High-throughput sequencing to decipher the genetic heterogeneity of deafness

Genome Biology

Volumn 13, Issue 5, 2012, Pages

  Brownstein, Zippora ^a   Bhonker, Yoni ^a   Avraham, Karen B ^a  

^a TEL AVIV UNIVERSITY   (Israel)

Author keywords

Deep sequencing; Exome sequencing; Genomics; Hearing loss; Homozygosity mapping; Massive parallel sequencing; Next generation sequencing

Indexed keywords

AUDITORY SYSTEM; DIAGNOSTIC PROCEDURE; EXOME; GENE LOCUS; GENE MUTATION; GENETIC COUNSELING; GENETIC HETEROGENEITY; GENETIC IDENTIFICATION; GENETIC SCREENING; GENOMICS; HEARING IMPAIRMENT; HEARING LOSS; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN GENOME; REVIEW; DNA SEQUENCE; GENETICS; METHODOLOGY; MUTATION;

DEAFNESS; GENETIC HETEROGENEITY; HEARING LOSS; HUMANS; MUTATION; SEQUENCE ANALYSIS, DNA;

EID: 84861699180     PISSN: None     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2012-13-5-245     Document Type: Review

References (58)

1. Estivill X, Fortina P, Surrey S, Rabionet R, Melchionda S, D'Agruma L, Mansfield E, Rappaport E, Govea N, Mila M, Zelante L, Gasparini P. Connexin-26 mutations in sporadic and inherited sensorineural deafness. Lancet 1998, 351:394-398. 10.1016/S0140-6736(97)11124-2, 9482292.
2. Nadol JB. Hearing loss. N Engl J Med 1993, 329:1092-1102. 10.1056/NEJM199310073291507, 8371732.
3. Morton CC, Nance WE. Newborn hearing screening-a silent revolution. N Engl J Med 2006, 354:2151-2164. 10.1056/NEJMra050700, 16707752.
4. Smith RJ, Bale JF, White KR. Sensorineural hearing loss in children. Lancet 2005, 365:879-890. 10.1016/S0140-6736(05)71047-3, 15752533.
5. Walsh T, Lee MK, Casadei S, Thornton AM, Stray SM, Pennil C, Nord AS, Mandell JB, Swisher EM, King MC. Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing. Proc Natl Acad Sci USA 2010, 107:12629-12633. 10.1073/pnas.1007983107, 2906584, 20616022.
6. Worthey EA, Mayer AN, Syverson GD, Helbling D, Bonacci BB, Decker B, Serpe JM, Dasu T, Tschannen MR, Veith RL, Basehore MJ, Broeckel U, Tomita-Mitchell A, Arca MJ, Casper JT, Margolis DA, Bick DP, Hessner MJ, Routes JM, Verbsky JW, Jacob HJ, Dimmock DP. Making a definitive diagnosis: successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease. Genet Med 2011, 13:255-262. 10.1097/GIM.0b013e3182088158, 21173700.
7. Ng SB, Bigham AW, Buckingham KJ, Hannibal MC, McMillin MJ, Gildersleeve HI, Beck AE, Tabor HK, Cooper GM, Mefford HC, Lee C, Turner EH, Smith JD, Rieder MJ, Yoshiura K, Matsumoto N, Ohta T, Niikawa N, Nickerson DA, Bamshad MJ, Shendure J. Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat Genet 2010, 42:790-793. 10.1038/ng.646, 2930028, 20711175.
8. Hereditary Hearing loss Homepage. , http://hereditaryhearingloss.org/
9. Richardson GP, de Monvel JB, Petit C. How the genetics of deafness illuminates auditory physiology. Annu Rev Physiol 2011, 73:311-334. 10.1146/annurev-physiol-012110-142228, 21073336.
10. Dror AA, Avraham KB. Hearing loss: mechanisms revealed by genetics and cell biology. Annu Rev Genet 2009, 43:411-437. 10.1146/annurev-genet-102108-134135, 19694516.
11. Deafness Variation Database. , http://deafnessvariationdatabase.com/
12. Hilgert N, Smith RJ, Van Camp G. Forty-six genes causing nonsyndromic hearing impairment: which ones should be analyzed in DNA diagnostics?. Mutat Res 2009, 681:189-196. 10.1016/j.mrrev.2008.08.002, 2847850, 18804553.
13. Lander ES, Botstein D. Homozygosity mapping: a way to map human recessive traits with the DNA of inbred children. Science 1987, 236:1567-1570. 10.1126/science.2884728, 2884728.
14. Christianson A, Modell B. Medical genetics in developing countries. Annu Rev Genomics Hum Genet 2004, 5:219-265. 10.1146/annurev.genom.5.061903.175935, 15485349.
15. Rodriguez-Paris J, Pique L, Colen T, Roberson J, Gardner P, Schrijver I. Genotyping with a 198 mutation arrayed primer extension array for hereditary hearing loss: assessment of its diagnostic value for medical practice. PLoS One 2010, 5:e11804. 10.1371/journal.pone.0011804, 2909915, 20668687.
16. Walsh T, Pierce SB, Lenz DR, Brownstein Z, Dagan-Rosenfeld O, Shahin H, Roeb W, McCarthy S, Nord AS, Gordon CR, Ben-Neriah Z, Sebat J, Kanaan M, Lee MK, Frydman M, King MC, Avraham KB. Genomic duplication and overexpression of TJP2/ZO-2 leads to altered expression of apoptosis genes in progressive nonsyndromic hearing loss DFNA51. Am J Hum Genet 2010, 87:101-109. 10.1016/j.ajhg.2010.05.011, 2896780, 20602916.
17. Brownstein Z, Friedlander Y, Peritz E, Cohen T. Estimated number of loci for autosomal recessive severe nerve deafness within the Israeli Jewish population, with implications for genetic counseling. Am J Med Genet 1991, 41:306-312. 10.1002/ajmg.1320410309, 1789284.
18. Brownstein Z, Avraham KB. Deafness genes in Israel: implications for diagnostics in the clinic. Pediatr Res 2009, 66:128-134. 10.1203/PDR.0b013e3181aabd7f, 19390476.
19. Brownstein Z, Friedman LM, Shahin H, Oron-Karni V, Kol N, Rayyan AA, Parzefall T, Lev D, Shalev S, Frydman M, Davidov B, Shohat M, Rahile M, Lieberman S, Levy-Lahad E, Lee MK, Shomron N, King MC, Walsh T, Kanaan M, Avraham KB. Targeted genomic capture and massively parallel sequencing to identify genes for hereditary hearing loss in middle eastern families. Genome Biol 2011, 12:R89. 10.1186/gb-2011-12-9-r89, 3308052, 21917145.
20. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437:376-380. 1464427, 16056220.
21. Ju J, Kim DH, Bi L, Meng Q, Bai X, Li Z, Li X, Marma MS, Shi S, Wu J, Edwards JR, Romu A, Turro NJ. Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators. Proc Natl Acad Sci USA 2006, 103:19635-19640. 10.1073/pnas.0609513103, 1702316, 17170132.
22. Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K, Sidow A, Fire A, Johnson SM. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res 2008, 18:1051-1063. 10.1101/gr.076463.108, 2493394, 18477713.
23. Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010, 11:31-46. 10.1038/nrg2626, 19997069.
24. Shearer AE, Hildebrand MS, Sloan CM, Smith RJ. Deafness in the genomics era. Hear Res 2011, 282:1-9. 10.1016/j.heares.2011.10.001, 22016077.
25. Shearer AE, DeLuca AP, Hildebrand MS, Taylor KR, Gurrola J, Scherer S, Scheetz TE, Smith RJ. Comprehensive genetic testing for hereditary hearing loss using massively parallel sequencing. Proc Natl Acad Sci USA 2010, 107:21104-21109. 10.1073/pnas.1012989107, 3000272, 21078986.
26. Rehman AU, Morell RJ, Belyantseva IA, Khan SY, Boger ET, Shahzad M, Ahmed ZM, Riazuddin S, Khan SN, Friedman TB. Targeted capture and next-generation sequencing identifies C9orf75, encoding taperin, as the mutated gene in nonsyndromic deafness DFNB79. Am J Hum Genet 2010, 86:378-388. 10.1016/j.ajhg.2010.01.030, 2833391, 20170899.
27. Lin X, Tang W, Ahmad S, Lu J, Colby CC, Zhu J, Yu Q. Applications of targeted gene capture and next-generation sequencing technologies in studies of human deafness and other genetic disabilities. Hear Res 2012, doi:10.1016/j.heares.2012.01.004.
28. Gilissen C, Hoischen A, Brunner HG, Veltman JA. Disease gene identification strategies for exome sequencing. Eur J Hum Genet 2012, 20:490-497. 10.1038/ejhg.2011.258, 22258526.
29. Walsh T, Shahin H, Elkan-Miller T, Lee MK, Thornton AM, Roeb W, Abu Rayyan A, Loulus S, Avraham KB, King MC, Kanaan M. Whole exome sequencing and homozygosity mapping identify mutation in the cell polarity protein GPSM2 as the cause of nonsyndromic hearing loss DFNB82. Am J Hum Genet 2010, 87:90-94. 10.1016/j.ajhg.2010.05.010, 2896776, 20602914.
30. Sirmaci A, Edwards YJ, Akay H, Tekin M. Challenges in whole exome sequencing: an example from hereditary deafness. PLoS One 2012, 7:e32000. 10.1371/journal.pone.0032000, 3283682, 22363784.
31. Schraders M, Haas SA, Weegerink NJ, Oostrik J, Hu H, Hoefsloot LH, Kannan S, Huygen PL, Pennings RJ, Admiraal RJ, Kalscheuer VM, Kunst HP, Kremer H. Next-generation sequencing identifies mutations of SMPX, which encodes the small muscle protein, X-linked, as a cause of progressive hearing impairment. Am J Hum Genet 2011, 88:628-634. 10.1016/j.ajhg.2011.04.012, 3146715, 21549342.
32. Huebner AK, Gandia M, Frommolt P, Maak A, Wicklein EM, Thiele H, Altmuller J, Wagner F, Vinuela A, Aguirre LA, Moreno F, Maier H, Rau I, Giesselmann S, Nurnberg G, Gal A, Nurnberg P, Hubner CA, del Castillo I, Kurth I. Nonsense mutations in SMPX, encoding a protein responsive to physical force, result in X-chromosomal hearing loss. Am J Hum Genet 2011, 88:621-627. 10.1016/j.ajhg.2011.04.007, 3146719, 21549336.
33. Scully JL. Disability and genetics in the era of genomic medicine. Nat Rev Genet 2008, 9:797-802.
34. Christiansen JB. Sociological implications of hearing loss. Ann NY Acad Sci 1991, 630:230-235. 10.1111/j.1749-6632.1991.tb19592.x, 1835330.
35. Grundfast KM, Rosen J. Ethical and cultural considerations in research on hereditary deafness. Otolaryngol Clin North Am 1992, 25:973-978.
36. Stern SJ, Arnos KS, Murrelle L, Welch KO, Nance WE, Pandya A. Attitudes of deaf and hard of hearing subjects towards genetic testing and prenatal diagnosis of hearing loss. J Med Genet 2002, 39:449-453. 10.1136/jmg.39.6.449, 1735146, 12070258.
37. Dagan O, Hochner H, Levi H, Raas-Rothschild A, Sagi M. Genetic testing for hearing loss: different motivations for the same outcome. Am J Med Genet 2002, 113:137-143. 10.1002/ajmg.10676, 12407703.
38. Bunnik EM, Schermer MH, Janssens AC. Personal genome testing: test characteristics to clarify the discourse on ethical, legal and societal issues. BMC Med Ethics 2011, 12:11. 10.1186/1472-6939-12-11, 3141793, 21672210.
39. Kaye J, Heeney C, Hawkins N, de Vries J, Boddington P. Data sharing in genomics - re-shaping scientific practice. Nat Rev Genet 2009, 10:331-335. 10.1038/nrg2573, 2672783, 19308065.
40. Pierce SB, Walsh T, Chisholm KM, Lee MK, Thornton AM, Fiumara A, Opitz JM, Levy-Lahad E, Klevit RE, King MC. Mutations in the DBP-deficiency protein HSD17B4 cause ovarian dysgenesis, hearing loss, and ataxia of Perrault Syndrome. Am J Hum Genet 2010, 87:282-288. 10.1016/j.ajhg.2010.07.007, 2917704, 20673864.
41. Sirmaci A, Walsh T, Akay H, Spiliopoulos M, Sakalar YB, Hasanefendioglu-Bayrak A, Duman D, Farooq A, King MC, Tekin M. MASP1 mutations in patients with facial, umbilical, coccygeal, and auditory findings of Carnevale, Malpuech, OSA, and Michels syndromes. Am J Hum Genet 2010, 87:679-686. 10.1016/j.ajhg.2010.09.018, 2978960, 21035106.
42. Zheng J, Miller KK, Yang T, Hildebrand MS, Shearer AE, DeLuca AP, Scheetz TE, Drummond J, Scherer SE, Legan PK, Goodyear RJ, Richardson GP, Cheatham MA, Smith RJ, Dallos P. Carcinoembryonic antigen-related cell adhesion molecule 16 interacts with α-tectorin and is mutated in autosomal dominant hearing loss (DFNA4). Proc Natl Acad Sci USA 2011, 108:4218-4223. 10.1073/pnas.1005842108, 3054008, 21368133.
43. Pierce SB, Chisholm KM, Lynch ED, Lee MK, Walsh T, Opitz JM, Li W, Klevit RE, King MC. Mutations in mitochondrial histidyl tRNA synthetase HARS2 cause ovarian dysgenesis and sensorineural hearing loss of Perrault syndrome. Proc Natl Acad Sci USA 2011, 108:6543-6548. 10.1073/pnas.1103471108, 3081023, 21464306.
44. Klein CJ, Botuyan MV, Wu Y, Ward CJ, Nicholson GA, Hammans S, Hojo K, Yamanishi H, Karpf AR, Wallace DC, Simon M, Lander C, Boardman LA, Cunningham JM, Smith GE, Litchy WJ, Boes B, Atkinson EJ, Middha S, PJ BD, Parisi JE, Mer G, Smith DI, Dyck PJ. Mutations in DNMT1 cause hereditary sensory neuropathy with dementia and hearing loss. Nat Genet 2011, 43:595-600. 10.1038/ng.830, 3102765, 21532572.
45. Calvo SE, Compton AG, Hershman SG, Lim SC, Lieber DS, Tucker EJ, Laskowski A, Garone C, Liu S, Jaffe DB, Christodoulou J, Fletcher JM, Bruno DL, Goldblatt J, Dimauro S, Thorburn DR, Mootha VK. Molecular diagnosis of infantile mitochondrial disease with targeted next-generation sequencing. Sci Transl Med 2012, 4:118ra10. 10.1126/scitranslmed.3003310, 22277967.
46. Winkelmann J, Lin L, Schormair B, Kornum BR, Faraco J, Plazzi G, Melberg A, Cornelio F, Urban AE, Pizza F, Poli F, Grubert F, Wieland T, Graf E, Hallmayer J, Strom TM, Mignot E. Mutations in DNMT1 cause autosomal dominant cerebellar ataxia, deafness and narcolepsy. Hum Mol Genet 2012, 15:2205-2210.
47. Dror AA and AKB. Hearing impairment: a panoply of genes and functions. Neuron 2010, 68:293-308. 10.1016/j.neuron.2010.10.011, 20955936.
48. 1000 Genomes. , http://www.1000genomes.org/home
49. NCBI dbSNP. , http://www.ncbi.nlm.nih.gov/projects/SNP/
50. NHLBI Exome Sequencing Project. , http://evs.gs.washington.edu/EVS/
51. UCSC - Genome Bioinformatics. , http://genome.ucsc.edu
52. PolyPhen-2. , http://genetics.bwh.harvard.edu/pph2/
53. SIFT Human Protein. , http://sift.jcvi.org/www/SIFT_enst_submit.html
54. The ConSurf Server. , http://consurf.tau.ac.il/
55. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 1977, 74:5463-5467. 10.1073/pnas.74.12.5463, 431765, 271968.
56. Bartlett JM, Stirling D. A short history of the polymerase chain reaction. Methods Mol Biol 2003, 226:3-6. 10.1007/978-1-4612-0055-0_1, 12958470.
57. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, et al. Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921. 10.1038/35057062, 11237011.
58. Shearer AE, Hildebrand MS, Sloan CM, Smith RJ. Deafness in the genomics era. Hear Res 2011, 282:1-9. 10.1016/j.heares.2011.10.001, 22016077.