Whole genome sequencing approach for the detection of rare protein-altering variants associated with familial male infertility

Abstract Background Whole-genome sequencing (WGS) is an efficient, accurate, and high-throughput technique used for the discovery of exonic as well as non-exonic variants causing different genetic anomalies, improving clinical management for the disease. This study was designed to evaluate pathogenic genetic variants related to male infertility in male infertile families in remote rural areas of Pakistan. Methods For the five families recruited, WGS was conducted on 14 patients and 6healthy controls. WGS was performed using the Illumina TruSeq DNA Nano Library Prep workflow protocol. DNA was assessed with TapeStation and sequenced using the TruSeq kit (Illumina). Bioinformatics tools were then used to identify potential causative variants, including indels and single-nucleotide variants. Results In family 1, five homozygous nonsynonymous SNVs were identified in FMR1 , PHF8 , TOPBP1 , and DAB2IP . These X-linked or recessive variants cause amino acid changes that affect key cellular pathways. In family 10, homozygous nonsynonymous SNVs were detected in FOS , MIR452 , PDHA1 , and SERPINB1 , implicating roles in structural, transcriptional, metabolic, and synaptic processes. In family 11, a frameshift deletion in PRDM9 and nonsynonymous SNVs in KIAA1210 , suggesting possible disruption of gene regulation and protein stability. In family 13, multiple nonsynonymous variants were identified in SPATA20 , and G6PD ,, with implications in reproductive function, angiogenesis, enzymatic activity, and neuromuscular disorders. SNV Variant was detected in SLC12A4 in Family 15. Conclusion The study contributes to a systematic understanding of the problem and provides a basis for identifying causal variations in idiopathic cases of male infertility, setting targets for future therapeutic development.