Understanding Male Infertility Causes through Long-Read Sequencing

Thomas Garcia from Baylor College of Medicine spoke at the Nanopore Community Meeting in Boston on “Long-read sequencing for comprehensive profiling of infertile men.” There are pre and post-testicular causes of infertility, Garcia mentioned. Pre-testicular causes include Kallmann syndrome, Beta thalassemia, and sickle disease. Intrinsic testicular causes of infertility include chromosomal abnormalities, Y-chromosome microdeletions/duplications, and monogenic causes. Post-testicular causes, Garcia explained, include cystic fibrosis. Karyotyping, y-chromosome microdeletion testing, and CFTR gene mutation testing are recommended based on guidance from the 2021 AUA/ASRM Guidelines. Garcia used the PromethION flow cells and LSK114 kit to obtain >30X coverage and >100 Gbases per male. They used the EPI2ME human variation workflow to analyze SNVs, SVs, and CNVs. One case study that Garcia shared was a 27-year-old male with delayed puberty, low testosterone, and azoospermia. Sequencing identified a mutation that was found to cause the phenotype. In other cases, Garcia shared how they found a variant that was annotated as benign but was incorrect. Their literature reviews helped identify errors in ClinVar. In another case, Garcia identified the loss of an entire long arm of the y-chromosome that the clinical lab PCR-based systems missed. Garcia ended by stating how long-read sequencing is very informative and helps to build better detection and diagnosis systems.

How does long-read sequencing help improve the diagnosis of male infertility? AI-generated image.