High-throughput detection of mutations responsible for childhood hearing loss using resequencing microarrays

Kothiyal, Prachi; Cox, Stephanie; Ebert, Jonathan; Husami, Ammar; Kenna, Margaret A.; Greinwald, John H.; Aronow, Bruce J.; Rehm, Heidi L.

doi:10.1186/1472-6750-10-10

Cited by 50 publications

(53 citation statements)

References 34 publications

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“…However, the SureSelectIllumina method is superior in terms of scalability, cost, and increased sensitivity. Our results compare very favorably with recent reports of high-throughput diagnostic tests for NSHL that rely on primer extension arrays (26) or targeted resequencing arrays (27), which are appealing due to low cost but are limited in terms of capacity (not all NSHL genes can be screened simultaneously) and therefore sensitivity.…”

Section: Discussionsupporting

confidence: 76%

Comprehensive genetic testing for hereditary hearing loss using massively parallel sequencing

Shearer

DeLuca²,

Hildebrand³

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

314

302

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The extreme genetic heterogeneity of nonsyndromic hearing loss (NSHL) makes genetic diagnosis expensive and time consuming using available methods. To assess the feasibility of targetenrichment and massively parallel sequencing technologies to interrogate all exons of all genes implicated in NSHL, we tested nine patients diagnosed with hearing loss. Solid-phase (NimbleGen) or solution-based (SureSelect) sequence capture, followed by 454 or Illumina sequencing, respectively, were compared. Sequencing reads were mapped using GSMAPPER, BFAST, and BOWTIE, and pathogenic variants were identified using a custom-variant calling and annotation pipeline (ASAP) that incorporates publicly available in silico pathogenicity prediction tools (SIFT, BLOSUM, Polyphen2, and Align-GVGD). Samples included one negative control, three positive controls (one biological replicate), and six unknowns (10 samples total), in which we genotyped 605 single nucleotide polymorphisms (SNPs) by Sanger sequencing to measure sensitivity and specificity for SureSelect-Illumina and NimbleGen-454 methods at saturating sequence coverage. Causative mutations were identified in the positive controls but not in the negative control. In five of six idiopathic hearing loss patients we identified the pathogenic mutation. Massively parallel sequencing technologies provide sensitivity, specificity, and reproducibility at levels sufficient to perform genetic diagnosis of hearing loss.deafness | genomics | Usher syndrome | diagnostics | next-generation sequencing H ereditary sensorineural hearing loss (SNHL) is the most common sensory impairment in humans (1, 2). In developed countries, two-thirds of prelingual-onset SNHL is estimated to have a genetic etiology, of which ∼70% is nonsyndromic hearing loss (NSHL). Eighty percent of NSHL is autosomal recessive nonsyndromic hearing loss (ARNSHL), ∼20% is autosomal dominant (AD), and the remainder is composed of X-linked and mitochondrial forms (1, 3). To date, 134 deafness loci have been identified, and 32 recessive (DFNB), 23 dominant (DFNA) and 2 X-linked (DFNX) genes have been cloned; 8 genes are associated with both ARNSHL and ADNSHL (4).Establishing a genetic diagnosis of NSHL is a critical component of the clinical evaluation of deaf and hard-of-hearing persons and their families. If a genetic cause of hearing loss is determined, it is possible to provide families with prognostic information, recurrence risks, and improved habilitation options. For persons diagnosed with Usher syndrome, preventative measures including sunlight protection and vitamin therapy can be implemented to minimize the rate of progression of retinitis pigmentosa (5). Most current genetic testing strategies for NSHL rely on a gene-specific Sanger sequencing approach. Because mutations in a single gene, GJB2 (DFNB1), account for up to 50% of ARNSHL in many world populations (6), this approach has changed the evaluation of patients with presumed ARNSHL. However, the mutation frequency in other genes in persons with NSHL in outbred populat...

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Section: Discussionsupporting

confidence: 76%

Comprehensive genetic testing for hereditary hearing loss using massively parallel sequencing

Shearer

DeLuca²,

Hildebrand³

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

314

302

View full text Add to dashboard Cite

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“…For our ResAT data, the detection rate of nucleotide substitutions in the automated mode was higher, and that in the manual mode was slightly lower, compared with detection rates in previous studies (82.1 vs. 81%, respectively, in automated mode, and 97.4 vs. 100%, respectively, in manual mode) (Bruce et al 2010;Chiou et al 2011). Our ResAT analysis was unable to detect any small indel mutations; this is similar to other studies (Hartmann et al 2009;Kothiyal et al 2010). In the human gene mutation database (HGMD; http://www.hgmd.cf.ac.uk/ac/index.…”

Section: Discussionsupporting

confidence: 66%

“…This technology has been used for multiple-gene analysis in childhood hearing loss (Kothiyal et al 2010), breast-ovarian cancer syndrome (Schroeder et al 2010), dilated cardiomyopathy (Zimmerman et al 2010), X-linked intellectual disability (Jensen et al 2011), familial hypercholesterolemia (Chiou et al 2011), and hypertrophic cardiomyopathy (Fokstuen et al 2011). DiVerent research groups have shown ResAT to be a highly eYcient, relatively accurate, cost-eVective, and rapid method.…”

Section: Introductionmentioning

confidence: 99%

Rapid detection of gene mutations responsible for non-syndromic aortic aneurysm and dissection using two different methods: resequencing microarray technology and next-generation sequencing

et al. 2011

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Aortic aneurysm and/or dissection (AAD) is a life-threatening condition, and several syndromes are known to be related to AAD. In this study, two new technologies, resequencing array technology (ResAT) and next-generation sequencing (NGS), were used to analyze eight genes associated with syndromic AAD in 70 patients with non-syndromic AAD. Eighteen sequence variants were detected using both ResAT and NGS. In addition one of these sequence variants was detected by ResAT only and two additional variants by NGS only. Three of the 18 variants are likely to be pathogenic (in 4.3% of AAD patients and in 8.6% of a subset of patients with thoracic AAD), highlighting the importance of genetic analysis in non-syndromic AAD. ResAT and NGS similarly detected most, but not all, of the variants. Resequencing array technology was a rapid and efficient method for detecting most nucleotide substitutions, but was unable to detect short insertions/deletions, and it is impractical to update custom arrays frequently. Next-generation sequencing was able to detect almost all types of mutation, but requires improved informatics methods.

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“…For instance, Laboratory for Molecular Medicine of Partners Healthcare Center for Personalized Genetic Medicine (PCPGM) offers physicians access to 33 genetic diagnostic and screening tests for hearing loss [46] or University of Iowa that have developed a software, AudioGene, to predict AD non-syndromic HL [47].…”

Section: Diagnostic Methods and Screeningmentioning

confidence: 99%

Genetics of hearing loss: where are we standing now?

Mahboubi

Dwabe

Fradkin

et al. 2012

Eur Arch Otorhinolaryngol

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Hearing loss (HL) is the most common sensory impairment and is caused by a broad range of inherited to environmental causes. Inherited HL consists 50-60% of all HL cases. The inherited form of HL is further classified to different categories. More than 300 syndromes and 40 genes have been identified to result in different levels of HL. Although several diagnostic or screening tests have been developed, yet there are controversies around their use.

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High-throughput detection of mutations responsible for childhood hearing loss using resequencing microarrays

Cited by 50 publications

References 34 publications

Comprehensive genetic testing for hereditary hearing loss using massively parallel sequencing

Comprehensive genetic testing for hereditary hearing loss using massively parallel sequencing

Rapid detection of gene mutations responsible for non-syndromic aortic aneurysm and dissection using two different methods: resequencing microarray technology and next-generation sequencing

Genetics of hearing loss: where are we standing now?

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