Cardiac structural and sarcomere genes associated with cardiomyopathy exhibit marked intolerance of genetic variation

Circulation: Cardiovascular Genetics

Volumn 5, Issue 6, 2012, Pages 602-610

  Pan, Stephen ^a,b   Caleshu, Colleen A ^a   Dunn, Kyla E ^a   Ashley, Euan A ^a,c  

^a STANFORD UNIVERSITY MEDICAL CENTER   (United States)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Cardiomyopathy; Genetic heart disease; Genetic testing; Genetic variation; Genomics

Indexed keywords

CONNECTIN;

ALGORITHM; AMINO ACID SUBSTITUTION; ARTICLE; COHORT ANALYSIS; CONGESTIVE CARDIOMYOPATHY; EXOME; GENE FREQUENCY; GENETIC VARIABILITY; HUMAN; HYPERTROPHIC CARDIOMYOPATHY; MAJOR CLINICAL STUDY; MISSENSE MUTATION; NONSENSE MUTATION; NUCLEOTIDE SEQUENCE; PATHOGENICITY; PREDICTION; PREVALENCE; PRIORITY JOURNAL; SARCOMERE; SINGLE NUCLEOTIDE POLYMORPHISM;

CARDIOMYOPATHIES; CODON, NONSENSE; DATABASES, GENETIC; EXOME; GENE FREQUENCY; GENETIC ASSOCIATION STUDIES; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; HUMANS; MUTATION, MISSENSE; RNA, MESSENGER; ROC CURVE; SARCOMERES;

EID: 84873884826     PISSN: 1942325X     EISSN: 19423268     Source Type: Journal    
DOI: 10.1161/CIRCGENETICS.112.963421     Document Type: Article

References (43)

1. 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature. 2010;467:1061-1073.
2. MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, et al. A systematic survey of loss-of-function variants in human protein-coding genes. Science. 2012;335:823-828.
3. Li Y, Vinckenbosch N, Tian G, Huerta-Sanchez E, Jiang T, Jiang H, et al. Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nat Genet. 2010;42:969-972.
4. Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, et al. Paired-end mapping reveals extensive structural variation in the human genome. Science. 2007;318:420-426.
5. Gersh BJ, Maron BJ, Bonow RO, Dearani JA, Fifer MA, Link MS, et al. 2011 ACCF/AHA guideline for the diagnosis and treatment of hypertrophic cardiomyopathy: Executive summary: A report of the American College of Cardiology Foundation/American Heart Association Task Force on Practice Guidelines. Circulation. 2011;124:2761-2796.
6. Ackerman MJ, Priori SG, Willems S, Berul C, Brugada R, Calkins H, et al. HRS/EHRA expert consensus statement on the state of genetic testing for the channelopathies and cardiomyopathies this document was developed as a partnership between the Heart Rhythm Society (HRS) and the European Heart Rhythm Association (EHRA). Heart Rhythm. 2011;8:1308-1339.
7. Wheeler M, Pavlovic A, DeGoma E, Salisbury H, Brown C, Ashley EA. A new era in clinical genetic testing for hypertrophic cardiomyopathy. J Cardiovasc Transl Res. 2009;2:381-391.
8. Cirulli ET, Goldstein DB. Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nat Rev Genet. 2010;11:415-425.
9. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, et al. Finding the missing heritability of complex diseases. Nature. 2009;461:747-753.
10. Ashley EA, Butte AJ, Wheeler MT, Chen R, Klein TE, Dewey FE, et al. Clinical assessment incorporating a personal genome. Lancet. 2010;375:1525-1535.
11. Dewey FE, Chen R, Cordero SP, Ormond KE, Caleshu C, Karczewski KJ, et al. Phased whole-genome genetic risk in a family quartet using a major allele reference sequence. PLoS Genet. 2011;7:e1002280.
12. Pan S, Dewey FE, Perez MV, Knowles JW, Chen R, Butte AJ, et al. Personalized medicine and cardiovascular disease: From genome to bedside. Curr Cardiovasc Risk Rep. 2011;5:542-551.
13. Tennessen JA, Bigham AW, O'Connor TD, Fu W, Kenny EE, Gravel S, et al. Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science. 2012;337:64-69.
14. Norton N, Robertson PD, Rieder MJ, Züchner S, Rampersaud E, Martin E, et al. Evaluating pathogenicity of rare variants from dilated cardiomyopathy in the exome era. Circ Cardiovasc Genet. 2012;5:167-174.
15. Zhang J, Feuk L, Duggan GE, Khaja R, Scherer SW. Development of bioinformatics resources for display and analysis of copy number and other structural variants in the human genome. Cytogenet Genome Res. 2006;115:205-214.
16. Online Mendelian Inheritance in Man, OMIM®. Online Mendelian Inheritance in Man. Retrieved December 11, 2011, from http://omim.org
17. Pruitt KD, Tatusova T, Klimke W, Maglott DR. NCBI Reference Sequences: Current status, policy and new initiatives. Nucleic Acids Res. 2009;37(Database issue):D32-D36.
18. Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, et al. The UCSC Genome Browser database: Update 2011. Nucleic Acids Res. 2011;39(Database issue):D876-D882.
19. Wang K, Li M, Hakonarson H. ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38:e164.
20. NHLBI Program for Genomic Applications, Harvard Medical School. Genomics of Cardiovascular Development, Adaptation, and Remodeling. Retrieved January 20, 2012, from http://www.cardiogenomics.org
21. Cooper GM, Stone EA, Asimenos G, Green ED, Batzoglou S, Sidow A. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res. 2005;15:901-913.
22. 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.
23. 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.
24. Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc. 2009;4:1073-1081.
25. Hughes AL, Yeager M. Natural selection at major histocompatibility complex loci of vertebrates. Annu Rev Genet. 1998;32:415-435.
26. Menashe I, Man O, Lancet D, Gilad Y. Different noses for different people. Nat Genet. 2003;34:143-144.
27. Bashyam MD, Purushotham G, Chaudhary AK, Rao KM, Acharya V, Mohammad TA, et al. A low prevalence of MYH7/MYBPC3 mutations among familial hypertrophic cardiomyopathy patients in India. Mol Cell Biochem. 2012;360:373-382.
28. 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.
29. Politano L, Nigro V, Nigro G, Petretta VR, Passamano L, Papparella S, et al. Development of cardiomyopathy in female carriers of Duchenne and Becker muscular dystrophies. JAMA. 1996;275:1335-1338.
30. Sylvius N, Tesson F, Gayet C, Charron P, Bénaïche A, Peuchmaurd M, et al. A new locus for autosomal dominant dilated cardiomyopathy identified on chromosome 6q12-q16. Am J Hum Genet. 2001;68:241-246.
31. Van Driest SL, Jaeger MA, Ommen SR, Will ML, Gersh BJ, Tajik AJ, et al. Comprehensive analysis of the beta-myosin heavy chain gene in 389 unrelated patients with hypertrophic cardiomyopathy. J Am Coll Cardiol. 2004;44:602-610.
32. Jin JP, Chong SM. Localization of the two tropomyosin-binding sites of troponin T. Arch Biochem Biophys. 2010;500:144-150.
33. Palm T, Graboski S, Hitchcock-DeGregori SE, Greenfield NJ. Disease-causing mutations in cardiac troponin T: Identification of a critical tropomyosin-binding region. Biophys J. 2001;81:2827-2837.
34. Andersen PS, Havndrup O, Hougs L, Sørensen KM, Jensen M, Larsen LA, et al. Diagnostic yield, interpretation, and clinical utility of mutation screening of sarcomere encoding genes in Danish hypertrophic cardiomyopathy patients and relatives. Hum Mutat. 2009;30:363-370.
35. Richard P, Charron P, Carrier L, Ledeuil C, Cheav T, Pichereau C, et al. Hypertrophic cardiomyopathy: Distribution of disease genes, spectrum of mutations, and implications for a molecular diagnosis strategy. Circulation. 2003;107:2227-2232.
36. Goh KI, Cusick ME, Valle D, Childs B, Vidal M, Barabási AL. The human disease network. Proc Natl Acad Sci USA. 2007;104:8685-8690.
37. Erdmann J, Daehmlow S, Wischke S, Senyuva M, Werner U, Raible J, et al. Mutation spectrum in a large cohort of unrelated consecutive patients with hypertrophic cardiomyopathy. Clin Genet. 2003;64:339-349.
38. Maron BJ, Gardin JM, Flack JM, Gidding SS, Kurosaki TT, Bild DE. Prevalence of hypertrophic cardiomyopathy in a general population of young adults: Echocardiographic analysis of 4111 subjects in the CARDIA Study. Coronary Artery Risk Development in (Young) Adults. Circulation. 1995;92:785-789.
39. Zou Y, Song L, Wang Z, Ma A, Liu T, Gu H, et al. Prevalence of idiopathic hypertrophic cardiomyopathy in China: A population-based echocardiographic analysis of 8080 adults. Am J Med. 2004;116:14-18.
40. Maron BJ. Hypertrophic cardiomyopathy: A systematic review. JAMA. 2002;287:1308-1320.
41. Refsgaard L, Holst AG, Sadjadieh G, Haunsø S, Nielsen JB, Olesen MS. High prevalence of genetic variants previously associated with LQT syndrome in new exome data. Eur J Hum Genet. 2012;20:905-908.
42. Holm H, Gudbjartsson DF, Sulem P, Masson G, Helgadottir HT, Zanon C, et al. A rare variant in MYH6 is associated with high risk of sick sinus syndrome. Nat Genet. 2011;43:316-320.
43. Lupski JR, Belmont JW, Boerwinkle E, Gibbs RA. Clan genomics and the complex architecture of human disease. Cell. 2011;147:32-43.