A de novo paradigm for male infertility

Abstract

De novo mutations are known to play a prominent role in sporadic disorders with reduced fitness. We hypothesize that de novo mutations play an important role in severe male infertility and explain a portion of the genetic causes of this understudied disorder. To test this hypothesis, we utilize trio-based exome sequencing in a cohort of 185 infertile males and their unaffected parents. Following a systematic analysis, 29 of 145 rare (MAF < 0.1%) protein-altering de novo mutations are classified as possibly causative of the male infertility phenotype. We observed a significant enrichment of loss-of-function de novo mutations in loss-of-function-intolerant genes (p-value = 1.00 × 10−5) in infertile men compared to controls. Additionally, we detected a significant increase in predicted pathogenic de novo missense mutations affecting missense-intolerant genes (p-value = 5.01 × 10−4) in contrast to predicted benign de novo mutations. One gene we identify, RBM5, is an essential regulator of male germ cell pre-mRNA splicing and has been previously implicated in male infertility in mice. In a follow-up study, 6 rare pathogenic missense mutations affecting this gene are observed in a cohort of 2,506 infertile patients, whilst we find no such mutations in a cohort of 5,784 fertile men (p-value = 0.03). Our results provide evidence for the role of de novo mutations in severe male infertility and point to new candidate genes affecting fertility.

Phasing of de novo mutations using a scaled‐up multiple amplicon long‐read sequencing approach

“…In our cohort of 77 patients, 51 patients were confirmed to suffer from nonobstructive severe oligospermic or azoospermic phenotypes. In the original publication related to this study (Oud et al, 2022), we showed that six out of the eight likely causative DNMs identified in these patients were of paternal origin (Supporting Information: Tables S9 and S14, Figure S7). As DNMs predominantly cause a dominant effect, it suggests that DNMs with a deleterious effect on the health of an individual can escape negative selection in spermatids from the paternal germline.…”

“…). It has been shown that approximately 80% of DNMs are of paternal origin (Goldmann et al, 2016;Kong et al, 2012;Oud et al, 2022;Yuen et al, 2016). A major factor known to contribute to an increase in DMNs in individuals is advanced parental age at the time of conception, particularly paternal age (Goldmann et al, 2016;Kong et al, 2012).…”

“…However, despite these challenges with longrange PCR enrichment, the approach is arguably more effective for scaled-up targeted phasing at present. This study aims to identify the DNM parent-of-origin and zygosity using a targeted long-range and standard PCR approach for phasing 109 distinct DNMs previously identified in infertile men by patient-parent trio exome sequencing (Oud et al, 2022). Targeted amplification of regions encompassing each unique DNM is performed using an optimized PCR workflow designed to quickly increase PCR success rates and reduce presequencing base error from standard and long-range PCR.…”

Diverse monogenic subforms of human spermatogenic failure

“…Second, we provide a higher confidence list of 21 genes which have all been observed in multiple NOA cases and have nominally significant association with NOA in a comparison with 11,587 fertile controls (Supplementary Table 4 ). The observed detection rate of possible causes of NOA in GEMINI (20%) remains a conservative estimate, as our approach did not consider genes exclusively involved in fetal gonad development, excluded genes with broad expression across the body, and did not address dominant or additive defects likely to contribute to the manifestation of NOA as well 47 , 48 . A more detailed analysis of X-linked genes is reported in a companion paper focusing exclusively on the X chromosome, using a different method of prioritization than described here 49 .…”

Genetic landscape of a large cohort of Primary Ovarian Insufficiency: New genes and pathways and implications for personalized medicine

“…It should be noted that in our study, the segregation of the identified variants could only be achieved in 40% of cases because the parents were not available for the other patients. The absence of available trios has hampered the assessment of de novo mutations that might explain a subset of POI as has been observed in infertile men 66 or other conditions 67 and may improve the diagnostic performance of NGS studies in POI.…”