The Role of Copy Number Variants in Severe Idiopathic Male Infertility

PhD ThesisVery few genetic variants are currently known to cause severe male infertility phenotypes in a dominant fashion. This is explained by an absence of cohorts of patient-parent trios, which impedes the study of this genetic inheritance model. It has been demonstrated that de novo copy number variants (CNVs) on chromosome Y cause severe male infertility, but up to now, such variants have not been identified on the autosomes. In this thesis, I used whole-exome sequencing (WES) in a large cohort of male infertility patient-parent trios to study the possible role of de novo and maternally inherited CNVs as causes of quantitative sperm defects. I also used the same method to identify likely pathogenic CNVs in two patients-only cohorts affected by quantitative as well as qualitative sperm defects. We identified several possibly causative de novo and maternally inherited CNVs, pointing us to novel candidate genes for male infertility. Moreover, my findings contributed to the identification of the first gene on chromosome X associated with a male infertility phenotype characterised by multiple morphological abnormalities of the sperm flagella. This study reveals unique insight into the genetic aetiology of severe male infertility. Also, it illustrates the value of WES as a tool for CNV detection and supports the increasing use of this genomic technique in the field of male infertility genetics

A de novo paradigm for male infertility

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. Germline de novo mutations can impact individual fitness, but their role in human male infertility is understudied. Trio-based exome sequencing identifies many new candidate genes affecting male fertility, including an essential regulator of male germ cell pre-mRNA splicing