Next generation sequencing-based copy number analysis reveals low prevalence of deletions and duplications in 46 genes associated with genetic cardiomyopathies

Molecular Genetics and Genomic Medicine

Volumn 4, Issue 2, 2016, Pages 143-151

  Ceyhan Birsoy, Ozge ^a,b   Pugh, Trevor J ^c   Bowser, Mark J ^a   Hynes, Elizabeth ^a   Frisella, Ashley L ^a   Mahanta, Lisa M ^a   Lebo, Matt S ^a,b   Amr, Sami S ^a,b   Funke, Birgit H ^a,d  

^a LABORATORY FOR MOLECULAR MEDICINE   (United States)

^b BRIGHAM AND WOMEN S HOSPITAL   (United States)

^c PRINCESS MARGARET HOSPITAL   (Canada)

^d MASSACHUSETTS GENERAL HOSPITAL   (United States)

Author keywords

Cardiomyopathies; DNA copy number variants; Genetic heterogeneity; Molecular diagnostics; Next generation sequencing

Indexed keywords

EID: 84992481731     PISSN: None     EISSN: 23249269     Source Type: Journal    
DOI: 10.1002/mgg3.187     Document Type: Article

References (45)

1. Adalsteinsdottir, B., P. Teekakirikul, B. J. Maron, M. A. Burke, D. F. Gudbjartsson, H. Holm, et al. 2014. Nationwide study on hypertrophic cardiomyopathy in Iceland: evidence of a MYBPC3 founder mutation. Circulation 130:1158-1167.
2. Alfares, A. A., M. A. Kelly, G. McDermott, B. H. Funke, M. S. Lebo, S. B. Baxter, et al. 2015. Results of clinical genetic testing of 2,912 probands with hypertrophic cardiomyopathy: expanded panels offer limited additional sensitivity. Genet. Med. doi: 10.1038/gim.2014.205.
3. Bagci, P., S. Erdamar, Y. Erzin, A. Karatas, and M. Tuncer. 2009. A case of polyarteritis nodosa diagnosed after recurrent, multiple intestinal perforations. Turk. J. Gastroenterol. 20:71-72.
4. Biagini, E., F. Coccolo, M. Ferlito, E. Perugini, G. Rocchi, L. Bacchi-Reggiani, et al. 2005. Dilated-hypokinetic evolution of hypertrophic cardiomyopathy: prevalence, incidence, risk factors, and prognostic implications in pediatric and adult patients. J. Am. Coll. Cardiol. 46:1543-1550.
5. Boucek, D., J. Jirikowic, and M. Taylor. 2011. Natural history of Danon disease. Genet. Med. 13:563-568.
6. Chanavat, V., M. F. Seronde, P. Bouvagnet, P. Chevalier, R. Rousson, and G. Millat. 2012. Molecular characterization of a large MYBPC3 rearrangement in a cohort of 100 unrelated patients with hypertrophic cardiomyopathy. Eur. J. Med. Genet. 55:163-166.
7. Duzkale, H., J. Shen, H. McLaughlin, A. Alfares, M. A. Kelly, T. J. Pugh, et al. 2013. A systematic approach to assessing the clinical significance of genetic variants. Clin. Genet. 84:453-463.
8. Eisenberger, T., C. Neuhaus, A. O. Khan, C. Decker, M. N. Preising, C. Friedburg, et al. 2013. Increasing the yield in targeted next-generation sequencing by implicating CNV analysis, non-coding exons and the overall variant load: the example of retinal dystrophies. PLoS ONE 8:e78496.
9. Elliott, P., C. O'Mahony, P. Syrris, A. Evans, C. Rivera Sorensen, M. N. Sheppard, et al. 2010. Prevalence of desmosomal protein gene mutations in patients with dilated cardiomyopathy. Circ. Cardiovasc. Genet. 3:314-322.
10. Fanin, M., A. C. Nascimbeni, L. Fulizio, M. Spinazzi, P. Melacini, and C. Angelini. 2006. Generalized lysosome-associated membrane protein-2 defect explains multisystem clinical involvement and allows leukocyte diagnostic screening in Danon disease. Am. J. Pathol. 168:1309-1320.
11. Feng, Y., D. Chen, G. L. Wang, V. W. Zhang, and L. J. Wong. 2015. Improved molecular diagnosis by the detection of exonic deletions with target gene capture and deep sequencing. Genet. Med. 17:99-107.
12. Germain, D. P. 2010. Fabry disease. Orphanet J Rare Dis 5:30.
13. Groeneweg, J. A., P. A. van der Zwaag, L. R. Olde Nordkamp, H. Bikker, J. D. Jongbloed, R. Jongbloed, et al. 2013. Arrhythmogenic right ventricular dysplasia/cardiomyopathy according to revised 2010 task force criteria with inclusion of non-desmosomal phospholamban mutation carriers. Am. J. Cardiol. 112:1197-1206.
14. Groeneweg, J. A., A. Bhonsale, C. A. James, A. S. Te Riele, D. Dooijes, C. Tichnell, et al. 2015. Clinical Presentation, Long-Term Follow-Up, and Outcomes of 1001 Arrhythmogenic Right Ventricular Dysplasia/Cardiomyopathy Patients and Family Members. Circ. Cardiovasc. Genet. 8:437-446.
15. Gupta, P., Z. T. Bilinska, N. Sylvius, E. Boudreau, J. P. Veinot, S. Labib, et al. 2010. Genetic and ultrastructural studies in dilated cardiomyopathy patients: a large deletion in the lamin A/C gene is associated with cardiomyocyte nuclear envelope disruption. Basic Res. Cardiol. 105:365-377.
16. den Haan, A. D., B. Y. Tan, M. N. Zikusoka, L. I. Llado, R. Jain, A. Daly, et al. 2009. Comprehensive desmosome mutation analysis in north americans with arrhythmogenic right ventricular dysplasia/cardiomyopathy. Circ. Cardiovasc. Genet. 2:428-435.
17. Hassel, D., T. Dahme, J. Erdmann, B. Meder, A. Huge, M. Stoll, et al. 2009. Nexilin mutations destabilize cardiac Z-disks and lead to dilated cardiomyopathy. Nat. Med. 15:1281-1288.
18. Haverty, C. E., A. E. Lin, E. Simpson, M. A. Spence, and R. A. Martin. 2004. 47, XXX associated with malformations. Am. J. Med. Genet. A 125A:108-111.; author reply 112
19. Herman, D. S., L. Lam, M. R. Taylor, L. Wang, P. Teekakirikul, D. Christodoulou, et al. 2012. Truncations of titin causing dilated cardiomyopathy. N. Engl. J. Med. 366:619-628.
20. Hindson, B. J., K. D. Ness, D. A. Masquelier, P. Belgrader, N. J. Heredia, A. J. Makarewicz, et al. 2011. High-throughput droplet digital PCR system for absolute quantitation of DNA copy number. Anal. Chem. 83:8604-8610.
21. Jouven, X., A. Hagege, P. Charron, L. Carrier, O. Dubourg, J. M. Langlard, et al. 2002. Relation between QT duration and maximal wall thickness in familial hypertrophic cardiomyopathy. Heart 88:153-157.
22. Kang, S. H., C. Shaw, Z. Ou, P. A. Eng, M. L. Cooper, A. N. Pursley, et al. 2010. Insertional translocation detected using FISH confirmation of array-comparative genomic hybridization (aCGH) results. Am. J. Med. Genet. A 152A:1111-1126.
23. Kapplinger, J. D., A. P. Landstrom, B. A. Salisbury, T. E. Callis, G. D. Pollevick, D. J. Tester, et al. 2011. Distinguishing arrhythmogenic right ventricular cardiomyopathy/dysplasia-associated mutations from background genetic noise. J. Am. Coll. Cardiol. 57:2317-2327.
24. Lacoste-Collin, L., V. Garcia, E. Uro-Coste, M. C. Arne-Bes, D. Durand, T. Levade, et al. 2002. Danon's disease (X-linked vacuolar cardiomyopathy and myopathy): a case with a novel Lamp-2 gene mutation. Neuromuscul. Disord. 12:882-885.
25. Lazzarini, E., J. D. Jongbloed, K. Pilichou, G. Thiene, C. Basso, H. Bikker, et al. 2015. The ARVD/C Genetic Variants Database: 2014 Update. Hum. Mutat. 36:403-410.
26. Li Mura, I. E., B. Bauce, A. Nava, M. Fanciulli, G. Vazza, E. Mazzotti, et al. 2013. Identification of a PKP2 gene deletion in a family with arrhythmogenic right ventricular cardiomyopathy. Eur. J. Hum. Genet. 21:1226-1231.
27. McKenna, A., M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis, A. Kernytsky, et al. 2010. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20:1297-1303.
28. Neill, N. J., B. C. Ballif, A. N. Lamb, S. Parikh, J. B. Ravnan, R. A. Schultz, et al. 2011. Recurrence, submicroscopic complexity, and potential clinical relevance of copy gains detected by array CGH that are shown to be unbalanced insertions by FISH. Genome Res. 21:535-544.
29. Newman, S., K. E. Hermetz, B. Weckselblatt, and M. K. Rudd. 2015. Next-Generation Sequencing of Duplication CNVs Reveals that Most Are Tandem and Some Create Fusion Genes at Breakpoints. Am. J. Hum. Genet. 96:208-220.
30. Norton, N., D. Li, M. J. Rieder, J. D. Siegfried, E. Rampersaud, S. Zuchner, et al. 2011. Genome-wide studies of copy number variation and exome sequencing identify rare variants in BAG3 as a cause of dilated cardiomyopathy. Am. J. Hum. Genet. 88:273-282.
31. Nowakowska, B. A., N. de Leeuw, C. A. Ruivenkamp, B. Sikkema-Raddatz, J. A. Crolla, R. Thoelen, et al. 2012. Parental insertional balanced translocations are an important cause of apparently de novo CNVs in patients with developmental anomalies. Eur. J. Hum. Genet. 20:166-170.
32. Pugh, T. J., S. S. Amr, M. J. Bowser, S. Gowrisankar, E. Duffy, L. M. Mahanta, et al. VisCap: Inference and visualization of germline copy number variants from targeted clinical sequencing data. Genet. Med., in press.
33. Pugh, T. J., M. A. Kelly, S. Gowrisankar, E. Hynes, M. A. Seidman, S. M. Baxter, et al. 2014. The landscape of genetic variation in dilated cardiomyopathy as surveyed by clinical DNA sequencing. Genet. Med. 16:601-608.
34. Retterer, K., J. Scuffins, D. Schmidt, R. Lewis, D. Pineda-Alvarez, A. Stafford, et al. 2014. Assessing copy number from exome sequencing and exome array CGH based on CNV spectrum in a large clinical cohort. Genet. Med. 17:623-629.
35. Richards, S., N. Aziz, S. Bale, D. Bick, S. Das, J. Gastier-Foster, et al. 2015. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet. Med. 17:405-424.
36. Roth, W., D. Bucsenez, H. Blaker, I. Berger, and P. A. Schnabel. 2006. Misalignment of pulmonary vessels with alveolar capillary dysplasia: association with atrioventricular septal defect and quadricuspid pulmonary valve. Virchows Arch. 448:375-378.
37. Sen-Chowdhry, S., P. Syrris, S. K. Prasad, S. E. Hughes, R. Merrifield, D. Ward, et al. 2008. Left-dominant arrhythmogenic cardiomyopathy: an under-recognized clinical entity. J. Am. Coll. Cardiol. 52:2175-2187.
38. Shearer, A. E., D. L. Kolbe, H. Azaiez, C. M. Sloan, K. L. Frees, A. E. Weaver, et al. 2014. Copy number variants are a common cause of non-syndromic hearing loss. Genome Med. 6:37.
39. Stankiewicz, P., and J. R. Lupski. 2010. Structural variation in the human genome and its role in disease. Annu. Rev. Med. 61:437-455.
40. Teekakirikul, P., M. A. Kelly, H. L. Rehm, N. K. Lakdawala, and B. H. Funke. 2013. Inherited cardiomyopathies: molecular genetics and clinical genetic testing in the postgenomic era. J. Mol. Diagn. 15:158-170.
41. Wang, H., Z. Li, J. Wang, K. Sun, Q. Cui, L. Song, et al. 2010. Mutations in NEXN, a Z-disc gene, are associated with hypertrophic cardiomyopathy. Am. J. Hum. Genet. 87:687-693.
42. Yang, Z., B. H. Funke, L. H. Cripe, G. W. III Vick, D. Mancini-Dinardo, L. S. Pena, et al. 2010. LAMP2 microdeletions in patients with Danon disease. Circ. Cardiovasc. Genet. 3:129-137.
43. Zhang, F., W. Gu, M. E. Hurles, and J. R. Lupski. 2009. Copy number variation in human health, disease, and evolution. Annu. Rev. Genomics Hum. Genet. 10:451-481.
44. Zhao, M., Q. Wang, P. Jia, and Z. Zhao. 2013. Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives. BMC Bioinformatics 14(Suppl 11):S1.
45. van der Zwaag, P. A., I. A. van Rijsingen, A. Asimaki, J. D. Jongbloed, D. J. van Veldhuisen, A. C. Wiesfeld, et al. 2012. Phospholamban R14del mutation in patients diagnosed with dilated cardiomyopathy or arrhythmogenic right ventricular cardiomyopathy: evidence supporting the concept of arrhythmogenic cardiomyopathy. Eur. J. Heart Fail. 14:1199-1207.