Next generation sequencing in cardiomyopathy: Towards personalized genomics and medicine

Molecular Biology Reports

Volumn 41, Issue 8, 2014, Pages 4881-4888

  Biswas, Amitabh ^a   Rao, V R ^a   Seth, Sandeep ^b   Maulik, S K ^b  

^a UNIVERSITY OF DELHI   (India)

^b ALL INDIA INSTITUTE OF MEDICAL SCIENCES   (India)

Author keywords

Cardiomyopathies; Next generation sequencing; Pathogenicity; Phenotypic heterogeneity

Indexed keywords

ARTICLE; CARDIOMYOPATHY; COST EFFECTIVENESS ANALYSIS; GENE IDENTIFICATION; GENE MUTATION; GENE SEQUENCE; GENE TARGETING; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOMICS; HUMAN; INFORMATION PROCESSING DEVICE; NEXT GENERATION SEQUENCING; PERSONALIZED MEDICINE; PHENOTYPE; SEQUENCE ANALYSIS; GENETICS; HIGH THROUGHPUT SEQUENCING; PROCEDURES; TRENDS;

CARDIOMYOPATHIES; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INDIVIDUALIZED MEDICINE; PHENOTYPE;

EID: 84905046604     PISSN: 03014851     EISSN: 15734978     Source Type: Journal    
DOI: 10.1007/s11033-014-3418-9     Document Type: Article

References (67)

1. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci 74(12):5463-5467
2. Zhou X, Ren L, Meng Q, Li Y, Yu Y, Yu J (2010) The next-generation sequencing technology and application. Protein Cell 1:520-536
3. Metzker ML (2010) Applications of next-generation sequencing, sequencing technologies: the next generation. Nat Rev Genet 11:31-46
4. Morozova O, Marra MA (2008) Applications of next-generation sequencing technologies in functional genomics. Genomics 92:255-264
5. Mardis ER (2013) Next-generation sequencing platforms. Annu Rev Anal Chem 6:287-303
6. Miller FA, Hayeems RZ, Bytautas JP (2013) Testing personalized medicine: patient and physician expectations of next-generation genomic sequencing in late-stage cancer care. Eur J Hum Genet 22:391-395. doi:10.1038/ejhg.2013.158
7. Papasavva T, van Ijcken WF, Kockx CE et al (2013) Next generation sequencing of SNPs for non-invasive prenatal diagnosis: challenges and feasibility as illustrated by an application to β-thalassaemia. Eur J Hum Genet 21(12):1403-1410
8. Sobreira NL, Cirulli ET, Avramopoulos D et al (2010) Whole-genome sequencing of a single proband together with linkage analysis identifies a Mendelian disease gene. PLoS Genet. doi:10.1371/journal.pgen.100099
9. Chen Z, Wang JL, Tang BS et al (2011) Using next-generation sequencing as a genetic diagnostic tool in rare autosomal recessive neurologic Mendelian disorders. Neurobiol Aging 34(10):2442.e11-7. doi:10.1016/j.neurobiolaging.2013. 04.029
10. Yang Y, Muzny DM, Jeffrey GR et al (2013) Clinical whole-exome sequencing for the diagnosis of Mendelian disorders. N Engl J Med 369:1502-1511
11. Mutai H, Suzuki N, Shimizu A et al (2013) Diverse spectrum of rare deafness genes underlies early-childhood hearing loss in Japanese patients: a cross-sectional, multi-center next-generation sequencing study. Orphanet J Rare Dis 8:172
12. Sankaran VG, Ghazvinian R, Do R et al (2012) Exome sequencing identifies GATA1 mutations resulting in Diamond-Blackfan anemia. J Clin Invest 122:2439-2443
13. Boycott KM, Vanstone MR, Bulman DE, Mackenzie AE (2013) Rare-disease genetics in the era of next-generation sequencing: discovery to translation. Nat Rev Genet 14:681-691
14. Harris TD, Buzby PR, Babcock H et al (2008) Single-molecule DNA sequencing of a viral genome. Science 320(5872):106-109 (Pubitemid 351490765)
15. Chaisson MJ, Pevzner PA (2008) Short read fragment assembly of bacterial genomes. Genome Res 18(2):324-330 (Pubitemid 351240742)
16. Pickrell JK, Marioni JC, Pai AA et al (2010) Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464(7289):768-772
17. Hiller D, Jiang H, Xu W, Wong WH (2009) Identifiability of isoform deconvolution from junction arrays and RNA-Seq. Bio-informatics 25(23):3056-3059
18. Kharchenko PV, Tolstorukov MY, Park PJ (2008) Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol 26(12):1351-1359
19. Veeramah KR, Hammer MF (2014) The impact of whole-genome sequencing on the reconstruction of human population history. Nat Rev Genet 15:149-162
20. Gravel S, Zakharia F, Moreno-Estrada A et al (2013) Reconstructing native American migrations from whole-genome and whole-exome data. PLoS Genet 9(12):e1004023
21. Ingolia NT (2014) Ribosome profiling: new views of translation, from single codons to genome scale. Nat Rev Genet 15:205-213
22. Bragg L, Tyson GW (2014) Metagenomics using next-generation sequencing environmental microbiology. Methods Mol Biol 1096:183-201
23. Rogers GB, Bruce KD (2010) Next-generation sequencing in the analysis of human microbiota: essential considerations for clinical application. Mol Diagn Ther 14(6):343-350
24. Ross JS, Cronin M (2011) Whole cancer genome sequencing by next-generation methods. Am J Clin Pathol 136(4):527-539
25. Ullah S, John P, Bhatti A (2014) MicroRNAs with a role in gene regulation and in human diseases. Mol Biol Rep 41:225-232
26. Zywicki M, Bakowska-Zywicka K, Polacek N (2012) Revealing stable processing products fromribosome-associated small RNAs by deep-sequencing data analysis. Nucleic Acids Res 40:4013-4024
27. Friedländer MR, Chen W, Adamidi C et al (2008) Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol 26:407-415 (Pubitemid 351501815)
28. Biesecker LG, Spinner NB (2013) A genomic view of mosaicism and human disease. Nat Rev Genet 14:307-320. doi:10.1038/nrg3424
29. Sekirov I, Russell SL, Antunes LC, Finlay BB (2010) Gut microbiota in health and disease. Physiol Rev 90(3):859-904. doi:10.1152/physrev.00045.2009
30. Albert TJ, Molla MN, Muzny DM et al (2007) Direct selection of human genomic loci by microarray hybridization. Nat Methods 4:903-905 (Pubitemid 350042375)
31. Hodges E, Xuan Z, Balija V et al (2007) Genome-wide in situ exon capture for selective resequencing. Nat Genet 39(12):1522-1527 (Pubitemid 350191350)
32. Quail MA, Smith M, Coupland P et al (2012) A tale of three next generation sequencing platforms: comparison of ion torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genom 13:341
33. Mook ORF, Haagmans MA, Soucy JF et al (2013) Targeted sequence capture and GS-FLX Titanium sequencing of 23 hypertrophic and dilated cardiomyopathy genes: implementation into diagnostics. J Med Genet 50:614-626. doi:10.1136/jmedgenet-2012-101231
34. Ng SB, Turner EH, Robertson PD et al (2009) Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461(7261):272-276
35. Botstein D, Risch N (2003) Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nat Genet 33(Suppl):228-237 (Pubitemid 36278833)
36. Reinhardt JA, Baltrus DA, Nishimura MT, Jeck WR, Jones CD, Dangl JL (2009) De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. Genome Res 19(2):294-305
37. Nowrousian M, Stajich JE, Chu M et al (2010) De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis. PLoS Genet 6(4):e1000891
38. Shin SC, Ahn DH, Kim SJ, Lee H et al (2013) Advantages of single-molecule real-time sequencing in high-GC content genomes. PLoS One 8(7):e68824. doi:10.1371/journal.pone.0068824
39. Maron BJ, Doerer JJ, Haas TS, Tierney DM, Mueller FO (2009) Sudden deaths in young competitive athletes: analysis of 1866 deaths in the United States, 1980-2006. Circulation 119:1085-1092
40. Elliott PM, Poloniecki J, Dickie S, Sharma S et al (2000) Sudden death in hypertrophic cardiomyopathy: identification of high risk patients. J Am Coll Cardiol 36:2212-2218
41. Lopes LR, Zekavati A, Syrris P et al (2013) Genetic complexity in hypertrophic cardiomyopathy revealed by high-throughput sequencing. J Med Genet 50:228-239
42. Meder B, Haas J, Keller A et al (2011) Targeted next-generation sequencing for the molecular genetic diagnostics of cardiomyopathies. Circ Cardiovasc Genet 4:110-122
43. Maron BJ, Towbin JA, Thiene G et al (2006) Contemporary definitions and classification of the cardiomyopathies: an American Heart Association Scientific Statement from the Council on Clinical Cardiology, Heart Failure and Transplantation Committee; Quality of Care and Outcomes Research and Functional Genomics and Translational Biology Interdisciplinary Working Groups; and Council on Epidemiology and Prevention. Circulation 113:1807-1816 (Pubitemid 43958474)
44. Richardson P, McKenna W, Bristow M et al (1996) Report of the 1995 World Health Organization/International Society and Federation of Cardiology task force on the definition and classification of cardiomyopathies. Circulation 93(5):841-842 (Pubitemid 26074816)
45. Elliott P, Anderson B, Arbustini E et al (2008) Classification of cardiomyopathies: a position statement from the European working group on myocardial and pericardial diseases. Eur Heart J 29:270-276
46. ARVD/C Genetic Variants Database. Accessed 6 March 2014
47. Human Genetic Mutation Database [HGMD]. Accessed June 2013.
48. Teare D (1958) Asymmetrical hypertrophy of the heart in young adults. Br Heart J 20:1-8
49. Hollman A, Goodwin JF, Teare D, Renwick JW (1960) A family with obstructive cardiomyopathy (asymmetrical hypertrophy). Br Heart J 321:1372-1378
50. Greaves SC, Roche AHG, Neutze JM, Whitlock RML, Veale AMO (1987) Inheritance of hypertrophic cardiomyopathy: a cross sectional and Mmode echocardiographic study of 50 families. Br Heart J 58:259-266 (Pubitemid 17131907)
51. Geisterfer-Lowrance AA, Kass S, Tanigawa G et al (1990) A molecular basis for familial hypertrophic cardiomyopathy: a beta cardiac myosin heavy chain gene missense mutation. Cell 62:999-1006
52. Elliot P (2000) Diagnosis and management of dilated cardiomyopathy. Heart 84:106
53. Ku L, Feiger J, Taylor M, Mestroni L (2003) Familial dilated cardiomyopathy. Circulation 108:e118-e121
54. Hershberger RE, Morales A, Siegfried JD (2010) Clinical and genetic issues in dilated cardiomyopathy: a review for genetics professionals. Genet Med 12(11):655-667
55. Biswas A, Das S, Seth S et al (2012) Role of modifying genes on the severity of rare mutation of MYH7 gene in hypertrophic obstructive cardiomyopathy. J Clin Exp Cardiol 3:225. doi:10.4172/2155-9880.1000225
56. Raju H, Alberg C, Sagoo GS, Burton H, Behr ER (2011) Inherited cardiomyopathies. BMJ 343:d6966
57. Wells QS, Becker JR, Su YR et al (2013) Whole exome sequencing identifies a causal RBM20 mutation in a large pedigree with familial dilated cardiomyopathy. Circ Cardiovasc Genet 6(4):317-326. doi:10.1161/CIRCGENETICS. 113.000011
58. Campbell N, Sinagra G, Jones KL et al (2013) Whole exome sequencing identifies a troponin T mutation hot spot in familial dilated cardiomyopathy. PLoS One 8(10):e78104
59. Andreasen C, Neilsen JB, Refsgaard L et al (2013) New population-based exome data are questioning the pathogenicity of previously cardiomyopathy- associated genetic variants. Eur J Hum Genet 21:918-928
60. Majewski J, Schwartzentruber J, Lalonde E, Montpetit A, Jabado N (2011) What can exome sequencing do for you? J Med Genet 48:580-589
61. Hershberger RE, Lindenfeld J, Mestroni L, Seidman CE, Taylor MR, Towbin JA (2009) Genetic evaluation of cardiomyopathy: a Heart Failure Society of America practice guideline. J Card Fail 15(2):83-97
62. Yancy CW, Jesup M, Bozkurt B et al (2013) 2013 ACCF/AHA guideline for the management of heart failure a report of the American College of Cardiology Foundation/American Heart Association task force on practice guidelines. Circulation 128:e240-e327
63. Michels M, Hoedemaekers YM, Kofflard MJ et al (2007) Familial screening and genetic counseling in hypertrophic cardiomyopathy: the Rotterdam experience. Neth Heart J 15:184-190 (Pubitemid 47260412)
64. Taylor MRG, Carniel E, Mestroni L (2004) Familial hypertrophic cardiomyopathy: clinical features, molecular genetics and molecular genetic testing. Expert Rev Mol Diagn 4(1):99-113 (Pubitemid 38089646)
65. Ghezzi D, Baruffini E, Haack TB et al (2012) Mutations of the mitochondrial-tRNA modifier MTO1 cause hypertrophic cardiomyopathy and lactic acidosis. Am J Hum Genet 90:1079-1087
66. Arimura T, Ishikawa T, Nunoda S et al (2011) Dilated cardiomyopathy- associated BAG3 mutations impair Z-disc assembly and enhance sensitivity to apoptosis in cardiomyocytes. Hum Mutat 32(12):1481-1491
67. Theis JL, Sharpe KM, Matsumoto ME et al (2011) Homozygosity mapping and exome sequencing reveal GATAD1 mutation in autosomal recessive dilated cardiomyopathy. Circ Cardiovasc Genet 4(6):585-594