9dd2c156aedfe1b408b2f8f430dab829 310171.pdf 6f90aa7d7f556702c8c62294f7186acc5e897eea 310171.pdf 583a75410d6b2cf71d9bd12a563ec95dce0d785282d9580dd0d436c300874b38 310171.pdf Title: A comprehensive study of common and rare genetic variants in spermatogenesis-related loci identifies new risk factors for idiopathic severe spermatogenic failure Subject: Doi: 10.1093/hropen/hoae069 Human Reproduction Open, 2024, 4, 2024 Publication Date: 13/11/2024 Abstract STUDY QUESTION Can genome-wide genotyping data be analysed using a hypothesis-driven approach to enhance the understanding of the genetic basis of severe spermatogenic failure (SPGF) in male infertility?SUMMARY ANSWER Our findings revealed a significant association between SPGF and the SHOC1 gene and identified three novel genes (PCSK4, AP3B1, and DLK1) along with 32 potentially pathogenic rare variants in 30 genes that contribute to this condition.WHAT IS KNOWN ALREADY SPGF is a major cause of male infertility, often with an unknown aetiology. SPGF can be due to either multifactorial causes, including both common genetic variants in multiple genes and environmental factors, or highly damaging rare variants. Next-generation sequencing methods are useful for identifying rare mutations that explain monogenic forms of SPGF. Genome-wide association studies (GWASs) have become essential approaches for deciphering the intricate genetic landscape of complex diseases, offering a cost-effective and rapid means to genotype millions of genetic variants. Novel methods have demonstrated that GWAS datasets can be used to infer rare coding variants that are causal for male infertility phenotypes. However, this approach has not been previously applied to characterize the genetic component of a whole case–control cohort.STUDY DESIGN, SIZE, DURATION We employed a hypothesis-driven approach focusing on all genetic variation identified, using a GWAS platform and subsequent genotype imputation, encompassing over 20 million polymorphisms and a total of 1571 SPGF patients and 2431 controls. Both common (minor allele frequency, MAF > 0.01) and rare (MAF < 0.01) variants were investigated within a total of 1797 loci with a reported role in spermatogenesis. This gene panel was meticulously assembled through comprehensive searches in the literature and various databases focused on male infertility genetics.PARTICIPANTS/MATERIALS, SETTING, METHODS This study involved a European cohort using previously and newly generated data. Our analysis consisted of three independent methods: (i) variant-wise association analyses using logistic regression models, (ii) gene-wise association analyses using combined multivariate and collapsing burden tests, and (iii) identification and characterisation of highly damaging rare coding variants showing homozygosity only in SPGF patients.MAIN RESULTS AND THE ROLE OF CHANCE The variant-wise analyses revealed an association between SPGF and SHOC1-rs12347237 (P = 4.15E−06, odds ratio = 2.66), which was likely explained by an altered binding affinity of key transcription factors in regulatory regions and the disruptive effect of coding variants within the gene. Three additional genes (PCSK4, AP3B1, and DLK1) were identified as novel relevant players in human male infertility using the gene-wise burden test approach (P < 5.56E−04). Furthermore, we linked a total of 32 potentially pathogenic and recessive coding variants of the selected genes to 35 different cases.LARGE SCALE DATA Publicly available via GWAS catalog (accession number: GCST90239721).LIMITATIONS, REASONS FOR CAUTION The analysis of low-frequency variants presents challenges in achieving sufficient statistical power to detect genetic associations. Consequently, independent studies with larger sample sizes are essential to replicate our results. Additionally, the specific roles of the identified variants in the pathogenic mechanisms of SPGF should be assessed through functional experiments.WIDER IMPLICATIONS OF THE FINDINGS Our findings highlight the benefit of using GWAS genotyping to screen for both common and rare variants potentially implicated in idiopathic cases of SPGF, whether due to complex or monogenic causes. The discovery of novel genetic risk factors for SPGF and the elucidation of the underlying genetic causes provide new perspectives for personalized medicine and reproductive counselling.STUDY FUNDING/COMPETING INTEREST(S) This work was supported by the Spanish Ministry of Science and Innovation through the Spanish National Plan for Scientific and Technical Research and Innovation (PID2020-120157RB-I00) and the Andalusian Government through the research projects of ‘Plan Andaluz de Investigación, Desarrollo e Innovación (PAIDI 2020)’ (ref. PY20_00212) and ‘Proyectos de Investigación aplicada FEDER-UGR 2023’ (ref. C-CTS-273-UGR23). S.G.-M. was funded by the previously mentioned projects (ref. PY20_00212 and PID2020-120157RB-I00). A.G.-J. was funded by MCIN/AEI/10.13039/501100011033 and FSE ‘El FSE invierte en tu futuro’ (grant ref. FPU20/02926). IPATIMUP integrates the i3S Research Unit, which is partially supported by the Portuguese Foundation for Science and Technology (FCT), financed by the European Social Funds (COMPETE-FEDER) and National Funds (projects PEstC/SAU/LA0003/2013 and POCI-01-0145-FEDER-007274). S.S. is supported by FCT funds (10.54499/DL57/2016/CP1363/CT0019), ToxOmics-Centre for Toxicogenomics and Human Health, Genetics, Oncology and Human Toxicology, and is also partially supported by the Portuguese Foundation for Science and Technology (UIDP/00009/2020 and UIDB/00009/2020). S. Larriba received support from Instituto de Salud Carlos III (grant: DTS18/00101), co-funded by FEDER funds/European Regional Development Fund (ERDF)—a way to build Europe) and from ‘Generalitat de Catalunya’ (grant 2021SGR052). S. Larriba is also sponsored by the ‘Researchers Consolidation Program’ from the SNS-Dpt. Salut Generalitat de Catalunya (Exp. CES09/020). All authors declare no conflict of interest related to this study. Keywords: spermatogenesis; idiopathic spermatogenic failure; genetics; male infertility; polygenic susceptibility; monogenic mutations Creator: Servigistics Arbortext Advanced Print Publisher 11.1.4667/W Producer: PDFlib+PDI 9.0.7p3 (C++/Win32) CreationDate: Fri Nov 29 08:34:32 2024 CET ModDate: Fri Nov 29 08:34:42 2024 CET Custom Metadata: yes Metadata Stream: yes Tagged: yes UserProperties: no Suspects: no Form: none JavaScript: no Pages: 12 Encrypted: no Page size: 612 x 792 pts (letter) Page rot: 0 File size: 1336272 bytes Optimized: no PDF version: 1.5 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- XMMKFD+CaeciliaLTStd-Bold Type 1C Custom yes yes yes 1317 0 MFLIMS+CaeciliaLTStd-Roman Type 1C Custom yes yes yes 1322 0 TeX_CM_Roman Type 1 Builtin yes no yes 1327 0 TeX_CM_Maths_Symbols Type 1 Builtin yes no yes 1331 0 HMFMAP+CaeciliaLTStd-Light Type 1C Custom yes yes yes 1335 0 LAOMZA+CaeciliaLTStd-Heavy Type 1C Custom yes yes yes 1340 0 LGZQYS+CaeciliaLTStd-Italic Type 1C Custom yes yes yes 1345 0 QATUCC+STIX-Regular Type 1C Custom yes yes yes 1350 0 TeX_CM_Maths_Italic Type 1 Builtin yes no yes 54 0 TFDTCE+STIXTwoMath-Regular CID TrueType Identity-H yes yes yes 58 0 AIKSFZ+CaeciliaLTStd-LightItalic Type 1C Custom yes yes yes 63 0 SNSHHX+CaeciliaLTStd-BoldItalic Type 1C Custom yes yes yes 142 0 QNDZZS+STIX-Bold Type 1C Custom yes yes yes 191 0 Jhove (Rel. 1.28.0, 2023-05-18) Date: 2025-04-04 02:43:18 CEST RepresentationInformation: 310171.pdf ReportingModule: PDF-hul, Rel. 1.12.4 (2023-03-16) LastModified: 2025-04-03 14:11:40 CEST Size: 1336272 Format: PDF Version: 1.5 Status: Well-Formed, but not valid SignatureMatches: PDF-hul ErrorMessage: Invalid indirect destination - referenced object 'lhoae069-FM2' cannot be found ID: PDF-HUL-149 ErrorMessage: Invalid indirect destination - referenced object 'lhoae069-FM1' cannot be found ID: PDF-HUL-149 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'lhoae069-FM1' cannot be found ID: PDF-HUL-122 Offset: 1208250 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'lhoae069-FM2' cannot be found ID: PDF-HUL-122 Offset: 1208250 MIMEtype: application/pdf Profile: Tagged PDF PDFMetadata: Objects: 1444 FreeObjects: 1 IncrementalUpdates: 2 DocumentCatalog: ViewerPreferences: HideToolbar: false HideMenubar: false HideWindowUI: false FitWindow: false CenterWindow: false DisplayDocTitle: true NonFullScreenPageMode: UseNone Direction: L2R ViewArea: CropBox ViewClip: CropBox PrintArea: CropBox PageClip: CropBox PageLayout: SinglePage PageMode: UseOutlines Language: en Outlines: Item: Title: Active Content List Destination: mkchap_artid Children: Item: Title: Introduction Destination: mkchap11__sec Item: Title: Materials and methods Destination: mkchap12__sec Item: Title: Results Destination: mkchap19__sec Item: Title: Discussion Destination: mkchap24__sec Item: Title: Supplementary data Destination: mkchap25__sec Item: Title: Data availability Destination: mkchap26__sec Item: Title: Acknowledgements Destination: mkchap27_ack1_ack Item: Title: Authors' roles Destination: mkchap27__sec Item: Title: Funding Destination: mkchap28__sec Item: Title: Conflict of interest Destination: mkchap29__sec Item: Title: References Destination: mkchap30_ref1_ref-list Info: Title: A comprehensive study of common and rare genetic variants in spermatogenesis-related loci identifies new risk factors for idiopathic severe spermatogenic failure Subject: Doi: 10.1093/hropen/hoae069 Human Reproduction Open, 2024, 4, 2024 Publication Date: 13/11/2024 Abstract STUDY QUESTION Can genome-wide genotyping data be analysed using a hypothesis-driven approach to enhance the understanding of the genetic basis of severe spermatogenic failure (SPGF) in male infertility?SUMMARY ANSWER Our findings revealed a significant association between SPGF and the SHOC1 gene and identified three novel genes (PCSK4, AP3B1, and DLK1) along with 32 potentially pathogenic rare variants in 30 genes that contribute to this condition.WHAT IS KNOWN ALREADY SPGF is a major cause of male infertility, often with an unknown aetiology. SPGF can be due to either multifactorial causes, including both common genetic variants in multiple genes and environmental factors, or highly damaging rare variants. Next-generation sequencing methods are useful for identifying rare mutations that explain monogenic forms of SPGF. Genome-wide association studies (GWASs) have become essential approaches for deciphering the intricate genetic landscape of complex diseases, offering a cost-effective and rapid means to genotype millions of genetic variants. Novel methods have demonstrated that GWAS datasets can be used to infer rare coding variants that are causal for male infertility phenotypes. However, this approach has not been previously applied to characterize the genetic component of a whole case–control cohort.STUDY DESIGN, SIZE, DURATION We employed a hypothesis-driven approach focusing on all genetic variation identified, using a GWAS platform and subsequent genotype imputation, encompassing over 20 million polymorphisms and a total of 1571 SPGF patients and 2431 controls. Both common (minor allele frequency, MAF > 0.01) and rare (MAF < 0.01) variants were investigated within a total of 1797 loci with a reported role in spermatogenesis. This gene panel was meticulously assembled through comprehensive searches in the literature and various databases focused on male infertility genetics.PARTICIPANTS/MATERIALS, SETTING, METHODS This study involved a European cohort using previously and newly generated data. Our analysis consisted of three independent methods: (i) variant-wise association analyses using logistic regression models, (ii) gene-wise association analyses using combined multivariate and collapsing burden tests, and (iii) identification and characterisation of highly damaging rare coding variants showing homozygosity only in SPGF patients.MAIN RESULTS AND THE ROLE OF CHANCE The variant-wise analyses revealed an association between SPGF and SHOC1-rs12347237 (P = 4.15E−06, odds ratio = 2.66), which was likely explained by an altered binding affinity of key transcription factors in regulatory regions and the disruptive effect of coding variants within the gene. Three additional genes (PCSK4, AP3B1, and DLK1) were identified as novel relevant players in human male infertility using the gene-wise burden test approach (P < 5.56E−04). Furthermore, we linked a total of 32 potentially pathogenic and recessive coding variants of the selected genes to 35 different cases.LARGE SCALE DATA Publicly available via GWAS catalog (accession number: GCST90239721).LIMITATIONS, REASONS FOR CAUTION The analysis of low-frequency variants presents challenges in achieving sufficient statistical power to detect genetic associations. Consequently, independent studies with larger sample sizes are essential to replicate our results. Additionally, the specific roles of the identified variants in the pathogenic mechanisms of SPGF should be assessed through functional experiments.WIDER IMPLICATIONS OF THE FINDINGS Our findings highlight the benefit of using GWAS genotyping to screen for both common and rare variants potentially implicated in idiopathic cases of SPGF, whether due to complex or monogenic causes. The discovery of novel genetic risk factors for SPGF and the elucidation of the underlying genetic causes provide new perspectives for personalized medicine and reproductive counselling.STUDY FUNDING/COMPETING INTEREST(S) This work was supported by the Spanish Ministry of Science and Innovation through the Spanish National Plan for Scientific and Technical Research and Innovation (PID2020-120157RB-I00) and the Andalusian Government through the research projects of ‘Plan Andaluz de Investigación, Desarrollo e Innovación (PAIDI 2020)’ (ref. PY20_00212) and ‘Proyectos de Investigación aplicada FEDER-UGR 2023’ (ref. C-CTS-273-UGR23). S.G.-M. was funded by the previously mentioned projects (ref. PY20_00212 and PID2020-120157RB-I00). A.G.-J. was funded by MCIN/AEI/10.13039/501100011033 and FSE ‘El FSE invierte en tu futuro’ (grant ref. FPU20/02926). IPATIMUP integrates the i3S Research Unit, which is partially supported by the Portuguese Foundation for Science and Technology (FCT), financed by the European Social Funds (COMPETE-FEDER) and National Funds (projects PEstC/SAU/LA0003/2013 and POCI-01-0145-FEDER-007274). S.S. is supported by FCT funds (10.54499/DL57/2016/CP1363/CT0019), ToxOmics-Centre for Toxicogenomics and Human Health, Genetics, Oncology and Human Toxicology, and is also partially supported by the Portuguese Foundation for Science and Technology (UIDP/00009/2020 and UIDB/00009/2020). S. Larriba received support from Instituto de Salud Carlos III (grant: DTS18/00101), co-funded by FEDER funds/European Regional Development Fund (ERDF)—a way to build Europe) and from ‘Generalitat de Catalunya’ (grant 2021SGR052). S. Larriba is also sponsored by the ‘Researchers Consolidation Program’ from the SNS-Dpt. Salut Generalitat de Catalunya (Exp. CES09/020). All authors declare no conflict of interest related to this study. Keywords: spermatogenesis; idiopathic spermatogenic failure; genetics; male infertility; polygenic susceptibility; monogenic mutations Creator: Servigistics Arbortext Advanced Print Publisher 11.1.4667/W Producer: PDFlib+PDI 9.0.7p3 (C++/Win32) CreationDate: Fri Nov 29 09:04:32 CET 2024 ModDate: Fri Nov 29 09:04:42 CET 2024 ID: 0x4769bd7f9a9759da158dbefcc73c4259, 0x241cd3caa04a0eb13285264a263c1a22 Filters: FilterPipeline: DCTDecode Images: Image: NisoImageMetadata: FormatName: image/jpg CompressionScheme: JPEG ImageWidth: 2000 ImageHeight: 1032 BitsPerSample: 8 BitsPerSampleUnit: integer Image: NisoImageMetadata: FormatName: image/jpg CompressionScheme: JPEG ImageWidth: 2000 ImageHeight: 746 BitsPerSample: 8 BitsPerSampleUnit: integer Image: NisoImageMetadata: FormatName: image/jpg CompressionScheme: JPEG ImageWidth: 1750 ImageHeight: 933 BitsPerSample: 8 BitsPerSampleUnit: integer Fonts: Type0: Font: BaseFont: TFDTCE+STIXTwoMath-Regular Encoding: Identity-H ToUnicode: true Type1: Font: BaseFont: LGZQYS+CaeciliaLTStd-Italic FontSubset: true FirstChar: 1 LastChar: 29 FontDescriptor: FontName: LGZQYS+CaeciliaLTStd-Italic Flags: Nonsymbolic, Italic FontBBox: -166, -270, 1053, 915 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true ToUnicode: true Font: BaseFont: TeX_CM_Maths_Symbols FirstChar: 1 LastChar: 138 FontDescriptor: FontName: TeX_CM_Maths_Symbols Flags: Symbolic FontBBox: -50, -180, 1000, 720 FontFile: true ToUnicode: true Font: BaseFont: XMMKFD+CaeciliaLTStd-Bold FontSubset: true FirstChar: 1 LastChar: 62 FontDescriptor: FontName: XMMKFD+CaeciliaLTStd-Bold Flags: Nonsymbolic, ForceBold FontBBox: -166, -273, 1141, 938 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true ToUnicode: true Font: BaseFont: QATUCC+STIX-Regular FontSubset: true FirstChar: 1 LastChar: 1 FontDescriptor: FontName: QATUCC+STIX-Regular Flags: Nonsymbolic FontBBox: -970, -486, 2208, 1023 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true ToUnicode: true Font: BaseFont: TeX_CM_Maths_Italic FirstChar: 1 LastChar: 127 FontDescriptor: FontName: TeX_CM_Maths_Italic Flags: Symbolic FontBBox: -50, -180, 1000, 720 FontFile: true ToUnicode: true Font: BaseFont: HMFMAP+CaeciliaLTStd-Light FontSubset: true FirstChar: 1 LastChar: 89 FontDescriptor: FontName: HMFMAP+CaeciliaLTStd-Light Flags: Nonsymbolic FontBBox: -164, -266, 1130, 908 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true ToUnicode: true Font: BaseFont: MFLIMS+CaeciliaLTStd-Roman FontSubset: true FirstChar: 1 LastChar: 79 FontDescriptor: FontName: MFLIMS+CaeciliaLTStd-Roman Flags: Nonsymbolic FontBBox: -167, -270, 1136, 926 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true ToUnicode: true Font: BaseFont: LAOMZA+CaeciliaLTStd-Heavy FontSubset: true FirstChar: 1 LastChar: 65 FontDescriptor: FontName: LAOMZA+CaeciliaLTStd-Heavy Flags: Nonsymbolic, ForceBold FontBBox: -170, -277, 1146, 970 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true ToUnicode: true Font: BaseFont: SNSHHX+CaeciliaLTStd-BoldItalic FontSubset: true FirstChar: 1 LastChar: 19 FontDescriptor: FontName: SNSHHX+CaeciliaLTStd-BoldItalic Flags: Nonsymbolic, Italic, ForceBold FontBBox: -169, -273, 1082, 932 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true ToUnicode: true Font: BaseFont: TeX_CM_Roman FirstChar: 1 LastChar: 127 FontDescriptor: FontName: TeX_CM_Roman Flags: Symbolic FontBBox: -50, -180, 1000, 720 FontFile: true ToUnicode: true Font: BaseFont: AIKSFZ+CaeciliaLTStd-LightItalic FontSubset: true FirstChar: 1 LastChar: 58 FontDescriptor: FontName: AIKSFZ+CaeciliaLTStd-LightItalic Flags: Nonsymbolic, Italic FontBBox: -166, -267, 1033, 909 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true ToUnicode: true Font: BaseFont: QNDZZS+STIX-Bold FontSubset: true FirstChar: 1 LastChar: 1 FontDescriptor: FontName: QNDZZS+STIX-Bold Flags: Nonsymbolic, ForceBold FontBBox: -998, -552, 2000, 1055 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true ToUnicode: true CIDFontType2: Font: BaseFont: TFDTCE+STIXTwoMath-Regular CIDSystemInfo: Registry: Adobe Registry: Identity Supplement: 0 FontDescriptor: FontName: TFDTCE+STIXTwoMath-Regular Flags: Nonsymbolic FontBBox: -978, -1641, 3072, 2627 FontFile2: true XMP: uuid:fb9eec24-579c-2871-771c-dedfae05cf6a uuid:F5680D21-60AE-1851-CE42-0F80290B6476 2024-11-29T13:04:32+05:30 2024-11-29T13:04:42+05:30 Servigistics Arbortext Advanced Print Publisher 11.1.4667/W 2024-11-29T13:04:42+05:30 PDFlib+PDI 9.0.7p3 (C++/Win32) spermatogenesis; idiopathic spermatogenic failure; genetics; male infertility; polygenic susceptibility; monogenic mutations A comprehensive study of common and rare genetic variants in spermatogenesis-related loci identifies new risk factors for idiopathic severe spermatogenic failure Andrea Guzmán-Jiménez Sara González-Muñoz Miriam Cerván-Martín Nicolás Garrido José A Castilla M Carmen Gonzalvo Ana Clavero Marta Molina Saturnino Luján Samuel Santos-Ribeiro Miguel Ángel Vilches Andrea Espuch Vicente Maldonado Noelia Galiano-Gutiérrez Esther Santamaría-López Cristina González-Ravina Fernando Quintana-Ferraz Susana Gómez David Amorós Luis Martínez-Granados Yanira Ortega-González Miguel Burgos Iris Pereira-Caetano Ozgur Bulbul Stefano Castellano Massimo Romano Elena Albani Lluís Bassas Susana Seixas João Gonçalves Alexandra M Lopes Sara Larriba Rogelio J Palomino-Morales F David Carmona Lara Bossini-Castillo Doi: 10.1093/hropen/hoae069 Human Reproduction Open, 2024, 4, 2024 Publication Date: 13/11/2024 Abstract STUDY QUESTION Can genome-wide genotyping data be analysed using a hypothesis-driven approach to enhance the understanding of the genetic basis of severe spermatogenic failure (SPGF) in male infertility?SUMMARY ANSWER Our findings revealed a significant association between SPGF and the SHOC1 gene and identified three novel genes (PCSK4, AP3B1, and DLK1) along with 32 potentially pathogenic rare variants in 30 genes that contribute to this condition.WHAT IS KNOWN ALREADY SPGF is a major cause of male infertility, often with an unknown aetiology. SPGF can be due to either multifactorial causes, including both common genetic variants in multiple genes and environmental factors, or highly damaging rare variants. Next-generation sequencing methods are useful for identifying rare mutations that explain monogenic forms of SPGF. Genome-wide association studies (GWASs) have become essential approaches for deciphering the intricate genetic landscape of complex diseases, offering a cost-effective and rapid means to genotype millions of genetic variants. Novel methods have demonstrated that GWAS datasets can be used to infer rare coding variants that are causal for male infertility phenotypes. However, this approach has not been previously applied to characterize the genetic component of a whole case–control cohort.STUDY DESIGN, SIZE, DURATION We employed a hypothesis-driven approach focusing on all genetic variation identified, using a GWAS platform and subsequent genotype imputation, encompassing over 20 million polymorphisms and a total of 1571 SPGF patients and 2431 controls. Both common (minor allele frequency, MAF > 0.01) and rare (MAF < 0.01) variants were investigated within a total of 1797 loci with a reported role in spermatogenesis. This gene panel was meticulously assembled through comprehensive searches in the literature and various databases focused on male infertility genetics.PARTICIPANTS/MATERIALS, SETTING, METHODS This study involved a European cohort using previously and newly generated data. Our analysis consisted of three independent methods: (i) variant-wise association analyses using logistic regression models, (ii) gene-wise association analyses using combined multivariate and collapsing burden tests, and (iii) identification and characterisation of highly damaging rare coding variants showing homozygosity only in SPGF patients.MAIN RESULTS AND THE ROLE OF CHANCE The variant-wise analyses revealed an association between SPGF and SHOC1-rs12347237 (P = 4.15E−06, odds ratio = 2.66), which was likely explained by an altered binding affinity of key transcription factors in regulatory regions and the disruptive effect of coding variants within the gene. Three additional genes (PCSK4, AP3B1, and DLK1) were identified as novel relevant players in human male infertility using the gene-wise burden test approach (P < 5.56E−04). Furthermore, we linked a total of 32 potentially pathogenic and recessive coding variants of the selected genes to 35 different cases.LARGE SCALE DATA Publicly available via GWAS catalog (accession number: GCST90239721).LIMITATIONS, REASONS FOR CAUTION The analysis of low-frequency variants presents challenges in achieving sufficient statistical power to detect genetic associations. Consequently, independent studies with larger sample sizes are essential to replicate our results. Additionally, the specific roles of the identified variants in the pathogenic mechanisms of SPGF should be assessed through functional experiments.WIDER IMPLICATIONS OF THE FINDINGS Our findings highlight the benefit of using GWAS genotyping to screen for both common and rare variants potentially implicated in idiopathic cases of SPGF, whether due to complex or monogenic causes. The discovery of novel genetic risk factors for SPGF and the elucidation of the underlying genetic causes provide new perspectives for personalized medicine and reproductive counselling.STUDY FUNDING/COMPETING INTEREST(S) This work was supported by the Spanish Ministry of Science and Innovation through the Spanish National Plan for Scientific and Technical Research and Innovation (PID2020-120157RB-I00) and the Andalusian Government through the research projects of ‘Plan Andaluz de Investigación, Desarrollo e Innovación (PAIDI 2020)’ (ref. PY20_00212) and ‘Proyectos de Investigación aplicada FEDER-UGR 2023’ (ref. C-CTS-273-UGR23). S.G.-M. was funded by the previously mentioned projects (ref. PY20_00212 and PID2020-120157RB-I00). A.G.-J. was funded by MCIN/AEI/10.13039/501100011033 and FSE ‘El FSE invierte en tu futuro’ (grant ref. FPU20/02926). IPATIMUP integrates the i3S Research Unit, which is partially supported by the Portuguese Foundation for Science and Technology (FCT), financed by the European Social Funds (COMPETE-FEDER) and National Funds (projects PEstC/SAU/LA0003/2013 and POCI-01-0145-FEDER-007274). S.S. is supported by FCT funds (10.54499/DL57/2016/CP1363/CT0019), ToxOmics-Centre for Toxicogenomics and Human Health, Genetics, Oncology and Human Toxicology, and is also partially supported by the Portuguese Foundation for Science and Technology (UIDP/00009/2020 and UIDB/00009/2020). S. Larriba received support from Instituto de Salud Carlos III (grant: DTS18/00101), co-funded by FEDER funds/European Regional Development Fund (ERDF)—a way to build Europe) and from ‘Generalitat de Catalunya’ (grant 2021SGR052). S. Larriba is also sponsored by the ‘Researchers Consolidation Program’ from the SNS-Dpt. Salut Generalitat de Catalunya (Exp. CES09/020). All authors declare no conflict of interest related to this study. © The Author(s) 2024. Published by Oxford University Press on behalf of European Society of Human Reproduction and Embryology. spermatogenesis idiopathic spermatogenic failure genetics male infertility polygenic susceptibility monogenic mutations application/pdf PStill version 1.84.42 True 3 A http://ns.adobe.com/pdf/1.3/ pdf Adobe PDF Schema internal A name object indicating whether the document has been modified to include trapping information Trapped Text http://ns.adobe.com/xap/1.0/mm/ xmpMM XMP Media Management Schema internal UUID based identifier for specific incarnation of a document InstanceID URI internal The common identifier for all versions and renditions of a document. 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