Screening of deafness-causing DNA variants that are common in patients of European ancestry using a microarray-based approach

Denise Yan; Guangxin Xiang; Xingping Chai; Jie Qing; Haiqiong Shang; Bing Zou; Rahul Mittal; Jun Shen; Richard J H Smith; Yao-Shan Fan; Susan H Blanton; Mustafa Tekin; Cynthia Morton; Wanli Xing; Jing Cheng; Xue Zhong Liu

doi:10.1371/journal.pone.0169219

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Screening of deafness-causing DNA variants that are common in patients of European ancestry using a microarray-based approach

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Screening of deafness-causing DNA variants that are common in patients of European ancestry using a microarray-based approach

Denise Yan, Guangxin Xiang, Xingping Chai, Jie Qing, Haiqiong Shang, Bing Zou, Rahul Mittal, Jun Shen, Richard J H Smith, Yao-Shan Fan, …

PloS one, Vol.12(3), pp.e0169219-e0169219

2017

DOI: 10.1371/journal.pone.0169219

PMCID: PMC5342170

PMID: 28273078

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Abstract

The unparalleled heterogeneity in genetic causes of hearing loss along with remarkable differences in prevalence of causative variants among ethnic groups makes single gene tests technically inefficient. Although hundreds of genes have been reported to be associated with nonsyndromic hearing loss (NSHL), GJB2, GJB6, SLC26A4, and mitochondrial (mt) MT-RNR1 and MTTS are the major contributors. In order to provide a faster, more comprehensive and cost effective assay, we constructed a DNA fluidic array, CapitalBioMiamiOtoArray, for the detection of sequence variants in five genes that are common in most populations of European descent. They consist of c.35delG, p.W44C, p.L90P, c.167delT (GJB2); 309kb deletion (GJB6); p.L236P, p.T416P (SLC26A4); and m.1555A>G, m.7444G>A (mtDNA). We have validated our hearing loss array by analyzing a total of 160 DNAs samples. Our results show 100% concordance between the fluidic array biochip-based approach and the established Sanger sequencing method, thus proving its robustness and reliability at a relatively low cost.

European Continental Ancestry Group - genetics

Genetic Predisposition to Disease - genetics

Deafness - genetics

DNA, Mitochondrial - metabolism

Humans

Connexins - genetics

Connexin 30

DNA - metabolism

Genetic Testing - methods

Sequence Analysis, DNA

Oligonucleotide Array Sequence Analysis - instrumentation

Connexins - metabolism

Sulfate Transporters

DNA - genetics

Deafness - pathology

DNA - isolation & purification

DNA - chemistry

DNA, Mitochondrial - genetics

Mitochondria - genetics

Membrane Transport Proteins - genetics

Polymerase Chain Reaction

DNA, Mitochondrial - chemistry

Details

Title: Subtitle: Screening of deafness-causing DNA variants that are common in patients of European ancestry using a microarray-based approach
Creators: Denise Yan - Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
Guangxin Xiang - National Engineering Research Center for Beijing Biochip Technology, Beijing, China
Xingping Chai - Tsinghua University School of Medicine, Beijing, China
Jie Qing - Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
Haiqiong Shang - Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
Bing Zou - Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
Rahul Mittal - Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
Jun Shen - Laboratory for Molecular Medicine, Partners Personalized Medicine, Cambridge, Massachusetts, United States of America
Richard J H Smith - Department of Otolaryngology - Head and Neck Surgery, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
Yao-Shan Fan - Dr. John T. Macdonald Department of Human Genetics and John P.Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, United States of America
Susan H Blanton - Department of Pathology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
Mustafa Tekin - Department of Pathology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
Cynthia Morton - Division of Evolution and Genomic Science, School of Biological Sciences, Manchester Academic Health Science Center, University of Manchester, United Kingdom
Wanli Xing - Tsinghua University School of Medicine, Beijing, China
Jing Cheng - Tsinghua University School of Medicine, Beijing, China
Xue Zhong Liu - Dr. John T. Macdonald Department of Human Genetics and John P.Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, United States of America
Resource Type: Journal article
Publication Details: PloS one, Vol.12(3), pp.e0169219-e0169219
DOI: 10.1371/journal.pone.0169219
PMID: 28273078
PMCID: PMC5342170
NLM abbreviation: PLoS One
ISSN: 1932-6203
eISSN: 1932-6203
Publisher: Public Library of Science; United States
Grant note: R01 DC015052 / NIDCD NIH HHS R01 DC009645 / NIDCD NIH HHS R01 DC012115 / NIDCD NIH HHS R01 DC005575 / NIDCD NIH HHS
Language: English
Date published: 2017
Academic Unit: Roy J. Carver Department of Biomedical Engineering; Molecular Physiology and Biophysics; Anatomy and Cell Biology; Stead Family Department of Pediatrics; Iowa Neuroscience Institute; Otolaryngology; Internal Medicine
Record Identifier: 9984007157702771

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