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

BMC Biotechnology

Research Article

Bruce J Aronow¹  Prachi Kothiyal¹  Ammar Husami²  Margaret A Kenna³  Jonathan Ebert⁴  John H Greinwald⁵  Stephanie Cox⁶  Heidi L Rehm⁷ 

[1] Biomedical Informatics, Cincinnati Children's Hospital Medical Center, 45229, Cincinnati, Ohio, USA;Department of Biomedical Engineering, University of Cincinnati, 45221, Cincinnati, Ohio, USA;Department of Biomedical Engineering, University of Cincinnati, 45221, Cincinnati, Ohio, USA;Ear and Hearing Center, Cincinnati Children's Hospital Medical Center, 45229, Cincinnati, Ohio, USA;Department of Otolaryngology and Communication Enhancement, Children's Hospital Boston, 02115, Massachusetts, USA;Department of Otology and Laryngology, Harvard Medical School, 02115, Boston, Massachusetts, USA;Ear and Hearing Center, Cincinnati Children's Hospital Medical Center, 45229, Cincinnati, Ohio, USA;Ear and Hearing Center, Cincinnati Children's Hospital Medical Center, 45229, Cincinnati, Ohio, USA;Department of Otolaryngology, Head and Neck Surgery, University of Cincinnati College of Medicine, 45221, Cincinnati, Ohio, USA;Partners Healthcare Center for Personalized Genetic Medicine, 02115, Boston, Massachusetts, USA;Partners Healthcare Center for Personalized Genetic Medicine, 02115, Boston, Massachusetts, USA;Department of Pathology, Brigham & Women's Hospital and Harvard Medical School, 02115, Boston, Massachusetts, USA;

关键词: Hearing Loss;    Variant Call;    Noonan Syndrome;    GJB2 Gene;    Usher Syndrome;   

DOI  :  10.1186/1472-6750-10-10

 received in 2009-09-15, accepted in 2010-02-10,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundDespite current knowledge of mutations in 45 genes that can cause nonsyndromic sensorineural hearing loss (SNHL), no unified clinical test has been developed that can comprehensively detect mutations in multiple genes. We therefore designed Affymetrix resequencing microarrays capable of resequencing 13 genes mutated in SNHL (GJB2, GJB6, CDH23, KCNE1, KCNQ1, MYO7A, OTOF, PDS, MYO6, SLC26A5, TMIE, TMPRSS3, USH1C). We present results from hearing loss arrays developed in two different research facilities and highlight some of the approaches we adopted to enhance the applicability of resequencing arrays in a clinical setting.ResultsWe leveraged sequence and intensity pattern features responsible for diminished coverage and accuracy and developed a novel algorithm, sPROFILER, which resolved >80% of no-calls from GSEQ and allowed 99.6% (range: 99.2-99.8%) of sequence to be called, while maintaining overall accuracy at >99.8% based upon dideoxy sequencing comparison.ConclusionsTogether, these findings provide insight into critical issues for disease-centered resequencing protocols suitable for clinical application and support the use of array-based resequencing technology as a valuable molecular diagnostic tool for pediatric SNHL and other genetic diseases with substantial genetic heterogeneity.

【 授权许可】

Unknown   
© Kothiyal et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.