The landscape of structural variants in male infertility identified by optical genome mapping

Abstract We aimed to determine what kind of structural genomic variants can be detected by optical genome mapping in patients with male infertility and whether such variants may contribute to male infertility. We performed a longitudinal case/control genetic study on patients with male infertility, negative for cytogenetic abnormalities using karyotyping, and molecular testing for chrY microdeletions, and CFTR gene variants, and compared them to healthy male individuals that underwent optical genomic mapping for other reasons. We tested a total of 220 individuals; 88 patients with male infertility and 132 control males. Exclusion criteria for the control cohort were low-sperm quality, known presence of cytogenetic rearrangements and/or inclusion in IVF procedures. We examined structural variants in 220 participants by using optical genome mapping, which was performed with DLE-1 SP-G2 chemistry and the Saphyr instrument. The de novo assembly and Variant Annotation Pipeline were executed on Bionano Solve3.7_20221013_25 while reporting and direct visualization of structural variants was done on Bionano Access 1.7.2. The male infertility cohort also underwent research whole exome analyses as previously reported. Results of optical genomic mapping were validated by multiple appropriate alternative methods where possible. We show that the overall number of structural variants in male infertility patients does not differ from that of healthy individuals. By looking in detail at genes and regions associated with MI, we identified 22 rare variants absent from controls in 25.0% of male infertility patients, of which five were likely causative, and two would be missed by using traditional approaches. These variants include inversions, duplications, amplifications, deletions (e.g. SPAG1 ), and insertions/expansions (e.g. DMPK ), that were validated using additional methods. Optical genome mapping can identify rare SV in male infertility patients that are absent from healthy controls. Most of the identified structural genomic variants cannot be currently classified as causative according to strict diagnostic criteria, and require a further functional characterization. Nevertheless, these findings open a new avenue in genetic research of SV involvement in MI.