Mate-pair genome sequencing reveals structural variants for idiopathic male infertility

Abstract Currently, routine genetic investigation for males with infertility includes karyotyping analysis and PCR for Y chromosomal microdeletions to provide prognostic information such as sperm retrieval success rate. However, over 85% of the cases remain idiopathic. We assessed 101 males with primary infertility in a retrospective cohort analysis who have previously received negative results from standard-of-care tests. Mate-pair genome sequencing (with ~ 5kb DNA fragment-size), an alternative long-DNA sequencing method was performed to detect clinically significant structural variants (SVs) and copy-number neutral absence of heterozygosity (AOH). Candidate SVs were filtered against our in-house cohort of 1,077 fertile men, and potentially clinically significant variants were correlated with gene expression profiles from single-cell RNA-seq datasets that curated human fetal and postnatal testicular development and adult germ cells. Follow-up studies were conducted for each patient with clinically relevant finding(s). Molecular diagnoses were made for 15.9% (10/63) of patients with non-obstructive azoospermia and 21.1% (8/38) of patients with severe oligozoospermia, respectively. Among them, 17 clinically significant SVs were identified in 16 cases, including five well-known syndromes, two inversions, and 10 SVs with direct disruption of genes by intragenic rearrangements or complex insertions. Importantly, a genetic defect related to Intracytoplasmic Sperm Injection (ICSI) failure was identified in a non-obstructive azoospermia patient illustrating the additional value of an etiologic diagnosis in addition to determining sperm retrieval rate. Our study reveals a landscape of various genomic variants in 101 males with idiopathic infertility, not only advancing understanding of the underlying mechanisms of male infertility, but also impacting clinical management.