Human Genetics最新文献

{"title":"Assessing the predicted impact of single amino acid substitutions in calmodulin for CAGI6 challenges.","authors":"Paola Turina, Giuditta Dal Cortivo, Carlos A Enriquez Sandoval, Emil Alexov, David B Ascher, Giulia Babbi, Constantina Bakolitsa, Rita Casadio, Piero Fariselli, Lukas Folkman, Akash Kamandula, Panagiotis Katsonis, Dong Li, Olivier Lichtarge, Pier Luigi Martelli, Shailesh Kumar Panday, Douglas E V Pires, Stephanie Portelli, Fabrizio Pucci, Carlos H M Rodrigues, Marianne Rooman, Castrense Savojardo, Martin Schwersensky, Yang Shen, Alexey V Strokach, Yuanfei Sun, Junwoo Woo, Predrag Radivojac, Steven E Brenner, Daniele Dell'Orco, Emidio Capriotti","doi":"10.1007/s00439-024-02720-y","DOIUrl":"https://doi.org/10.1007/s00439-024-02720-y","url":null,"abstract":"<p><p>Recent thermodynamic and functional studies have been conducted to evaluate the impact of amino acid substitutions on Calmodulin (CaM). The Critical Assessment of Genome Interpretation (CAGI) data provider at University of Verona (Italy) measured the melting temperature (T_m) and the percentage of unfolding (%unfold) of a set of CaM variants (CaM challenge dataset). Thermodynamic measurements for the equilibrium unfolding of CaM were obtained by monitoring far-UV Circular Dichroism as a function of temperature. These measurements were used to determine the T_m and the percentage of protein remaining unfolded at the highest temperature. The CaM challenge dataset, comprising a total of 15 single amino acid substitutions, was used to evaluate the effectiveness of computational methods in predicting the T_m and unfolding percentages associated with the variants, and categorizing them as destabilizing or not. For the sixth edition of CAGI, nine independent research groups from four continents (Asia, Australia, Europe, and North America) submitted over 52 sets of predictions, derived from various approaches. In this manuscript, we summarize the results of our assessment to highlight the potential limitations of current algorithms and provide insights into the future development of more accurate prediction tools. By evaluating the thermodynamic stability of CaM variants, this study aims to enhance our understanding of the relationship between amino acid substitutions and protein stability, ultimately contributing to more accurate predictions of the effects of genetic variants.</p>","PeriodicalId":13175,"journal":{"name":"Human Genetics","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142876860","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Further evidence of biallelic NAV3 variants associated with recessive neurodevelopmental disorder with dysmorphism, developmental delay, intellectual disability, and behavioral abnormalities.","authors":"Naseebullah Kakar, Selinda Mascarenhas, Asmat Ali, Azmatullah, Syed M Ijlal Haider, Vaishnavi Ashok Badiger, Mobina Shadman Ghofrani, Nathalie Kruse, Sohana Nadeem Hashmi, Jelena Pozojevic, Saranya Balachandran, Mathias Toft, Sajid Malik, Kristian Händler, Ambrin Fatima, Zafar Iqbal, Anju Shukla, Malte Spielmann, Periyasamy Radhakrishnan","doi":"10.1007/s00439-024-02718-6","DOIUrl":"https://doi.org/10.1007/s00439-024-02718-6","url":null,"abstract":"<p><p>Neuron navigators (NAVs) are cytoskeleton-associated proteins well known for their role in axonal guidance, neuronal migration, and neurite growth necessary for neurodevelopment. Neuron navigator 3 (NAV3) is one of the three NAV proteins highly expressed in the embryonic and adult brain. However, the role of the NAV3 gene in human disease is not well-studied. Recently, five bi-allelic and three mono-allelic variants in NAV3 were reported in 12 individuals from eight unrelated families with neurodevelopmental disorder (NDD). Here, we report five patients from three unrelated consanguineous families segregating autosomal recessive NDD. Patients have symptoms of dysmorphism, intellectual disability, developmental delay, and behavioral abnormalities. Exome sequencing (ES) was performed on two affected individuals from one large family, and one affected individual from each of the other two families. ES revealed two homozygous nonsense c.6325C > T; p.(Gln2109Ter) and c.6577C > T; p.(Arg2193Ter) and a homozygous splice site (c.243 + 1G > T) variants in the NAV3 (NM_001024383.2). Analysis of single-cell sequencing datasets from embryonic and young adult human brains revealed that NAV3 is highly expressed in the excitatory neurons, inhibitory neurons, and microglia, consistent with its role in neurodevelopment. In conclusion, in this study, we further validate biallelic protein truncating variants in NAV3 as a cause of NDD, expanding the spectrum of pathogenic variants in this newly discovered NDD gene.</p>","PeriodicalId":13175,"journal":{"name":"Human Genetics","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2024-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142871876","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Advancements and limitations in polygenic risk score methods for genomic prediction: a scoping review.","authors":"Dovini Jayasinghe, Setegn Eshetie, Kerri Beckmann, Beben Benyamin, S Hong Lee","doi":"10.1007/s00439-024-02716-8","DOIUrl":"10.1007/s00439-024-02716-8","url":null,"abstract":"<p><p>This scoping review aims to identify and evaluate the landscape of Polygenic Risk Score (PRS)-based methods for genomic prediction from 2013 to 2023, highlighting their advancements, key concepts, and existing gaps in knowledge, research, and technology. Over the past decade, various PRS-based methods have emerged, each employing different statistical frameworks aimed at enhancing prediction accuracy, processing speed and memory efficiency. Despite notable advancements, challenges persist, including unrealistic assumptions regarding sample sizes and the polygenicity of traits necessary for accurate predictions, as well as limitations in exploring hyper-parameter spaces and considering environmental interactions. We included studies focusing on PRS-based methods for risk prediction that underwent methodological evaluations using valid approaches and released computational tools/software. Additionally, we restricted our selection to studies involving human participants that were published in English language. This review followed the standard protocol recommended by Joanna Briggs Institute Reviewer's Manual, systematically searching Ovid MEDLINE, Ovid Embase, Scopus and Web of Science databases. Additionally, searches included grey literature sources like pre-print servers such as bioRxiv, and articles recommended by experts to ensure comprehensive and diverse coverage of relevant records. This study identified 34 studies detailing 37 genomic prediction methods, the majority of which rely on linkage disequilibrium (LD) information and necessitate hyper-parameter tuning. Nine methods integrate functional/gene annotation, while 12 are suitable for cross-ancestry genomic prediction, with only one considering gene-environment (GxE) interaction. While some methods require individual-level data, most leverage summary statistics, offering flexibility. Despite progress, challenges remain. These include computational complexity and the need for large sample sizes for high prediction accuracy. Furthermore, recent methods exhibit varying effectiveness across traits, with absolute accuracies often falling short of clinical utility. Transferability across ancestries varies, influenced by trait heritability and diversity of training data, while handling admixed populations remains challenging. Additionally, the absence of standard error measurements for individual PRSs, crucial in clinical settings, underscores a critical gap. Another issue is the lack of customizable graphical visualization tools among current software packages. While genomic prediction methods have advanced significantly, there is still room for improvement. Addressing current challenges and embracing future research directions will lead to the development of more universally applicable, robust, and clinically relevant genomic prediction tools.</p>","PeriodicalId":13175,"journal":{"name":"Human Genetics","volume":" ","pages":"1401-1431"},"PeriodicalIF":3.8,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142619298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biallelic germline DDX41 variants in a patient with bone dysplasia, ichthyosis, and dysmorphic features.","authors":"Prashant Sharma, Jason R McFadden, F Graeme Frost, Thomas C Markello, Dorothy K Grange, Wendy J Introne, William A Gahl, May Christine V Malicdan","doi":"10.1007/s00439-024-02708-8","DOIUrl":"10.1007/s00439-024-02708-8","url":null,"abstract":"<p><p>DDX41 (DEAD‑box helicase 41) is a member of the largest family of RNA helicases. The DEAD-box RNA helicases share a highly conserved core structure and regulate all aspects of RNA metabolism. The functional role of DDX41 in innate immunity is also highly conserved. DDX41 acts as a sensor of viral DNA and activates the STING-TBK1-IRF3-type I IFN signaling pathway. Germline heterozygous variants in DDX41 have been reported in familial myelodysplasia syndrome (MDS)/acute myeloid leukemia (AML) patients; most patients also acquired a somatic variant in the second DDX41 allele. Here, we report a patient who inherited compound heterozygous DDX41 variants and presented with bone dysplasia, ichthyosis, and dysmorphic features. Functional analyses of the patient-derived dermal fibroblasts revealed a reduced abundance of DDX41 and abrogated activation of the IFN genes through the STING-type I interferon pathway. Genome-wide transcriptome analyses in the patient's fibroblasts revealed significant gene dysregulation and changes in the RNA splicing events. The patient's fibroblasts also displayed upregulation of periostin mRNA expression. Using an RNA binding protein assay, we identified DDX41 as a novel regulator of periostin expression. Our results suggest that functional impairment of DDX41, along with dysregulated periostin expression, likely contributes to this patient's multisystem disorder.</p>","PeriodicalId":13175,"journal":{"name":"Human Genetics","volume":" ","pages":"1445-1457"},"PeriodicalIF":3.8,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11576897/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142499441","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The MorbidGenes panel: a monthly updated list of diagnostically relevant rare disease genes derived from diverse sources.","authors":"Robin-Tobias Jauss, Bernt Popp, Joachim Bachmann, Rami Abou Jamra, Konrad Platzer","doi":"10.1007/s00439-024-02711-z","DOIUrl":"10.1007/s00439-024-02711-z","url":null,"abstract":"<p><strong>Purpose: </strong>With exome sequencing now standard, diagnostic labs are in need of a, in principle, to-the-day-accurate list of genes associated with rare diseases. Manual curation efforts are slow and often disease specific, while efforts relying on single sources are too inaccurate and may result in false-positive or false-negative genes.</p><p><strong>Methods: </strong>We established the MorbidGenes panel based on a list of publicly available databases: OMIM, PanelApp, SysNDD, ClinVar, HGMD and GenCC. A simple logic allows inclusion of genes that are supported by at least one of these sources, providing a list of all genes with diagnostic relevance.</p><p><strong>Results: </strong>The panel is freely available at https://morbidgenes.uni-leipzig.de and currently includes 5037 genes (as of October 2024) with minimally sufficient evidence on disease causality to classify them as diagnostically relevant.</p><p><strong>Conclusion: </strong>The MorbidGenes panel is an open and comprehensive overview of diagnostically relevant rare disease genes based on a diverse set of resources. The panel is updated monthly to keep up with the ever increasing number of rare disease genes.</p>","PeriodicalId":13175,"journal":{"name":"Human Genetics","volume":" ","pages":"1459-1463"},"PeriodicalIF":3.8,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11576763/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142499443","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Polymorphic pseudogenes in the human genome - a comprehensive assessment.","authors":"Mónica Lopes-Marques, M João Peixoto, David N Cooper, M João Prata, Luísa Azevedo, L Filipe C Castro","doi":"10.1007/s00439-024-02715-9","DOIUrl":"10.1007/s00439-024-02715-9","url":null,"abstract":"<p><strong>Background: </strong>Over the past decade, variations of the coding portion of the human genome have become increasingly evident. In this study, we focus on polymorphic pseudogenes, a unique and relatively unexplored type of pseudogene whose inactivating mutations have not yet been fixed in the human genome at the global population level. Thus, polymorphic pseudogenes are characterized by the presence in the population of both coding alleles and non-coding alleles originating from Loss-of-Function (LoF) mutations. These alleles can be found both in heterozygosity and in homozygosity in different human populations and thus represent pseudogenes that have not yet been fixed in the population.</p><p><strong>Results: </strong>A methodical cross-population analysis of 232 polymorphic pseudogenes, including 35 new examples, reveals that human olfactory signalling, drug metabolism and immunity are among the systems most impacted by the variable presence of LoF variants at high frequencies. Within this dataset, a total of 179 genes presented polymorphic LoF variants in all analysed populations. Transcriptome and proteome analysis confirmed that although these genes may harbour LoF alleles, when the coding allele is present, the gene remains active and can play a functional role in various metabolic pathways, including drug/xenobiotic metabolism and immunity. The observation that many polymorphic pseudogenes are members of multigene families argues that genetic redundancy may play a key role in compensating for the inactivation of one paralogue.</p><p><strong>Conclusions: </strong>The distribution, expression and integration of cellular/biological networks in relation to human polymorphic pseudogenes, provide novel insights into the architecture of the human genome and the dynamics of gene gain and loss with likely functional impact.</p>","PeriodicalId":13175,"journal":{"name":"Human Genetics","volume":" ","pages":"1465-1479"},"PeriodicalIF":3.8,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11576641/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142564379","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic analysis of preaxial polydactyly: identification of novel variants and the role of ZRS duplications in a Chinese cohort of 102 cases.","authors":"Siyu Pu, Zhibo Wang, Xueyang Tang, Daoxi Wang, Xiaodong Yang, Jun Jiang, Yifan Deng, Bo Xiang, Jiayin Yang, Xiaoli Wang, Xuesong Guo, Miao Sun, Bin Wang, Jing Chen","doi":"10.1007/s00439-024-02709-7","DOIUrl":"10.1007/s00439-024-02709-7","url":null,"abstract":"<p><p>Preaxial polydactyly (PPD) is a congenital limb malformation, previously reported to be caused primarily by variants in the ZRS and upstream preZRS regions. This study investigated genetic variations associated with PPD, focusing on point variants and copy number variations (CNVs) in the ZRS and preZRS regions. Comprehensive genetic analyses were conducted on 102 patients with PPD, including detailed clinical examinations and Sanger sequencing of the ZRS and preZRS regions. Additionally, real-time quantitative PCR (qPCR) was used to detect CNVs in the ZRS region. The evolutionary conservation and population frequencies of identified variants were also evaluated. Six point variants were identified, among which four are likely pathogenic novel variants: 93G > T (g.156584477G > T), 106G > A (g.156584464G > A), 278G > A (g.156584292G > A), and 409A > C (g.156585378A > C). Additionally, qPCR analysis revealed that 66.67% of patients exhibited ZRS duplications. Notably, these duplications were also present in cases with newly identified potential pathogenic point variants. These findings suggest the possible interaction of point variants in ZRS and preZRS through a common pathogenic mechanism, leading jointly to PPD. The findings expand the variant spectrum associated with non-syndromic polydactyly and highlight that, despite different classifications, anterior polydactyly caused by variants in ZRS and nearby regions may share common pathogenic mechanisms. The incorporation of various variant types in genetic screening can effectively enhance the rate of pathogenic variant detection and contribute to the cost-effectiveness of genetic testing for limb developmental defects, thereby promoting healthy births.</p>","PeriodicalId":13175,"journal":{"name":"Human Genetics","volume":" ","pages":"1433-1444"},"PeriodicalIF":3.8,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142499442","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Homozygosity for a hypomorphic mutation in frizzled class receptor 5 causes syndromic ocular coloboma with microcornea in humans.","authors":"Vianney Cortés-González, Miguel Rodriguez-Morales, Paris Ataliotis, Claudine Mayer, Julie Plaisancié, Nicolas Chassaing, Hane Lee, Jean-Michel Rozet, Florencia Cavodeassi, Lucas Fares Taie","doi":"10.1007/s00439-024-02712-y","DOIUrl":"10.1007/s00439-024-02712-y","url":null,"abstract":"<p><p>Ocular coloboma (OC) is a congenital disorder caused by the incomplete closure of the embryonic ocular fissure. OC can present as a simple anomaly or, in more complex forms, be associated with additional ocular abnormalities. It can occur in isolation or as part of a broader syndrome, exhibiting considerable genetic heterogeneity. Diagnostic yield for OC remains below 30%, indicating the need for further genetic exploration. Mutations in the Wnt receptor FZD5, which is expressed throughout eye development, have been linked to both isolated and complex forms of coloboma. These mutations often result in a dominant-negative effect, where the mutated FZD5 protein disrupts WNT signaling by sequestering WNT ligands. Here, we describe a case of syndromic bilateral OC with additional features such as microcornea, bone developmental anomalies, and mild intellectual disability. Whole exome sequencing revealed a homozygous rare missense variant in FZD5. Consistent with a loss-of-function effect, overexpressing of fzd5 mRNA harboring the missense variant in zebrafish embryos does not influence embryonic development, whereas overexpression of wild-type fzd5 mRNA results in body axis duplications. However, in vitro TOPFlash assays revealed that the missense variant only caused partial loss-of-function, behaving as a hypomorphic mutation. We further showed that the mutant protein still localized to the cell membrane and maintained proper conformation when modeled in silico, suggesting that the impairment lies in signal transduction. This hypothesis is further supported by the fact that the variant affects a highly conserved amino acid known to be crucial for protein-protein interactions.</p>","PeriodicalId":13175,"journal":{"name":"Human Genetics","volume":" ","pages":"1509-1521"},"PeriodicalIF":3.8,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11576812/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142582716","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Interpreting the actionable clinical role of rare variants associated with short QT syndrome.","authors":"Estefanía Martínez-Barrios, Andrea Greco, José Cruzalegui, Sergi Cesar, Nuria Díez-Escuté, Patricia Cerralbo, Fredy Chipa, Irene Zschaeck, Leonel Slanovic, Alipio Mangas, Rocío Toro, Josep Brugada, Georgia Sarquella-Brugada, Oscar Campuzano","doi":"10.1007/s00439-024-02713-x","DOIUrl":"10.1007/s00439-024-02713-x","url":null,"abstract":"<p><p>Genetic testing is recommended in the diagnosis of short QT syndrome. This rare inherited lethal entity is characterized by structural normal hearts with short QT intervals in the electrocardiogram. Few families diagnosed with this arrhythmogenic disease have been reported worldwide so far, impeding a comprehensive understanding of this syndrome. Unraveling the origin of the disease helps to the early identification of genetic carriers at risk. However, only rare variants with a definite deleterious role should be actionable in clinical practice. Our aim was to perform a comprehensive update and reinterpretation, according to the American College of Medical Genetics and Genomics recommendations of all rare variants currently associated with short QT syndrome. We identified 34 rare variants. Reanalysis showed that only nine variants played a deleterious role associated with a definite short QT syndrome phenotype. These variants were located in the four main genes: KCNQ1, KCNH2, KCNJ2 or SLC4A3. Additional rare variants located in other genes were associated with other conditions with phenotypic shortened QT intervals, but not definite diagnosis of short QT syndrome. Periodically updating of rare variants, especially those previously classified as unknown, helps to clarify the role of rare variants and translate genetic data into clinical practice.</p>","PeriodicalId":13175,"journal":{"name":"Human Genetics","volume":" ","pages":"1499-1508"},"PeriodicalIF":3.8,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11576798/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142582718","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Germline copy number variants and endometrial cancer risk.","authors":"Cassie E Stylianou, George A R Wiggins, Vanessa L Lau, Joe Dennis, Andrew N Shelling, Michelle Wilson, Peter Sykes, Frederic Amant, Daniela Annibali, Wout De Wispelaere, Douglas F Easton, Peter A Fasching, Dylan M Glubb, Ellen L Goode, Diether Lambrechts, Paul D P Pharoah, Rodney J Scott, Emma Tham, Ian Tomlinson, Manjeet K Bolla, Fergus J Couch, Kamila Czene, Thilo Dörk, Alison M Dunning, Olivia Fletcher, Montserrat García-Closas, Reiner Hoppe, Helena Jernström, Rudolf Kaaks, Kyriaki Michailidou, Nadia Obi, Melissa C Southey, Jennifer Stone, Qin Wang, Amanda B Spurdle, Tracy A O'Mara, John Pearson, Logan C Walker","doi":"10.1007/s00439-024-02707-9","DOIUrl":"10.1007/s00439-024-02707-9","url":null,"abstract":"<p><p>Known risk loci for endometrial cancer explain approximately one third of familial endometrial cancer. However, the association of germline copy number variants (CNVs) with endometrial cancer risk remains relatively unknown. We conducted a genome-wide analysis of rare CNVs overlapping gene regions in 4115 endometrial cancer cases and 17,818 controls to identify functionally relevant variants associated with disease. We identified a 1.22-fold greater number of CNVs in DNA samples from cases compared to DNA samples from controls (p = 4.4 × 10^-63). Under three models of putative CNV impact (deletion, duplication, and loss of function), genome-wide association studies identified 141 candidate gene loci associated (p < 0.01) with endometrial cancer risk. Pathway analysis of the candidate loci revealed an enrichment of genes involved in the 16p11.2 proximal deletion syndrome, driven by a large recurrent deletion (chr16:29,595,483-30,159,693) identified in 0.15% of endometrial cancer cases and 0.02% of control participants. Together, these data provide evidence that rare copy number variants have a role in endometrial cancer susceptibility and that the proximal 16p11.2 BP4-BP5 region contains 25 candidate risk gene(s) that warrant further analysis to better understand their role in human disease.</p>","PeriodicalId":13175,"journal":{"name":"Human Genetics","volume":" ","pages":"1481-1498"},"PeriodicalIF":3.8,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11576655/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142567991","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}