Massively parallel sequencing: The new frontier of hematologic genomics

Blood

Volumn 122, Issue 19, 2013, Pages 3268-3275

  Johnsen, Jill M ^a,b   Nickerson, Deborah A ^c   Reiner, Alex P ^c,d  

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^b PUGET SOUND BLOOD CENTER   (United States)

^c UNIVERSITY OF WASHINGTON   (United States)

^d Fred Hutchinson Cancer Research Center   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

COMPARATIVE GENOMIC HYBRIDIZATION; DNA DAMAGE; DNA LIBRARY; DNA METHYLATION; DNA REPLICATION; DNA SEQUENCE; DNA TEMPLATE; GENE AMPLIFICATION; GENE EXPRESSION REGULATION; GENE TARGETING; GENETIC ASSOCIATION; GENETIC CODE; GENETIC VARIABILITY; GENOMICS; HEMATOLOGY; HUMAN; HUMAN GENETICS; MEDICINE; MUTAGENESIS; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 84888265056     PISSN: 00064971     EISSN: 15280020     Source Type: Journal    
DOI: 10.1182/blood-2013-07-460287     Document Type: Review

References (87)

1. Lander ES, Linton LM, Birren B, et al; International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome [published correction appears in Nature. 2001;411(6838):720]. Nature. 2001;409(6822):860-921.
2. Venter JC, Adams MD, Myers EW, et al. The sequence of the human genome. Science. 2001;291(5507):1304-1351.
3. ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science. 2004;306(5696):636-640.
4. Palstra RJ, De Laat W, Grosveld F. Beta-globin regulation and long-range interactions. Adv Genet. 2008;61:107-142.
5. Ballestar E. An introduction to epigenetics. Adv Exp Med Biol. 2011;711:1-11.
6. Abramowitz LK, Bartolomei MS. Genomic imprinting: recognition and marking of imprinted loci. Curr Opin Genet Dev. 2012;22(2):72-78.
7. Kunkel TA, Bebenek K. DNA replication fidelity. Annu Rev Biochem. 2000;69:497-529.
8. Jiricny J. Postreplicative mismatch repair. Cold Spring Harb Perspect Biol. 2013;5(4):a012633.
9. Jiricny J. The multifaceted mismatch-repair system. Nat Rev Mol Cell Biol. 2006;7(5):335-346.
10. Hirschhorn JN, Daly MJ. Genome-wide association studies for common diseases and complex traits. Nat Rev Genet. 2005;6(2):95-108.
11. McCarthy MI, Hirschhorn JN. Genome-wide association studies: potential next steps on a genetic journey. Hum Mol Genet. 2008;17(R2):R156-R165.
12. Manolio TA, Collins FS, Cox NJ, et al. Finding the missing heritability of complex diseases. Nature. 2009;461(7265):747-753.
13. Gieger C, Radhakrishnan A, Cvejic A, et al. New gene functions in megakaryopoiesis and platelet formation. Nature. 2011;480(7376):201-208.
14. Van Der Harst P, Zhang W, Mateo Leach I, et al. Seventy-five genetic loci influencing the human red blood cell. Nature. 2012;492(7429):369-375.
15. Alkan C, Coe BP, Eichler EE. Genome structural variation discovery and genotyping. Nat Rev Genet. 2011;12(5):363-376.
16. Weischenfeldt J, Symmons O, Spitz F, Korbel JO. Phenotypic impact of genomic structural variation: insights from and for human disease. Nat Rev Genet. 2013;14(2):125-138.
17. Stephens M, Sloan JS, Robertson PD, Scheet P, Nickerson DA. Automating sequence-based detection and genotyping of SNPs from diploid samples. Nat Genet. 2006;38(3):375-381.
18. Shendure J, Porreca GJ, Reppas NB, et al. Accurate multiplex polony sequencing of an evolved bacterial genome. Science. 2005;309(5741):1728-1732.
19. Margulies M, Egholm M, Altman WE, et al. Genome sequencing in microfabricated highdensity picolitre reactors [published correction appears in Nature. 2006;441(7089):120]. Nature. 2005;437(7057):376-380.
20. Bentley DR, Balasubramanian S, Swerdlow HP, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008;456(7218):53-59.
21. Wetterstrand KA. DNA sequencing costs: data from the NHGRI Genome Sequencing Program (GSP). www.genome.gov/sequencingcosts. Accessed June 24, 2013.
22. Ng SB, Turner EH, Robertson PD, et al. Targeted capture and massively parallel sequencing of 12 human exomes. Nature. 2009;461(7261):272-276.
23. Choi M, Scholl UI, Ji W, et al. Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc Natl Acad Sci U S A. 2009;106(45):19096-19101.
24. Worthey EA, Mayer AN, Syverson GD, 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(3):255-262.
25. Ley TJ, Mardis ER, Ding L, et al. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature. 2008;456(7218):66-72.
26. Pritchard CC, Smith C, Salipante SJ, et al. ColoSeq provides comprehensive lynch and polyposis syndrome mutational analysis using massively parallel sequencing. J Mol Diagn. 2012;14(4):357-366.
27. Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol. 2008;26(10):1135-1145.
28. Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet. 2010;11(1):31-46.
29. Adey A, Morrison HG, Asan, et al. Rapid, lowinput, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Biol. 2010;11(12):R119.
30. Aird D, Ross MG, Chen WS, et al. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol. 2011;12(2):R18.
31. Cibulskis K, Lawrence MS, Carter SL, et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol. 2013;31(3):213-219.
32. Drmanac R, Sparks AB, Callow MJ, et al. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science. 2010;327(5961):78-81.
33. McKernan KJ, Peckham HE, Costa GL, 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(9):1527-1541.
34. Rothberg JM, Hinz W, Rearick TM, et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature. 2011;475(7356):348-352.
35. Eid J, Fehr A, Gray J, et al. Real-time DNA sequencing from single polymerase molecules. Science. 2009;323(5910):133-138.
36. Flusberg BA, Webster DR, Lee JH, et al. Direct detection of DNA methylation during singlemolecule, real-time sequencing. Nat Methods. 2010;7(6):461-465.
37. Branton D, Deamer DW, Marziali A, et al. The potential and challenges of nanopore sequencing. Nat Biotechnol. 2008;26(10):1146-1153.
38. Manrao EA, Derrington IM, Laszlo AH, et al. Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase. Nat Biotechnol. 2012;30(4):349-353.
39. Cherf GM, Lieberman KR, Rashid H, Lam CE, Karplus K, Akeson M. Automated forward and reverse ratcheting of DNA in a nanopore at 5-A° precision. Nat Biotechnol. 2012;30(4):344-348.
40. Alkan C, Sajjadian S, Eichler EE. Limitations of next-generation genome sequence assembly. Nat Methods. 2011;8(1):61-65.
41. Ye K, Schulz MH, Long Q, Apweiler R, Ning Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics. 2009;25(21):2865-2871.
42. Hiatt JB, Patwardhan RP, Turner EH, Lee C, Shendure J. Parallel, tag-directed assembly of locally derived short sequence reads. Nat Methods. 2010;7(2):119-122.
43. Li Y, Hu Y, Bolund L, Wang J. State of the art de novo assembly of human genomes from massively parallel sequencing data. Hum Genomics. 2010;4(4):271-277.
44. Li H. Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly. Bioinformatics. 2012;28(14):1838-1844.
45. Kitzman JO, Mackenzie AP, Adey A, et al. Haplotype-resolved genome sequencing of a Gujarati Indian individual. Nat Biotechnol. 2011;29(1):59-63.
46. Peters BA, Kermani BG, Sparks AB, et al. Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells. Nature. 2012;487(7406):190-195.
47. De Pristo MA, Banks E, Poplin R, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011;43(5):491-498.
48. Karakoc E, Alkan C, O'Roak BJ, et al. Detection of structural variants and indels within exome data. Nat Methods. 2012;9(2):176-178.
49. Krumm N, Sudmant PH, Ko A, et al; NHLBI Exome Sequencing Project. Copy number variation detection and genotyping from exome sequence data. Genome Res. 2012;22(8):1525-1532.
50. Li W, Olivier M. Current analysis platforms and methods for detecting copy number variation. Physiol Genomics. 2013;45(1):1-16.
51. Schmitt MW, Kennedy SR, Salk JJ, Fox EJ, Hiatt JB, Loeb LA. Detection of ultra-rare mutations by next-generation sequencing. Proc Natl Acad Sci U S A. 2012;109(36):14508-14513.
52. Tennessen JA, Bigham AW, O'Connor TD, et al; Broad GO; Seattle GO; NHLBI Exome Sequencing Project. Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science. 2012;337(6090):64-69.
53. Nelson MR, Wegmann D, Ehm MG, et al. An abundance of rare functional variants in 202 drug target genes sequenced in 14, 002 people. Science. 2012;337(6090):100-104.
54. Fu W, O'Connor TD, Jun. G, et al; NHLBI Exome Sequencing Project. Analysis of 6, 515 exomes reveals the recent origin of most human proteincoding variants. Nature. 2013;493(7431):216-220.
55. [published Correction Appears in Nature. 2013;495(7440):270].
56. Turner EH, Ng SB, Nickerson DA, Shendure J. Methods for genomic partitioning. Annu Rev Genomics Hum Genet. 2009;10:263-284.
57. Turner EH, Lee C, Ng SB, Nickerson DA, Shendure J. Massively parallel exon capture and library-free resequencing across 16 genomes. Nat Methods. 2009;6(5):315-316.
58. O'Roak BJ, Vives L, Fu W, et al. Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders. Science. 2012;338(6114):1619-1622.
59. Pickrell JK, Marioni JC, Pai AA, et al. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature. 2010;464(7289):768-772.
60. Paul DS, Albers CA, Rendon A, et al; HaemGen Consortium. Maps of open chromatin highlight cell type-restricted patterns of regulatory sequence variation at hematological trait loci. Genome Res. 2013;23(7):1130-1141.
61. Li G, Ruan X, Auerbach RK, et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell. 2012;148(1-2):84-98.
62. Wang C, Krishnakumar S, Wilhelmy J, et al. Highthroughput, high-fidelity HLA genotyping with deep sequencing. Proc Natl Acad Sci U S A. 2012;109(22):8676-8681.
63. Robins HS, Campregher PV, Srivastava SK, et al. Comprehensive assessment of T-cell receptor beta-chain diversity in alphabeta T cells. Blood. 2009;114(19):4099-4107.
64. Freeman JD, Warren RL, Webb JR, Nelson BH, Holt RA. Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing. Genome Res. 2009;19(10):1817-1824.
65. Fowler DM, Araya CL, Fleishman SJ, et al. Highresolution mapping of protein sequence-function relationships. Nat Methods. 2010;7(9):741-746.
66. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008;5(7):621-628.
67. Bamshad MJ, Ng SB, Bigham AW, et al. Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet. 2011;12(11):745-755.
68. Auer PL, Johnsen JM, Johnson AD, et al. Imputation of exome sequence variants into population-based samples and blood-cell-trait-associated loci in African Americans: NHLBI GO Exome Sequencing Project. Am J Hum Genet. 2012;91(5):794-808.
69. Johnsen JM, Auer PL, Morrison AC, et al; NHLBI Exome Sequencing Project. Common and rare von Willebrand factor (VWF) coding variants, VWF levels, and factor VIII levels in African Americans: the NHLBI Exome Sequencing Project. Blood. 2013;122(4):590-597.
70. Varley KE, Gertz J, Bowling KM, et al. Dynamic DNA methylation across diverse human cell lines and tissues. Genome Res. 2013;23(3):555-567.
71. Duan Z, Andronescu M, Schutz K, et al. A three-dimensional model of the yeast genome. Nature. 2010;465(7296):363-367.
72. Lieberman-Aiden E, Van Berkum NL, Williams L, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009;326(5950):289-293.
73. Mercer TR, Edwards SL, Clark MB, et al. DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements. Nat Genet. 2013;45(8):852-859.
74. Li XY, Biggin MD. Genome-wide in vivo crosslinking of sequence-specific transcription factors. Methods Mol Biol. 2012;809:3-26.
75. Shendure J, Lieberman Aiden E. The expanding scope of DNA sequencing. Nat Biotechnol. 2012;30(11):1084-1094.
76. Trapnell C, Roberts A, Goff L, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012;7(3):562-578.
77. Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol. 2013;31(1):46-53.
78. Melnikov A, Murugan A, Zhang X, et al. Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay. Nat Biotechnol. 2012;30(3):271-277.
79. Patwardhan RP, Hiatt JB, Witten DM, et al. Massively parallel functional dissection of mammalian enhancers in vivo. Nat Biotechnol. 2012;30(3):265-270.
80. ENCODE Project Consortium; Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489(7414):57-74.
81. Manolio TA, Chisholm RL, Ozenberger B, et al. Implementing genomic medicine in the clinic: the future is here. Genet Med. 2013;15(4):258-267.
82. Biesecker LG. Opportunities and challenges for the integration of massively parallel genomic sequencing into clinical practice: lessons from the ClinSeq project. Genet Med. 2012;14(4):393-398.
83. Bamshad MJ, Shendure JA, Valle D, et al; Centers for Mendelian Genomics. The Centers for Mendelian Genomics: a new large-scale initiative to identify the genes underlying rare Mendelian conditions. Am J Med Genet A. 2012;158 A (7): 1523-1525.
84. Bell CJ, Dinwiddie DL, Miller NA, et al. Carrier testing for severe childhood recessive diseases by next-generation sequencing. Sci Transl Med. 2011;3(65):65ra4.
85. Stein LD. The case for cloud computing in genome informatics. Genome Biol. 2010;11(5):207.
86. Jamal SM, Yu JH, Chong JX, et al. Practices and policies of clinical exome sequencing providers: analysis and implications. Am J Med Genet A. 2013;161 A (5): 935-950.
87. Adzhubei IA, Schmidt S, Peshkin L, et al. A method and server for predicting damaging missense mutations. Nat Methods. 2010;7(4):248-249.