Abstract
Currently, routine genetic investigation for male infertility includes karyotyping analysis and PCR for Y chromosomal microdeletions to provide prognostic information such as sperm retrieval success rate. However, over 85% of male infertility remain idiopathic. We assessed 101 male patients with primary infertility in a retrospective cohort analysis who have previously received negative results from standard-of-care tests. Mate-pair genome sequencing (large-insert size library), 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 1077 fertile men. Genes disrupted by potentially clinically significant variants were correlated with single-cell gene expression profiles of human fetal and postnatal testicular developmental lineages and adult germ cells. Follow-up studies were conducted for each patient with clinically relevant finding(s). Molecular diagnoses were made in 11.1% (7/63) of patients with non-obstructive azoospermia and 13.2% (5/38) of patients with severe oligozoospermia. Among them, 12 clinically significant SVs were identified in 12 cases, including five known syndromes, one inversion, and six 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 patient with non-obstructive azoospermia, 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.
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Data sharing statement
The sequencing datasets generated during the current study are not publicly available because most patients did not consent to such sharing but are available from the corresponding author on reasonable request. All relative programs are publicly available: copy-number variant analysis at https://sourceforge.net/projects/increment-ratio-of-coverage-v2/files, structural variant analysis at https://sourceforge.net/projects/bca-analysis/files/ and absence of heterozygosity analysis at https://sourceforge.net/projects/lpgsaoh/files/.
Abbreviations
- CNV:
-
Copy-number variant
- SV:
-
Structural variant
- AOH:
-
Absence of heterozygosity
- IVF:
-
In vitro fertilization
- ICSI:
-
Intracytoplasmic sperm injection
- NOA:
-
Non-obstructive azoospermia
- GS:
-
Genome sequencing
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Acknowledgements
Drs. Dong and Cao acknowledge support from the Direct Grant, The Chinese University of Hong Kong. Dr. Morton acknowledges support from the NIHR Manchester Biomedical Research Centre.
Funding
This project is supported by the Natural Science Foundation of Guangdong Province, China (#2019A1515011042), the Health and Medical Research Fund (#09200236), and the Collaborative Research Fund (#C4062-21GF) and NIH P01 (#GM061354 to CCM).
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ZD, JQ, TSML and KWC designed this study. TSML, KN, DC, PKFC, CFN, CHSC, JSMM and JPWC collected samples. TYL and JPWC conducted genetic counselling. ZD, JQ, MHKC, YC and YKK conducted the analysis. JQ, SX, ST and YZ performed validation. ZD, JQ, TSML, CCM and KWC wrote the manuscript.
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Dong, Z., Qian, J., Law, T.S.M. et al. Mate-pair genome sequencing reveals structural variants for idiopathic male infertility. Hum Genet 142, 363–377 (2023). https://doi.org/10.1007/s00439-022-02510-4
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DOI: https://doi.org/10.1007/s00439-022-02510-4