Development of a novel next-generation sequencing panel for diagnosis of quantitative spermatogenic impairment

Maria Santa Rocca; Aichi Msaki; Marco Ghezzi; Ilaria Cosci; Kalliopi Pilichou; Rudy Celeghin; Carlo Foresta; Alberto Ferlin

doi:10.1007/s10815-020-01747-0

Male Fertility · Male Endocrine and Genetic Factors

Development of a novel next-generation sequencing panel for diagnosis of quantitative spermatogenic impairment

Rocca MS, Msaki A, Ghezzi M, Cosci I, Pilichou K, Celeghin R, Foresta C, Ferlin A

Published April 3, 2020 Journal of assisted reproduction and genetics

DOI 10.1007/s10815-020-01747-0 PMID 32242295 PMC PMC7183017

RRM Academy Synopsis

Gene panel finds rare variants in men with low or absent sperm counts

A custom nine-gene sequencing panel found rare variants in Italian men with low or absent sperm counts. About 9 out of 100 of these men carried a rare variant classified as pathogenic or of uncertain significance. The single-center study sequenced 241 men whose infertility had no identified cause. None of the 67 men with normal counts carried a missense variant.

Key Findings

The panel sequenced 239 of 241 men on the first attempt and the other two on a repeat run. Ten positive controls with known variants were sequenced correctly.
The panel detected 19 rare missense variants, in eight of its nine genes. Five had been described in earlier studies. Fourteen had no published studies and may be new findings.
Under American College of Medical Genetics and Genomics criteria, 1 variant was pathogenic, 11 were of uncertain significance, 5 were likely benign and 2 were benign.
Variants classified as pathogenic or of uncertain significance appeared in 16 of 174 men with abnormal sperm counts, against 0 of 67 men with normal counts (p = 0.007).

Interpretation

This is a single-center study that developed and tested a genetic panel. The study counts how often rare variants appear in a group of Italian men. Whether any variant causes low sperm counts remains open. The authors state that functional studies or animal models are needed. All 241 men had already passed standard genetic screening, and the study ran no head-to-head comparison with another test. The 67 men with normal counts came from the same group of 241 men whose infertility had no identified cause. The authors add that other genetic causes are possible and call for more genes and a larger cohort in future work.

RRM Context

Restorative reproductive medicine (RRM) looks for the cause of infertility in both partners. The authors note that a male factor is involved in about half of infertility cases. They also report that 30–60% of infertile men get no clear diagnosis. RRM calls that undiagnosed infertility and keeps looking for the cause. Gene panels like this one are candidate tools for that search.

Our editorial summary of this paper, not the article's abstract.

Abstract

Purpose

To develop and assess a novel custom next-generation sequencing (NGS) panel for male infertility genetic diagnosis.

Methods

A total of 241 subjects with diagnosis of idiopathic infertility ranging from azoospermia to normozoospermia were sequenced by a custom NGS panel including AR, FSHB, FSHR, KLHL10, NR5A1, NANOS1, SEPT12, SYCP3, TEX11 genes. Variants with minor allele frequency < 1% were confirmed by Sanger sequencing.

Results

Nineteen missense variants were detected in 23 subjects with abnormal sperm count, whilst no variants were identified in normozoospermic men. Of identified variants, we prioritized variants classified as pathogenic and of uncertain significance (VUS) (63.1%, 12/19). No missense variants were found in males with normal seminal parameters (0/67). Therefore, the prevalence of variants was significantly higher in patients with spermatogenic impairment (16/174 vs 0/67, p = 0.007).

Conclusion

This study confirms the utility to apply NGS panel for infertility diagnosis in order to find new genetic variants potentially linked to male infertility with much higher accuracy than standard tests suggested by guidelines. Indeed, based on biological significance, prevalence in the general population and clinical data of patients, it is plausible that identified variants in this study might be linked to quantitative spermatogenic impairment, although further studies are needed.

Topics

Male Fertility › Male Endocrine and Genetic Factors › Genetic Causes of Male Infertility · Genetics and Immunology › Reproductive Genetics › Single Gene Conditions

Maria Santa Rocca, Aichi Msaki, Marco Ghezzi, Ilaria Cosci, Kalliopi Pilichou, Rudy Celeghin, Carlo Foresta, Alberto Ferlin

M Rocca, A Msaki, M Ghezzi, I Cosci, K Pilichou, R Celeghin, C Foresta, A Ferlin

PMID 32242295 32242295 DOI 10.1007/s10815-020-01747-0 10.1007/s10815-020-01747-0 Rocca et al. 2020, Rocca 2020

Development of a novel next-generation sequencing panel for diagnosis of quantitative spermatogenic impairment

Gene panel finds rare variants in men with low or absent sperm counts

Key Findings

Interpretation

RRM Context

Abstract

Topics

By this author

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