menesses A, McDonough B, Roberts AE, Kucherlapati R, et al. Shared genetic causes of cardiac hypertrophy in children and adults. N Engl J Med 2008;358:1899-908.
87. Chiu RW, Chan KC, Gao Y, Lau VY, Zheng W, Leung TY, et al. Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma. Proc Natl Acad Sci U S A 2008;105: 20458-63.
88. Fan HC, Blumenfeld YJ, Chitkara U, Hudgins L, Quake SR. Noninvasive diagnosis of fetal aneu- ploidy by shotgun sequencing DNA from maternal blood. Proc Natl Acad Sci U S A 2008;105: 16266-71.
89. Fan HC, Quake SR. Detection of aneuploidy with digital polymerase chain reaction. Anal Chem 2007;79:7576-9.
90. Lo YM, Lun FM, Chan KC, Tsui NB, Chong KC, Lau TK, et al. Digital PCR for the molecular detection of fetal chromosomal aneuploidy. Proc Natl Acad Sci U S A 2007;104:13116-21.
91. Dennis Lo YM, Chiu RW. Prenatal diagnosis: progress through plasma nucleic acids. Nat Rev Genet 2007;8:71-7.
92. Korlach J, Marks PJ, Cicero RL, Gray JJ, Murphy DL, Roitman DB, et al. Selective aluminum pas- sivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures. Proc Natl Acad Sci U S A 2008;105:1176-81.
93. Levene MJ, Korlach J, Turner SW, Foquet M, Craig- head HG, Webb WW. Zero-mode waveguides for single-molecule analysis at high concentrations. Sci- ence 2003;299:682-6.
94. Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, et al. Real-time DNA sequencing from sin- gle polymerase molecules. Science 2008;323: 133-8.
95. Astier Y, Braha O, Bayley H. Toward single mol- ecule DNA sequencing: direct identification of ribonucleoside and deoxyribonucleoside 5- monophosphates by using an engineered protein nanopore equipped with a molecular adapter. J Am Chem Soc 2006;128:1705-10.
96. Wu HC, Astier Y, Maglia G, Mikhailova E, Bayley H. Protein nanopores with covalently attached molecular adapters. J Am Chem Soc 2007;129: 16142-8.
97. Gupta PK. Single-molecule DNA sequencing tech- nologies for future genomics research. Trends Biotechnol 2008;26:602-11.
98. Rhee M, Burns MA. Nanopore sequencing technology: research trends and applications. Trends Biotechnol 2006;24:580-6.