Advancing genetic testing for deafness with genomic technology

Journal of Medical Genetics

Volumn 50, Issue 9, 2013, Pages 627-634

  Shearer, A Eliot ^a,b   Black Ziegelbein, E Ann ^a   Hildebrand, Michael S ^a,c   Eppsteiner, Robert W ^a   Ravi, Harini ^d,e   Joshi, Swati ^d,e   Guiffre, Angelica C ^d,e   Sloan, Christina M ^a,b   Happe, Scott ^d,e   Howard, Susanna D ^a   Novak, Barbara ^f   DeLuca, Adam P ^f,g   Taylor, Kyle R ^f,g   Scheetz, Todd E ^b,f,g   Braun, Terry A ^b,f,g   Casavant, Thomas L ^f,g   Kimberling, William J ^a   LeProust, Emily M ^e,g   Smith, Richard J H ^a,b,f  

^a UNIVERSITY OF IOWA HOSPITALS AND CLINICS   (United States)

^b UNIVERSITY OF IOWA   (United States)

^c UNIVERSITY OF MELBOURNE   (Australia)

^d AGILENT TECHNOLOGIES   (United States)

^e AGILENT TECHNOLOGIES   (United States)

^f UNIVERSITY OF IOWA   (United States)

^g University of Iowa   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONNEXIN 26; MYOSIN VI; MYOSIN VIIA; PENDRIN; POTASSIUM CHANNEL KCNQ4;

ADULT; ARTICLE; BIOINFORMATICS; CLINICAL EVALUATION; CLINICAL FEATURE; EXON; FEMALE; GENE IDENTIFICATION; GENE MUTATION; GENE SEQUENCE; GENE TECHNOLOGY; GENETIC SCREENING; GENETIC VARIABILITY; GENOME; HEARING IMPAIRMENT; HUMAN; INHERITANCE; MAJOR CLINICAL STUDY; MALE; NON SYNDROMIC HEARING LOSS; PRIORITY JOURNAL; SENSITIVITY ANALYSIS;

DEAFNESS; HEARING LOSS; MASSIVELY PARALLEL SEQUENCING; SEQUENCE CAPTURE; TARGETED GENOMIC ENRICHMENT;

ADOLESCENT; ADULT; DEAFNESS; FEMALE; GENETIC TESTING; GENOMICS; HUMANS; MALE; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA;

EID: 84883200746     PISSN: 00222593     EISSN: 14686244     Source Type: Journal    
DOI: 10.1136/jmedgenet-2013-101749     Document Type: Article

References (19)

1. Morton N. Genetic epidemiology of hearing impairment. Ann N Y Acad Sci 1991;630:16-31.
2. Shearer AE, DeLuca AP, Hildebrand MS, Taylor KR, Gurrola J, Scherer S, Scheetz TE, Smith RJH. Comprehensive genetic testing for hereditary hearing loss using massively parallel sequencing. Proc Natl Acad Sci USA 2010;107:21104-9.
3. Tang W, Qian D, Ahmad S, Mattox D, Todd NW, Han H, Huang S, Li Y, Wang Y, Li H, Lin X. A low-cost exon capture method suitable for large-scale screening of genetic deafness by the massively-parallel sequencing approach. Genet Test Mol Biomark 2012;16:536-42.
4. Schrauwen I, Sommen M, Corneveaux JJ, Reiman RA, Hackett NJ, Claes C, Claes K, Bitner-Glindzicz M, Couck P, Van Camp G, Huentelman MJ. A sensitive and specific diagnostic test for hearing loss using a microdroplet PCR-based approach and next generation sequencing. Am J Med Genet A 2013;161A:145-52.
5. Brownstein Z, Friedman LM, Shahin H, Oron-Karni V, Kol N, Abu Rayyan A, Parzefall T, Avraham K. Targeted genomic capture and massively parallel sequencing to identify genes for hereditary hearing loss in Middle Eastern families. Genome Biol 2011;12:R89.
6. Shearer AE, Hildebrand MS, Smith RJ. Solution-based targeted genomic enrichment for precious DNA samples. BMC Biotechnol 2012;12:20.
7. Shearer AE, Hildebrand MS, Ravi H, Joshi S, Guiffre AC, Novak B, Happe S, LeProust EM, Smith RJH. Pre-capture multiplexing improves efficiency and cost-effectiveness of targeted genomic enrichment. BMC Genomics 2012;13:618.
8. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009;25:1754-60.
9. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010;20:1297-303.
10. Frommolt P, Abdallah AT, Altmuller J, Motameny S, Thiele H, Becker C, Stemshorn K, Fischer M, Freilinger T, NÜrnberg P. Assessing the enrichment performance in targeted resequencing experiments. Hum Mutat 2012;33:635-41.
11. Liu X, Jian X, Boerwinkle E. dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions. Hum Mutat 2011; 32:894-9.
12. Nord AS, Lee M, King M, Walsh T. Accurate and exact CNV identification from targeted high-throughput sequence data. BMC Genomics 2011;12:184.
13. Francey LJ, Conlin LK, Kadesch HE, Clark D, Berrodin D, Sun Y, Glessner J, Hakonarson H, Jalas C, Landau C, Spinner NB, Kenna M, Sagi M, Rehm HL, Krantz ID. Genome-wide SNP genotyping identifies the Stereocilin (STRC) gene as a major contributor to pediatric bilateral sensorineural hearing impairment. Am J Med Genet A 2011;158:298-308.
14. Knijnenburg J, Oberstein SAJL, Frei K, Lucas T, Gijsbers ACJ, Ruivenkamp CAL, Tanke HJ, Szuhai K. A homozygous deletion of a normal variation locus in a patient with hearing loss from non-consanguineous parents. J Med Genet 2009;46:412-17.
15. Redin C, Le Gras S, Mhamdi O, Geoffroy V, Stoetzel C, Vincent MC, Tanke HJ, Szuhai K. Targeted high-throughput sequencing for diagnosis of genetically heterogeneous diseases: efficient mutation detection in Bardet-Biedl and Alstrom syndromes. J Med Genet 2012;49:502-12.
16. Kohane IS, Hsing M, Kong SW. Taxonomizing, sizing, and overcoming the incidentalome. Genet Med 2012;14:399-404.
17. Tennessen JA, Bigham AW, O'Connor TD, Fu W, Kenny EE, Gravel S, McGee S, Do R, Liu X, Jun G, Kang HM, Jordan D, Leal SM, Gabriel S, Rieder MJ, Abecasis G, Altshuler D, Nickerson DA, Boerwinkle E, Sunyaev S, Bustamante CD, Bamshad MJ, Akey JM. Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 2012;337:64-9.
18. Korver AMH, Konings S, Dekker FW, Beers M, Wever CC, Frijns JHM, Oudesluys-Murphy AM. Newborn hearing screening vs later hearing screening and developmental outcomes in children with permanent childhood hearing impairment. JAMA 2010;304:1701-8.
19. Morton CC, Nance WE. Newborn hearing screening-a silent revolution. N Engl J Med 2006;354:2151-64.