Overview of high throughput sequencing technologies to elucidate molecular pathways in cardiovascular diseases

Circulation Research

Volumn 112, Issue 12, 2013, Pages 1613-1623

  Churko, Jared M ^a,b   Mantalas, Gary L ^a,b   Snyder, Michael P ^a   Wu, Joseph C ^a,b  

^a STANFORD UNIVERSITY   (United States)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

epigenetics; genetics; genomics; heart diseases; RNA; sequence analysis; transcriptome

Indexed keywords

GENOMIC DNA; MESSENGER RNA; RIBOSOME RNA; TRANSCRIPTOME;

CARDIOVASCULAR DISEASE; CHROMATIN IMMUNOPRECIPITATION; DNA METHYLATION; DNA SEQUENCE; EXOME; GENE MUTATION; HIGH THROUGHPUT SEQUENCING; HUMAN; NANOPORE; NONHUMAN; PRIORITY JOURNAL; REVIEW; RIBOSOME; RNA SEQUENCE; TRANSCRIPTOMICS;

EPIGENETICS; GENETICS; GENOMICS; HEART DISEASES; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME;

ANIMALS; CARDIOVASCULAR DISEASES; CHROMATIN IMMUNOPRECIPITATION; DIFFUSION OF INNOVATION; DNA METHYLATION; EPIGENESIS, GENETIC; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; GENETIC PREDISPOSITION TO DISEASE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; PHENOTYPE; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, RNA;

EID: 84880029194     PISSN: 00097330     EISSN: 15244571     Source Type: Journal    
DOI: 10.1161/CIRCRESAHA.113.300939     Document Type: Review

References (96)

1. Crick F. Central dogma of molecular biology. Nature. 1970;227:561-563
2. Temin HM. Reverse transcription in the eukaryotic genome: retroviruses, pararetroviruses, retrotransposons, and retrotranscripts. Mol Biol Evol. 1985;2:455-468 (Pubitemid 16234729)
3. Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA. A map of human genome variation from population- scale sequencing. Nature. 2010;467:1061-1073
4. Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. An integrated map of genetic variation from 1,092 human genomes. Nature 2012;491:56-65
5. Dunham I, Kundaje A, Aldred SF, et al. An integrated encyclopedia of DNA elements in the human genome. Nature 2012;489:57-74
6. Altshuler DM, Gibbs RA, Peltonen L, et al. Integrating common and rare genetic variation in diverse human populations. Nature 2010;467:52-58
7. Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010;11:31-46
8. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA. 1977;74:5463-5467
9. Kolata GB. The 1980 Nobel Prize in Chemistry. Science. 1980;210:887-889
10. Metzker ML. Emerging technologies in DNA sequencing. Genome Res. 2005;15:1767-1776 (Pubitemid 41780407)
11. Wilbanks EG, Facciotti MT. Evaluation of algorithm performance in ChIP-seq peak detection. PLoS One. 2010;5:e11471.
12. Karger BL, Guttman A. DNA sequencing by CE. Electrophoresis. 2009;30(suppl 1):S196-S202
13. Kircher M, Kelso J. High-throughput DNA sequencing-concepts and limitations. Bioessays. 2010;32:524-536
14. Stein LD. Human genome: end of the beginning. Nature. 2004;431:915-916
15. Wheeler DA, Srinivasan M, Egholm M, et al. The complete genome of an individual by massively parallel DNA sequencing. Nature. 2008;452:872-876 (Pubitemid 351550870)
16. Consortium IHGS. Finishing the euchromatic sequence of the human genome. Nature. 2004;431:931-945
17. Lander ES, Linton LM, Birren B, et al. Initial sequencing and analysis of the human genome. Nature. 2001;409:860-921 (Pubitemid 32165345)
18. Venter JC, Adams MD, Myers EW, et al. The sequence of the human genome. Science. 2001;291:1304-1351 (Pubitemid 32173090)
19. Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, Bertoni A, Swerdlow HP, Gu Y. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics. 2012;13:341.
20. Minoche AE, Dohm JC, Himmelbauer H. Evaluation of genomic highthroughput sequencing data generated on Illumina HiSeq and genome analyzer systems. Genome Biol. 2011;12:R112.
21. Schadt EE, Turner S, Kasarskis A. A window into third-generation sequencing. Hum Mol Genet. 2010;19:R227-R240
22. Eid J, Fehr A, Gray J, et al. Real-time DNA sequencing from single polymerase molecules. Science. 2009;323:133-138
23. Ziegler A, Koch A, Krockenberger K, Grosshennig A. Personalized medicine using DNA biomarkers: a review. Hum Genet. 2012;131:1627-1638
24. Moore LD, Le T, Fan G. DNA methylation and its basic function. Neuropsychopharmacology. 2013;38:23-38
25. Gabory A, Attig L, Junien C. Developmental programming and epigenetics. Am J Clin Nutr. 2011;94:1943S-1952S
26. Chou J, Ohsumi TK, Geha RS. Use of whole exome and genome sequencing in the identification of genetic causes of primary immunodeficiencies. Curr Opin Allergy Clin Immunol. 2012;12:623-628
27. Snyder M, Du J, Gerstein M. Personal genome sequencing: current approaches and challenges. Genes Dev. 2010;24:423-431
28. Alex Buerkle C, Gompert Z. Population genomics based on low coverage sequencing: How low should we go? Mol Ecol. 2012
29. Mir KU. Sequencing genomes: from individuals to populations. Brief Funct Genomic Proteomic. 2009;8:367-378
30. Koboldt DC, Ding L, Mardis ER, Wilson RK. Challenges of sequencing human genomes. Brief Bioinform. 2010;11:484-498
31. Ajay SS, Parker SC, Abaan HO, Fajardo KV, Margulies EH. Accurate and comprehensive sequencing of personal genomes. Genome Res. 2011;21:1498-1505
32. Lam HY, Clark MJ, Chen R, Natsoulis G, O'Huallachain M, Dewey FE, Habegger L, Ashley EA, Gerstein MB, Butte AJ, Ji HP, Snyder M. Performance comparison of whole-genome sequencing platforms. Nat Biotechnol. 2012;30:78-82
33. Gnirke A, Melnikov A, Maguire J, Rogov P, LeProust EM, Brockman W, Fennell T, Giannoukos G, Fisher S, Russ C, Gabriel S, Jaffe DB, Lander ES, Nusbaum C. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol. 2009;27:182-189
34. Lee H, O'Connor BD, Merriman B, Funari VA, Homer N, Chen Z, Cohn DH, Nelson SF. Improving the efficiency of genomic loci capture using oligonucleotide arrays for high throughput resequencing. BMC Genomics. 2009;10:646.
35. Krishnakumar S, Zheng J, Wilhelmy J, Faham M, Mindrinos M, Davis R. A comprehensive assay for targeted multiplex amplification of human DNA sequences. Proc Natl Acad Sci U S A. 2008;105:9296-9301
36. Li H, Durbin R. Fast and accurate short read alignment with Burrows- Wheeler transform. Bioinformatics. 2009;25:1754-1760
37. Liu CM, Wong T, Wu E, Luo R, Yiu SM, Li Y, Wang B, Yu C, Chu X, Zhao K, Li R, Lam TW. SOAP3: ultra-fast GPU-based parallel alignment tool for short reads. Bioinformatics. 2012;28:878-879
38. Homer N, Merriman B, Nelson SF. BFAST: an alignment tool for large scale genome resequencing. PLoS One. 2009;4:e7767.
39. DePristo MA, Banks E, Poplin R, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011;43:491-498
40. Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 2008;18:1851-1858
41. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078-2079
42. Lombardi R, Marian AJ. Molecular genetics and pathogenesis of arrhythmogenic right ventricular cardiomyopathy: a disease of cardiac stem cells. Pediatr Cardiol. 2011;32:360-365
43. Murray B. Arrhythmogenic right ventricular dysplasia/cardiomyopathy (ARVD/C): a review of molecular and clinical literature. J Genet Couns. 2012;21:494-504
44. Ohe T. Idiopathic ventricular fibrillation of the Brugada type: an atypical form of arrhythmogenic right ventricular cardiomyopathy? Intern Med. 1996;35:595.
45. Al-Aama JY, Bondagji NS, El-Harouni AA. Congenital heart defects in Down syndrome patients from western Saudi Arabia. Saudi Med J. 2012;33:1211-1215
46. Kobayashi D, Sallaam S, Humes RA. Tetralogy of fallot with complete digeorge syndrome: Report of a case and a review of the literature. Congenit Heart Dis. 2012. doi: 10.1111/j.1747-0803.2012.00694.x.
47. Strehle EM, Gruszfeld D, Schenk D, Mehta SG, Simonic I, Huang T. The spectrum of 4q- syndrome illustrated by a case series. Gene. 2012;506:387-391
48. Wat MJ, Shchelochkov OA, Holder AM, Breman AM, Dagli A, Bacino C, Scaglia F, Zori RT, Cheung SW, Scott DA, Kang SH. Chromosome 8p23.1deletions as a cause of complex congenital heart defects and diaphragmatic hernia. Am J Med. Genet A. 2009;149A:1661-1677
49. Redon R, Ishikawa S, Fitch KR, et al. Global variation in copy number in the human genome. Nature. 2006;444:444-454 (Pubitemid 44809057)
50. Feuk L, Carson AR, Scherer SW. Structural variation in the human genome. Nat Rev Genet. 2006;7:85-97 (Pubitemid 43128895)
51. Matkovich SJ, Van Booven DJ, Hindes A, Kang MY, Druley TE, Vallania FL, Mitra RD, Reilly MP, Cappola TP, Dorn GW II. Cardiac signaling genes exhibit unexpected sequence diversity in sporadic cardiomyopathy, revealing HSPB7 polymorphisms associated with disease. J Clin Invest. 2010;120:280-289
52. Cappola TP, Matkovich SJ, Wang W, van Booven D, Li M, Wang X, Qu L, Sweitzer NK, Fang JC, Reilly MP, Hakonarson H, Nerbonne JM, Dorn GW II. Loss-of-function DNA sequence variant in the CLCNKA chloride channel implicates the cardio-renal axis in interindividual heart failure risk variation. Proc Natl Acad Sci USA. 2011;108:2456-2461
53. Cooper GM, Johnson JA, Langaee TY, Feng H, Stanaway IB, Schwarz UI, Ritchie MD, Stein CM, Roden DM, Smith JD, Veenstra DL, Rettie AE, Rieder MJ. A genome-wide scan for common genetic variants with a large influence on warfarin maintenance dose. Blood. 2008;112:1022-1027
54. Poe BL, Haverstick DM, Landers JP. Warfarin genotyping in a single PCR reaction for microchip electrophoresis. Clin Chem. 2012;58:725-731
55. Jamieson D, Cresti N, Bray J, Sludden J, Griffin MJ, Hawsawi NM, Famie E, Mould EV, Verrill MW, May FE, Boddy AV. Two minor NQO1 and NQO2 alleles predict poor response of breast cancer patients to adjuvant doxorubicin and cyclophosphamide therapy. Pharmacogenet Genomics. 2011;21:808-819
56. Bains OS, Karkling MJ, Grigliatti TA, Reid RE, Riggs KW. Two nonsynonymous single nucleotide polymorphisms of human carbonyl reductase 1 demonstrate reduced in vitro metabolism of daunorubicin and doxorubicin. Drug Metab Dispos. 2009;37:1107-1114
57. Jamieson D, Boddy AV. Pharmacogenetics of genes across the doxorubicin pathway. Expert Opin Drug Metab Toxicol. 2011;7:1201-1210
58. Wells QS, Delaney JT, Roden DM. Genetic determinants of response to cardiovascular drugs. Curr Opin Cardiol. 2012;27:253-261
59. Lamond AI, Earnshaw WC. Structure and function in the nucleus. Science. 1998;280:547-553 (Pubitemid 28227750)
60. Thurman RE, Day N, Noble WS, Stamatoyannopoulos JA. Identification of higher-order functional domains in the human ENCODE regions. Genome Res. 2007;17:917-927 (Pubitemid 46919726)
61. Pauler FM, Sloane MA, Huang R, Regha K, Koerner MV, Tamir I, Sommer A, Aszodi A, Jenuwein T, Barlow DP. H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome. Genome Res. 2009;19:221-233
62. Mattout A, Biran A, Meshorer E. Global epigenetic changes during somatic cell reprogramming to iPS cells. J Mol Cell Biol. 2011;3:341-350
63. Furey TS. ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Nat Rev Genet. 2012;13:840-852
64. Blow MJ, McCulley DJ, Li Z, et al. ChIP-Seq identification of weakly conserved heart enhancers. Nat Genet. 2010;42:806-810
65. Elliott DA, Kirk EP, Yeoh T, Chandar S, McKenzie F, Taylor P, Grossfeld P, Fatkin D, Jones O, Hayes P, Feneley M, Harvey RP. Cardiac homeobox gene NKX2-5 mutations and congenital heart disease: associations with atrial septal defect and hypoplastic left heart syndrome. J Am Coll Cardiol. 2003;41:2072-2076 (Pubitemid 36677134)
66. Tanizawa H, Noma K. Unravelling global genome organization by 3C-seq. Semin Cell Dev Biol. 2012;23:213-221
67. Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science. 2002;295:1306-1311 (Pubitemid 34157624)
68. Korostowski L, Raval A, Breuer G, Engel N. Enhancer-driven chromatin interactions during development promote escape from silencing by a long non-coding RNA. Epigenetics Chromatin. 2011;4:21.
69. Friso S, Lotto V, Choi SW, Girelli D, Pinotti M, Guarini P, Udali S, Pattini P, Pizzolo F, Martinelli N, Corrocher R, Bernardi F, Olivieri O. Promoter methylation in coagulation F7 gene influences plasma FVII concentrations and relates to coronary artery disease. J Med Genet. 2012;49:192-199
70. Krueger F, Kreck B, Franke A, Andrews SR. DNA methylome analysis using short bisulfite sequencing data. Nat Methods. 2012;9:145-151
71. Movassagh M, Choy MK, Knowles DA, Cordeddu L, Haider S, Down T, Siggens L, Vujic A, Simeoni I, Penkett C, Goddard M, Lio P, Bennett MR, Foo RS. Distinct epigenomic features in end-stage failing human hearts. Circulation. 2011;124:2411-2422
72. ?abaj PP, Leparc GG, Linggi BE, Markillie LM, Wiley HS, Kreil DP. Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling. Bioinformatics. 2011;27:i383-i391
73. Matkovich SJ, Zhang Y, Van Booven DJ, Dorn GW II. Deep mRNA sequencing for in vivo functional analysis of cardiac transcriptional regulators: application to Galphaq. Circ Res. 2010;106:1459-1467
74. Hoeijmakers WA, Bártfai R, Stunnenberg HG. Transcriptome analysis using RNA-Seq. Methods Mol Biol. 2013;923:221-239
75. Sánchez-Pla A, Reverter F, Ruiz de Villa MC, Comabella M. Transcriptomics: mRNA and alternative splicing. J Neuroimmunol. 2012;248:23-31
76. Raz T, Causey M, Jones DR, Kieu A, Letovsky S, Lipson D, Thayer E, Thompson JF, Milos PM. RNA sequencing and quantitation using the Helicos Genetic Analysis System. Methods Mol Biol. 2011;733:37-49
77. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10:R25.
78. Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25:1105-1111
79. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28:511-515
80. Katz Y, Wang ET, Airoldi EM, Burge CB. Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat Methods. 2010;7:1009-1015
81. Anders S, Reyes A, Huber W. Detecting differential usage of exons from RNA-seq data. Genome Res. 2012;22:2008-2017
82. Lee JH, Gao C, Peng G, Greer C, Ren S, Wang Y, Xiao X. Analysis of transcriptome complexity through RNA sequencing in normal and failing murine hearts. Circ Res. 2011;109:1332-1341
83. Song HK, Hong SE, Kim T, Kim do H. Deep RNA sequencing reveals novel cardiac transcriptomic signatures for physiological and pathological hypertrophy. PLoS One. 2012;7:e35552.
84. Hu Y, Matkovich SJ, Hecker PA, Zhang Y, Edwards JR, Dorn GW II. Epitranscriptional orchestration of genetic reprogramming is an emergent property of stress-regulated cardiac microRNAs. Proc Natl Acad Sci USA. 2012;109:19864-19869
85. Shen T, Aneas I, Sakabe N, et al. Tbx20 regulates a genetic program essential to adult mouse cardiomyocyte function. J Clin Invest. 2011;121:4640-4654
86. Sakabe NJ, Aneas I, Shen T, Shokri L, Park SY, Bulyk ML, Evans SM, Nobrega MA. Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function. Hum Mol Genet. 2012;21:2194-2204
87. Wamstad JA, Alexander JM, Truty RM, et al. Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. Cell. 2012;151:206-220
88. Ingolia NT. Genome-wide translational profiling by ribosome footprinting. Methods Enzymol. 2010;470:119-142
89. Guo H, Ingolia NT, Weissman JS, Bartel DP. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature. 2010;466:835-840
90. Brar GA, Yassour M, Friedman N, Regev A, Ingolia NT, Weissman JS. High-resolution view of the yeast meiotic program revealed by ribosome profiling. Science. 2012;335:552-557
91. Schneider-Poetsch T, Ju J, Eyler DE, Dang Y, Bhat S, Merrick WC, Green R, Shen B, Liu JO. Inhibition of eukaryotic translation elongation by cycloheximide and lactimidomycin. Nat Chem Biol. 2010;6:209-217
92. Kalisky T, Blainey P, Quake SR. Genomic analysis at the single-cell level. Annu Rev Genet. 2011;45:431-445
93. Thompson JF, Oliver JS. Mapping and sequencing DNA using nanopores and nanodetectors. Electrophoresis. 2012;33:3429-3436
94. Branton D, Deamer DW, Marziali A, et al. The potential and challenges of nanopore sequencing. Nat Biotechnol. 2008;26:1146-1153
95. Boersma AJ, Brain KL, Bayley H. Real-time stochastic detection of multiple neurotransmitters with a protein nanopore. ACS Nano. 2012;6:5304-5308
96. Ayub M, Bayley H. Individual RNA base recognition in immobilized oligonucleotides using a protein nanopore. Nano Lett. 2012;12:5637-5643.