Targeted genomic capture and massively parallel sequencing to identify novel variants causing Chinese hereditary hearing loss.
BACKGROUND
Hereditary hearing loss is genetically heterogeneous, and hundreds of mutations in than 60 genes are involved in this disease. Therefore, it is difficult to identify the causative gene mutations involved. In this study, we combined targeted genomic capture and massively parallel sequencing (MPS) to address this issue.


METHODS
Using targeted genomic capture and MPS, 104 genes and three microRNA regions were selected and simultaneously sequenced in 23 unrelated probands of Chinese families with nonsyndromic hearing loss. The results were validated by Sanger sequencing for all available members of the probands' families. To analyze the possible pathogenic functional effects of the variants, three types of prediction programs (Mutation Taster, PROVEAN and SIFT) were used. A total of 195 healthy Chinese Han individuals were compared as controls to verify the novel causative mutations.


RESULTS
Of the 23 probands, six had mutations in DFNA genes [WFS1 (n = 2), COCH, ACTG1, TMC1, and POU4F3] known to cause autosomal dominant nonsyndromic hearing loss. These included one novel in-frame indel mutation, three novel missense mutations and two reported missense mutations. Furthermore, one proband from a family with recessive DFNB carried two monoallelic mutations in the GJB2 and USH2A genes. All of these mutations co-segregated with the hearing loss phenotype in 36 affected individuals from 7 families and were predicted to be pathogenic.


CONCLUSIONS
Mutations in uncommon deafness genes contribute to a portion of nonsyndromic deafness cases. In the future, critical gene mutations may be accurately and quickly identified in families with hereditary hearing loss by targeted genomic capture and MPS.
Department of Biotechnology, School of Basic Medical Science, Nanjing Medical University, Nanjing, 210029, PR China. wqj@njmu.edu.cn.
Qinjun
Q
Wei
Department of Otolaryngology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China. 8215013@qq.com.
Hongmei
H
Zhu
Department of Biotechnology, School of Basic Medical Science, Nanjing Medical University, Nanjing, 210029, PR China. goodmale2000@163.com.
Xuli
X
Qian
Department of Otolaryngology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China. czbwy71@163.com.
Zhibin
Z
Chen
Department of Biotechnology, School of Basic Medical Science, Nanjing Medical University, Nanjing, 210029, PR China. joelyao@163.com.
Jun
J
Yao
Department of Biotechnology, School of Basic Medical Science, Nanjing Medical University, Nanjing, 210029, PR China. 13851543104@163.com.
Yajie
Y
Lu
Department of Biotechnology, School of Basic Medical Science, Nanjing Medical University, Nanjing, 210029, PR China. caoxin@njmu.edu.cn.
Xin
X
Cao
Department of Otolaryngology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China. xing-gq@163.com.
Guangqian
G
Xing
D000072259:Connexin 26; D017630:Connexins; D005006:Ethnicity; D005260:Female; D015894:Genome, Human; D034381:Hearing Loss / Q000235:genetics*; D006801:Humans; D008297:Male; D009154:Mutation; D010375:Pedigree; D017421:Sequence Analysis
D017630:Connexins; C000607042:GJB2 protein, human; D000072259:Connexin 26