Long-read whole genome sequencing (WGS) may help simplify the complex genetic testing pathway often required for couples with unexplained subfertility and recurrent pregnancy loss (RPL), according to a multicenter study published as a preprint on medRxiv.
The study evaluated HiFi long-read sequencing across 96 individuals recruited from fertility and genomic medicine centers in Singapore, Thailand, Taiwan, and South Korea. Researchers investigated whether a single long-read WGS assay could identify clinically relevant genetic variants linked to unexplained infertility, subfertility, or recurrent miscarriage.
Subfertility affects approximately one in six people worldwide, while recurrent pregnancy loss affects 1–2 percent of women. Genetic abnormalities are known contributors, but current diagnostic workflows often require multiple separate tests, including karyotyping, chromosomal microarray analysis, Fragile X testing, and exome or genome sequencing.
According to the authors, long-read sequencing can detect multiple classes of genomic variation in a single assay, including single nucleotide variants, insertions and deletions, copy number variants, structural rearrangements, repeat expansions, and methylation changes.
Participants enrolled in the study had unexplained subfertility or recurrent pregnancy loss after other known causes had been excluded. Among the 84 individuals who completed sequencing and analysis, pathogenic or likely pathogenic variants related to the primary condition were identified in 4.8 percent of individuals. Variants of uncertain significance were also identified in additional participants. Overall, the researchers estimated that approximately one in 10 affected couples carried a clinically significant genetic variant.
The identified variants were associated with conditions including premature ovarian insufficiency, spermatogenic failure, hypogonadotropic hypogonadism, and ovarian dysgenesis. Clinically relevant findings were detected in both male and female partners, supporting the value of testing both individuals during fertility evaluation.
The sequencing workflow achieved an average genome coverage depth of 34.6× and identified millions of genomic variants per individual, including structural variants that may be difficult to detect using conventional short-read sequencing approaches.
Researchers also reviewed secondary findings and carrier status. Among 74 individuals analyzed, one participant carried a pathogenic variant associated with hypercholesterolemia, while more than one-third were carriers of at least one recessive genetic condition.
“One of the biggest challenges in reproductive genomics today is that patients often undergo multiple fragmented tests that still fail to provide clear answers,” says lead researcher Saumya Jamuar. “As long-read sequencing technologies mature, we see increasing potential for laboratories to move beyond sequential testing strategies toward a unified genomic workflow that can provide deeper and more clinically meaningful insights for patients.”
The authors said the findings support the potential role of long-read WGS as a more comprehensive early diagnostic approach for couples with unexplained subfertility or recurrent pregnancy loss. However, they noted that balanced chromosomal rearrangements remain difficult to identify reliably using current long-read datasets, meaning conventional karyotyping may still be required.
The study also highlighted cost as an ongoing limitation, although the authors suggested that falling sequencing costs and improving bioinformatics tools may support broader clinical use in the future. Additional studies with larger patient cohorts will be needed to further assess diagnostic yield, clinical utility, and cost-effectiveness before first-line implementation can be established.
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