Targeted analysis of whole genome sequence data to diagnose genetic cardiomyopathy

Circulation: Cardiovascular Genetics

Volumn 7, Issue 6, 2014, Pages 751-759

  Golbus, Jessica R ^a   Puckelwartz, Megan J ^a   Dellefave Castillo, Lisa ^a   Fahrenbach, John P ^a   Nelakuditi, Viswateja ^a   Pesce, Lorenzo L ^a   Pytel, Peter ^a,b   McNally, Elizabeth M ^a  

^a ARGONNE NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF CHICAGO   (United States)

Author keywords

Cardiomyopathies; Genetics; Genomics; Humans

Indexed keywords

ADOLESCENT; ADULT; ARTICLE; CARDIOMYOPATHY; CHILD; DISEASE SEVERITY; GENE MUTATION; GENE SEQUENCE; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENOMICS; HUMAN; HUMAN CELL; PRIORITY JOURNAL; SCHOOL CHILD; SEQUENCE ANALYSIS; ALGORITHM; CARDIOMYOPATHIES; DNA SEQUENCE; ECONOMICS; GENETIC DATABASE; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN GENOME; MIDDLE AGED; PEDIGREE; SINGLE NUCLEOTIDE POLYMORPHISM; YOUNG ADULT;

LDB3 PROTEIN, HUMAN; LIM PROTEIN; MYH11 PROTEIN, HUMAN; MYOSIN HEAVY CHAIN; SCN5A PROTEIN, HUMAN; SIGNAL TRANSDUCING ADAPTOR PROTEIN; SODIUM CHANNEL NAV1.5;

ADAPTOR PROTEINS, SIGNAL TRANSDUCING; ADOLESCENT; ADULT; ALGORITHMS; CARDIOMYOPATHIES; CHILD; DATABASES, GENETIC; GENOME, HUMAN; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; LIM DOMAIN PROTEINS; MIDDLE AGED; MYOSIN HEAVY CHAINS; NAV1.5 VOLTAGE-GATED SODIUM CHANNEL; PEDIGREE; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; YOUNG ADULT;

EID: 84922955673     PISSN: 1942325X     EISSN: 19423268     Source Type: Journal    
DOI: 10.1161/CIRCGENETICS.113.000578     Document Type: Article

References (45)

1. Cirino AL, Ho CY. Genetic testing for inherited heart disease. Circulation. 2013;128:e4-e8
2. Lakdawala NK, Thune JJ, Colan SD, Cirino AL, Farrohi F, Rivero J, et al. Subtle abnormalities in contractile function are an early manifestation of sarcomere mutations in dilated cardiomyopathy. Circ Cardiovasc Genet. 2012;5:503-510
3. Maron BJ, Roberts WC, Arad M, Haas TS, Spirito P, Wright GB, et al. Clinical outcome and phenotypic expression in LAMP2 cardiomyopathy. JAMA. 2009;301:1253-1259
4. Mestroni L, Taylor MR. Lamin A/C gene and the heart: how genetics may impact clinical care. J Am Coll Cardiol. 2008;52:1261-1262
5. Zimmerman RS, Cox S, Lakdawala NK, Cirino A, Mancini-DiNardo D, Clark E, Leon A, et al. A novel custom resequencing array for dilated cardiomyopathy. Genet Med. 2010;12:268-278
6. Meder B, Haas J, Keller A, Heid C, Just S, Borries A, et al. Targeted nextgeneration sequencing for the molecular genetic diagnostics of cardiomyopathies. Circ Cardiovasc Genet. 2011;4:110-122
7. Clark MJ, Chen R, Lam HY, Karczewski KJ, Chen R, Euskirchen G, Butte AJ, et al. Performance comparison of exome DNA sequencing technologies. Nat Biotechnol. 2011;29:908-914
8. Asan, Xu Y, Jiang H, Tyler-Smith C, Xue Y, Jiang T, Wang J, et al. Comprehensive comparison of three commercial human whole-exome capture platforms. Genome Biol. 2011;12:R95
9. 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;12:745-755
10. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, et al. A method and server for predicting damaging missense mutations. Nat Methods. 2010;7:248-249
11. Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005;15:1034-1050
12. Ng PC, Henikoff S. Predicting deleterious amino acid substitutions. Genome Res. 2001;11:863-874
13. Cooper GM, Stone EA, Asimenos G, Green ED, Batzoglou S, Sidow A; NISC Comparative Sequencing Program. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res. 2005;15:901-913
14. Thomas PD, Kejariwal A, Campbell MJ, Mi H, Diemer K, Guo N, Ladunga I, et al. PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification. Nucleic Acids Res. 2003;31:334-341
15. Ashkenazy H, Erez E, Martz E, Pupko T, Ben-Tal N. ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res. 2010;38(Web Server issue):W529-W533
16. A map of human genome variation from population-scale sequencing. Nature. 2010;467:1061-1073
17. Yeo G, Burge CB. Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J Comput Biol. 2004;11:377-394
18. Demonbreun AR, Fahrenbach JP, Deveaux K, Earley JU, Pytel P, McNally EM. Impaired muscle growth and response to insulin-like growth factor 1 in dysferlin-mediated muscular dystrophy. Hum Mol Genet. 2011;20:779-789
19. Herman DS, Lam L, Taylor MR, Wang L, Teekakirikul P, Christodoulou D, et al. Truncations of titin causing dilated cardiomyopathy. N Engl J Med. 2012;366:619-628
20. Golbus JR, Puckelwartz MJ, Fahrenbach JP, Dellefave-Castillo LM, Wolfgeher D, McNally EM. Population-based variation in cardiomyopathy genes. Circ Cardiovasc Genet. 2012;5:391-399
21. Dalakas MC, Park KY, Semino-Mora C, Lee HS, Sivakumar K, Goldfarb LG. Desmin myopathy, a skeletal myopathy with cardiomyopathy caused by mutations in the desmin gene. N Engl J Med. 2000;342:770-780
22. Park KY, Dalakas MC, Goebel HH, Ferrans VJ, Semino-Mora C, Litvak S, et al. Desmin splice variants causing cardiac and skeletal myopathy. J Med Genet. 2000;37:851-857
23. Gahl WA, Huizing M. Hermansky-Pudlak syndrome. 1993
24. Arimura T, Hayashi YK, Murakami T, Oya Y, Funabe S, Arikawa-Hirasawa E, Hattori N, et al. Mutational analysis of fukutin gene in dilated cardiomyopathy and hypertrophic cardiomyopathy. Circ J. 2009;73:158-161
25. Ruan Y, Liu N, Priori SG. Sodium channel mutations and arrhythmias. Nat Rev Cardiol. 2009;6:337-348
26. Schott JJ, Alshinawi C, Kyndt F, Probst V, Hoorntje TM, Hulsbeek M, et al. Cardiac conduction defects associate with mutations in SCN5A. Nat Genet. 1999;23:20-21
27. Olson TM, Michels VV, Ballew JD, Reyna SP, Karst ML, Herron KJ, et al. Sodium channel mutations and susceptibility to heart failure and atrial fibrillation. JAMA. 2005;293:447-454
28. Nguyen TP, Wang DW, Rhodes TH, George AL Jr. Divergent biophysical defects caused by mutant sodium channels in dilated cardiomyopathy with arrhythmia. Circ Res. 2008;102:364-371
29. Babu GJ, Warshaw DM, Periasamy M. Smooth muscle myosin heavy chain isoforms and their role in muscle physiology. Microsc Res Tech. 2000;50:532-540
30. Tajsharghi H, Ohlsson M, Palm L, Oldfors A. Myopathies associated with -tropomyosin mutations. Neuromuscul Disord. 2012;22:923-933
31. Chourbagi O, Bruston F, Carinci M, Xue Z, Vicart P, Paulin D, et al. Desmin mutations in the terminal consensus motif prevent synemin-desmin heteropolymer filament assembly. Exp Cell Res. 2011;317:886-897
32. Clemen CS, Herrmann H, Strelkov SV, Schröder R. Desminopathies: pathology and mechanisms. Acta Neuropathol. 2013;125:47-75
33. Hershberger RE, Parks SB, Kushner JD, Li D, Ludwigsen S, Jakobs P, Nauman D, et al. Coding sequence mutations identified in MYH7, TNNT2, SCN5A, CSRP3, LBD3, and TCAP from 313 patients with familial or idiopathic dilated cardiomyopathy. Clin Transl Sci. 2008;1:21-26
34. Schafer E, Baron K, Widmer U, Deegan P, Neumann HP, Sunder-Plassmann G, et al. Thirty-four novel mutations of the GLA gene in 121 patients with Fabry disease. Hum Mutat. 2005;25:412
35. Sheppard MN. The heart in Fabry's disease. Cardiovasc Pathol. 2011;20:8-14
36. Hershberger RE, Pinto JR, Parks SB, Kushner JD, Li D, Ludwigsen S, Cowan J, et al. Clinical and functional characterization of TNNT2 mutations identified in patients with dilated cardiomyopathy. Circ Cardiovasc Genet. 2009;2:306-313
37. Richard P, Charron P, Carrier L, Ledeuil C, Cheav T, Pichereau C, Benaiche A, et al; EUROGENE Heart Failure Project. Hypertrophic cardiomyopathy: distribution of disease genes, spectrum of mutations, and implications for a molecular diagnosis strategy. Circulation. 2003;107:2227-2232
38. Hanson EL, Jakobs PM, Keegan H, Coates K, Bousman S, Dienel NH, Litt M, et al. Cardiac troponin T lysine 210 deletion in a family with dilated cardiomyopathy. J Card Fail. 2002;8:28-32
39. Fürst DO, Goldfarb LG, Kley RA, Vorgerd M, Olivé M, van der Ven PF. Filamin C-related myopathies: pathology and mechanisms. Acta Neuropathol. 2013;125:33-46
40. Thompson TG, Chan YM, Hack AA, Brosius M, Rajala M, Lidov HG, et al. Filamin 2 (FLN2): A muscle-specific sarcoglycan interacting protein. J Cell Biol. 2000;148:115-126
41. Fujita M, Mitsuhashi H, Isogai S, Nakata T, Kawakami A, Nonaka I, Noguchi S, et al. Filamin C plays an essential role in the maintenance of the structural integrity of cardiac and skeletal muscles, revealed by the medaka mutant zacro. Dev Biol. 2012;361:79-89
42. Maerkens A, Kley RA, Olive M, Theis V, van der Ven PF, Reimann J, et al. Differential proteomic analysis of abnormal intramyoplasmic aggregates in desminopathy. J Proteomics. 2013;90:14-27
43. Lidove O, West ML, Pintos-Morell G, Reisin R, Nicholls K, Figuera LE, Parini R, et al. Effects of enzyme replacement therapy in Fabry disease-a comprehensive review of the medical literature. Genet Med. 2010;12:668-679
44. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008;456:53-59
45. Ajay SS, Parker SC, Abaan HO, Fajardo KV, Margulies EH. Accurate and comprehensive sequencing of personal genomes. Genome Res. 2011;21:1498-1505.