Sequence analysis of 37 candidate genes for male infertility: challenges in variant assessment and validating genes

Abstract

Background The routine genetic analysis for diagnosing male infertility has not changed over the last twenty years, and currently available tests can only determine the etiology of 4% of unselected infertile patients. Thus, to create new diagnostic assays, we must better understand the molecular and genetic mechanisms of male infertility. Although next‐generation sequencing allows for simultaneous analysis of hundreds of genes and the discovery of novel candidates related to male infertility, so far only a few gene candidates have enough sound evidence to support the gene–disease relationship. Objective Since complementary studies are required to validate genes, we aimed to analyze the presence of potentially pathogenic rare variants in a set of candidate genes related to azoospermia in a hitherto understudied South American population. Subjects and Methods We performed whole exome sequencing in a group of 16 patients with non‐obstructive azoospermia from Ribeirão Preto, Brazil. Based on a recent systematic review of monogenic causes of male infertility, we selected a set of 37 genes related to azoospermia, Sertoli‐Cell‐Only histology, and spermatogenic arrest to analyze. The identified variants were confirmed by Sanger sequencing, and their functional consequence was predicted by in silico programs. Results We identified potential pathogenic variants in seven genes in six patients. Two variants, c.671A>G (p.(Asn224Ser)) in DMRT1 and c.91C>T (p.(Arg31Cys)) in REC8, have already been described in association with azoospermia. We also found new variants in genes that already have moderate evidence of being linked to spermatogenic failure (TEX15, KLHL10), in genes with limited evidence (DNMT3B, TEX14) and in one novel promising candidate gene that has no evidence so far (SYCE1L). Discussion Although this study included a small number of patients, the process of rationally selecting genes allowed us to detect rare potentially pathogenic variants, providing supporting evidence for validating candidate genes associated with azoospermia.

Genetic dissection of spermatogenic arrest through exome analysis: clinical implications for the management of azoospermic men

“…We identified two homozygous LoF variants in TEX14 in two unrelated patients affected by incomplete spermatogonial arrest. Previously reported TEX14 variants were associated with testis histology ranging from SCO to complete SCA 20 – 22 . With the discovery of the two new TEX14 variant carriers, this gene can now be upgraded to strong clinical evidence.…”

Genetic Landscape of Nonobstructive Azoospermia and New Perspectives for the Clinic

“…One year later, Tewes and colleagues [110] analysed the DMRT1 sequence in 131 individuals diagnosed with NOA and 215 normozoospermic controls, reporting two cases of NOA (one of them with SCO) that showed heterozygosity for a putative pathogenic transition mutation in the third exon of the gene. The DMRT1 mutation observed in the SCO patient was detected in another NOA individual from Brazil (from a total of 16 azoospermic patients analysed) in a recent study [111].…”

“…Colombo and colleagues [127] performed exome sequencing in two infertile siblings affected by NOA, identifying another nonsense mutation and a single nucleotide deletion that led to premature stop codons in the TEX15 locus. Finally, the recent sequencing study of 16 Brazilian patients affected by NOA by Araujo et al [111] also reported novel rare variants in both TEX14 and TEX15.…”

Role of genetics and epigenetics in male infertility

“…The ancestral mammalian Y chromosome lost a vast number of genes, which moved to autosomes during evolution (Hughes, Skaletsky, Koutseva, Pyntikova, & Page, 2015;Mendez, Poznik, Castellano, & Bustamante, 2016). Numerous studies have shown that several genes expressed in the testis are associated with fertility potential (Araujo et al, 2019;van der Bijl et al, 2019). The expression of inserted gene copies was reported to be increased in the testis, thus suggesting a possible function in spermatogenesis (Ropke et al, 2013).…”