Correcting false-positive pathogenic categorization of benign variants by re-sequencing of the recessive deafness genes in carriers
10.3969/j.issn.1674-8115.2017.11.015
- VernacularTitle:运用耳聋基因隐性突变携带者重测序策略纠正假阳性变异的致病性误判
- Author:
Jun SHI
1
;
xia Long HE
;
Tao YANG
Author Information
1. 上海交通大学 医学院附属第九人民医院耳鼻咽喉-头颈外科
- Keywords:
exome sequencing;
deafness;
autosomal recessive inheritance;
carrier;
pathogenesis
- From:
Journal of Shanghai Jiaotong University(Medical Science)
2017;37(11):1534-1540
- CountryChina
- Language:Chinese
-
Abstract:
Objective· To correct the false-positive categorization of the rare and benign variants by re-sequencing of the recessive deafness genes in carriers. Methods · Heterozygous carriers of known causative mutations in recessive deafness genes were identified from normal hearing relatives of the deaf probands.Targeted next-generation sequencing was performed in those carriers to identify additional variants in trans,which was presumed to be benign. Results · A total of 30 normal-hearing carriers of heterozygous and known pathogenic mutations were identified. By targeted next-generation sequencing of corresponding genes,32 non-synonymous variants in trans were identified,which were categorized to benign mutations under the recessive and full-penetrant mode.Among those variants p.A434T in SLC26A4,p.R266Q in LOXHD1,p.K96Q in MYO15A,p.T123N in GJB2 and pV1299I in CDH23 were five rare variants with minor allele frequency of less than 0.005.Some of the 5 variants were predicted to be pathogenic by prediction programs including Polyphen-2, PROVEAN, SIFT and MutationTaster, or documented to be pathogenic by Deafness Variation Database or Human Genome Mutation Database. Conclusion · Re-sequencing of the recessive deafness genes in carriers may efficiently correct the false-positive categorization of some rare and benign variants to improve the accuracy and efficiency of the next-generation sequencing in diagnosis of monogenic recessive hereditary disorders.
