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A novel stopgain mutation c.G992A (p.W331X) in TACR3 gene was identified in nonobstructive azoospermia by targeted next-generation sequencing.

ABSTRACT: BACKGROUND:Nonobstructive azoospermia (NOA) is one of the most severe forms of male infertility because of impaired spermatogenesis with the absence of spermatozoa in the ejaculate. The causes of this disease can be partly attributed to genetic factors. Some common structural variants and single nucleotide polymorphisms (SNPs) were reported to be associated with NOA. However, the underlying etiology and genetic mechanism(s) remain largely unclear. The aim of this study was to investigate the associated mutations of spermatogenic genes in Chinese infertile men with NOA. METHODS:The entire coding region of 25 genes associated with spermatogenesis was sequenced from 200 infertile men with NOA. Screening was carried out using the targeted exome sequencing to identify genetic variations and SNPs of the entire coding region of these genes. RESULTS:After the targeted exome sequencing data were filtered through several currently existing variation databases, a series of variations were found. In this paper, we report one novel stopgain variation c.G992A (p.W331X) in the exon 4 of TACR3 gene. The variant was heterozygous and categorized as pathogenic. CONCLUSION:In conclusion, our study revealed a novel stopgain mutation c.G992A (p.W331X) in TACR3 which expanded the mutation spectrum of TACR3 in Chinese NOA infertile men and advanced our understanding of the genetic susceptibility to NOA.

SUBMITTER: Geng D

PROVIDER: S-EPMC6818563 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

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A novel stopgain mutation c.G992A (p.W331X) in TACR3 gene was identified in nonobstructive azoospermia by targeted next-generation sequencing.

Geng Dongfeng D Yang Xiao X Wang Ruixue R Deng Shu S Li Leilei L Hu Xiaonan X Jiang Yuting Y Liu Ruizhi R

Journal of clinical laboratory analysis 20181102 3

<h4>Background</h4>Nonobstructive azoospermia (NOA) is one of the most severe forms of male infertility because of impaired spermatogenesis with the absence of spermatozoa in the ejaculate. The causes of this disease can be partly attributed to genetic factors. Some common structural variants and single nucleotide polymorphisms (SNPs) were reported to be associated with NOA. However, the underlying etiology and genetic mechanism(s) remain largely unclear. The aim of this study was to investigate ...[more]

PMID: 30390321

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Project description:BackgroundWith the expanded availability of next generation sequencing (NGS)-based clinical genetic tests, clinicians seeking to test patients with Mendelian diseases must weigh the superior coverage of targeted gene panels with the greater number of genes included in whole exome sequencing (WES) when considering their first-tier testing approach. Here, we use an in silico analysis to predict the analytic sensitivity of WES using pathogenic variants identified on targeted NGS panels as a reference.MethodsCorresponding nucleotide positions for 1533 different alterations classified as pathogenic or likely pathogenic identified on targeted NGS multi-gene panel tests in our laboratory were interrogated in data from 100 randomly-selected clinical WES samples to quantify the sequence coverage at each position. Pathogenic variants represented 91 genes implicated in hereditary cancer, X-linked intellectual disability, primary ciliary dyskinesia, Marfan syndrome/aortic aneurysms, cardiomyopathies and arrhythmias.ResultsWhen assessing coverage among 100 individual WES samples for each pathogenic variant (153,300 individual assessments), 99.7% (n = 152,798) would likely have been detected on WES. All pathogenic variants had at least some coverage on exome sequencing, with a total of 97.3% (n = 1491) detectable across all 100 individuals. For the remaining 42 pathogenic variants, the number of WES samples with adequate coverage ranged from 35 to 99. Factors such as location in GC-rich, repetitive, or homologous regions likely explain why some of these alterations were not detected across all samples. To validate study findings, a similar analysis was performed against coverage data from 60,706 exomes available through the Exome Aggregation Consortium (ExAC). Results from this validation confirmed that 98.6% (91,743,296/93,062,298) of pathogenic variants demonstrated adequate depth for detection.ConclusionsResults from this in silico analysis suggest that exome sequencing may achieve a diagnostic yield similar to panel-based testing for Mendelian diseases.

Dataset Information

A novel stopgain mutation c.G992A (p.W331X) in TACR3 gene was identified in nonobstructive azoospermia by targeted next-generation sequencing.

Publications

A novel stopgain mutation c.G992A (p.W331X) in TACR3 gene was identified in nonobstructive azoospermia by targeted next-generation sequencing.

Similar Datasets

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