American journal of human genetics最新文献

{"title":"Role of X chromosome and dosage-compensation mechanisms in complex trait genetics.","authors":"Yu Fu, Aino Kenttämies, Sanni Ruotsalainen, Matti Pirinen, Taru Tukiainen","doi":"10.1016/j.ajhg.2025.04.004","DOIUrl":"https://doi.org/10.1016/j.ajhg.2025.04.004","url":null,"abstract":"<p><p>The X chromosome (chrX) is often excluded from genome-wide association studies due to its unique biology complicating the analysis and interpretation of genetic data. Consequently, the influence of chrX on human complex traits remains debated. Here, we systematically assessed the relevance of chrX and the effect of its biology on complex traits by analyzing 48 quantitative traits in 343,695 individuals in UK Biobank with replication in 412,181 individuals from FinnGen. We show that, in the general population, chrX contributes to complex trait heritability at a rate of 3% of the autosomal heritability, consistent with the amount of genetic variation observed in chrX. We find that a pronounced male bias in chrX heritability supports the presence of near-complete dosage compensation between sexes through X chromosome inactivation (XCI). However, we also find subtle yet plausible evidence of escape from XCI contributing to human height. Assuming full XCI, the observed chrX contribution to complex trait heritability in both sexes is greater than expected given the presence of only a single active copy of chrX, mirroring potential dosage compensation between chrX and the autosomes. We find this enhanced contribution attributable to systematically larger active allele effects from chrX compared to autosomes in both sexes, independent of allele frequency and variant deleteriousness. Together, these findings support a model in which the two dosage-compensation mechanisms work in concert to balance the influence of chrX across the population while preserving sex-specific differences at a manageable level. Overall, our study advocates for more comprehensive locus discovery efforts in chrX.</p>","PeriodicalId":7659,"journal":{"name":"American journal of human genetics","volume":" ","pages":""},"PeriodicalIF":8.1,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143959638","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"First steps toward building natural history of diseases computationally: Lessons learned from the Noonan syndrome use case.","authors":"Tudor Groza, Warittha Rayabsri, Dylan Gration, Harshini Hariram, Saumya Shekhar Jamuar, Gareth Baynam","doi":"10.1016/j.ajhg.2025.03.014","DOIUrl":"https://doi.org/10.1016/j.ajhg.2025.03.014","url":null,"abstract":"<p><p>Rare diseases (RDs) are conditions affecting fewer than 1 in 2,000 people, with over 7,000 identified, primarily genetic in nature, and more than half impacting children. Although each RD affects a small population, collectively, between 3.5% and 5.9% of the global population, or 262.9-446.2 million people, live with an RD. Most RDs lack established treatment protocols, highlighting the need for proper care pathways addressing prognosis, diagnosis, and management. Advances in generative AI and large language models (LLMs) offer new opportunities to document the temporal progression of phenotypic features, addressing gaps in current knowledge bases. This study proposes an LLM-based framework to capture the natural history of diseases, specifically focusing on Noonan syndrome. The framework aims to document phenotypic trajectories, validate against RD knowledge bases, and integrate insights into care coordination using electronic health record (EHR) data from the Undiagnosed Diseases Program Singapore.</p>","PeriodicalId":7659,"journal":{"name":"American journal of human genetics","volume":"112 5","pages":"1158-1172"},"PeriodicalIF":8.1,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143953688","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Interplay and cooperation between GLI2 and master transcription factors promote progression of esophageal squamous cell carcinoma.","authors":"Yin-Qiao Liu, Ze-Jun Zheng, Wang-Kai Fang, Yan-Shang Li, Chun Li, Min Yang, Dong-Chen Han, Jun-Hua Zhou, Ying-Hua Xie, Yu-Ying Zhang, Zhuo-Ying Kang, Yi-Wei Xu, Jian-Jun Xie","doi":"10.1016/j.ajhg.2025.03.001","DOIUrl":"10.1016/j.ajhg.2025.03.001","url":null,"abstract":"<p><p>The establishment of gene expression programs that drive cell identity is governed by tightly regulated transcription factors (TFs) that engage in auto- and cross-regulation in a feedforward manner, forming core regulatory circuitries (CRCs). Here, we identify and validate an important interconnected CRC formed by three master TFs-GLI2, TP63, and RUNX1-in esophageal squamous cell carcinoma (ESCC). Furthermore, master TFs co-bind to their own and each other's super-enhancers, forming an interconnected auto-regulatory loop. Mechanistically, these master TFs occupy the majority of ESCC super-enhancers and cooperatively orchestrate the ESCC transcription program. Functionally, GLI2, a master TF, is essential for ESCC viability, migration, invasion, and the growth of xenograft tumors. Moreover, the overexpression of GLI2 is significantly associated with shorter overall survival of patients with ESCC. Downstream, this CRC apparatus coordinately regulates gene expression networks in ESCC, controlling important cancer-promoting pathways, including Hedgehog, glycolysis, and epidermal growth factor receptor signaling pathways. Together, these findings offer significant mechanistic insights into the transcriptional dysregulation in ESCC and recognize GLI2 as a potential therapeutic target and prognostic marker for ESCC. More importantly, CRC-downstream genes and signaling pathways may contain potential therapeutic targets for this malignancy.</p>","PeriodicalId":7659,"journal":{"name":"American journal of human genetics","volume":" ","pages":"1039-1061"},"PeriodicalIF":8.1,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143741947","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bi-allelic pathogenic variants in TRMT1 disrupt tRNA modification and induce a neurodevelopmental disorder.","authors":"Stephanie Efthymiou, Cailyn P Leo, Chenghong Deng, Sheng-Jia Lin, Reza Maroofian, Renee Lin, Irem Karagoz, Kejia Zhang, Rauan Kaiyrzhanov, Annarita Scardamaglia, Daniel Owrang, Valentina Turchetti, Friederike Jahnke, Kevin Huang, Cassidy Petree, Anna V Derrick, Mark I Rees, Javeria Raza Alvi, Tipu Sultan, Chumei Li, Marie-Line Jacquemont, Frederic Tran-Mau-Them, Maria Valenzuela-Palafoll, Rich Sidlow, Grace Yoon, Michelle M Morrow, Deanna Alexis Carere, Mary O'Connor, Julie Fleischer, Erica H Gerkes, Chanika Phornphutkul, Bertrand Isidor, Clotilde Rivier-Ringenbach, Christophe Philippe, Semra Hiz Kurul, Didem Soydemir, Bulent Kara, Deniz Sunnetci-Akkoyunlu, Viktoria Bothe, Konrad Platzer, Dagmar Wieczorek, Margarete Koch-Hogrebe, Nils Rahner, Ann-Charlotte Thuresson, Hans Matsson, Carina Frykholm, Sevcan Tuğ Bozdoğan, Atil Bisgin, Nicolas Chatron, Gaetan Lesca, Sara Cabet, Zeynep Tümer, Tina D Hjortshøj, Gitte Rønde, Thorsten Marquardt, Janine Reunert, Erum Afzal, Mina Zamani, Reza Azizimalamiri, Hamid Galehdari, Pardis Nourbakhsh, Niloofar Chamanrou, Seo-Kyung Chung, Mohnish Suri, Paul J Benke, Maha S Zaki, Joseph G Gleeson, Daniel G Calame, Davut Pehlivan, Halil I Yilmaz, Alper Gezdirici, Aboulfazl Rad, Iman Sabri Abumansour, Gabriela Oprea, Muhammed Burak Bereketoğlu, Guillaume Banneau, Sophie Julia, Jawaher Zeighami, Saeed Ashoori, Gholamreza Shariati, Alireza Sedaghat, Alihossein Sabri, Mohammad Hamid, Sahere Parvas, Tajul Arifin Tajudin, Uzma Abdullah, Shahid Mahmood Baig, Wendy K Chung, Olga O Glazunova, Sigaudy Sabine, Huma Arshad Cheema, Giovanni Zifarelli, Peter Bauer, Jai Sidpra, Kshitij Mankad, Barbara Vona, Andrew E Fry, Gaurav K Varshney, Henry Houlden, Dragony Fu","doi":"10.1016/j.ajhg.2025.03.015","DOIUrl":"https://doi.org/10.1016/j.ajhg.2025.03.015","url":null,"abstract":"<p><p>The post-transcriptional modification of tRNAs plays a crucial role in tRNA structure and function. Pathogenic variants in tRNA-modification enzymes have been implicated in a wide range of human neurodevelopmental and neurological disorders. However, the molecular basis for many of these disorders remains unknown. Here, we describe a comprehensive cohort of 43 individuals from 31 unrelated families with bi-allelic variants in tRNA methyltransferase 1 (TRMT1). These individuals present with a neurodevelopmental disorder universally characterized by developmental delay and intellectual disability, accompanied by variable behavioral abnormalities, epilepsy, and facial dysmorphism. The identified variants include ultra-rare TRMT1 variants, comprising missense and predicted loss-of-function variants, which segregate with the observed clinical pathology. Our findings reveal that several variants lead to mis-splicing and a consequent loss of TRMT1 protein accumulation. Moreover, cells derived from individuals harboring TRMT1 variants exhibit a deficiency in tRNA modifications catalyzed by TRMT1. Molecular analysis reveals distinct regions of TRMT1 required for tRNA-modification activity and binding. Notably, depletion of Trmt1 protein in zebrafish is sufficient to induce developmental and behavioral phenotypes along with gene-expression changes associated with disrupted cell cycle, immune response, and neurodegenerative disorders. Altogether, these findings demonstrate that loss of TRMT1-catalyzed tRNA modifications leads to intellectual disability and provides insight into the molecular underpinnings of tRNA-modification deficiency caused by pathogenic TRMT1 variants.</p>","PeriodicalId":7659,"journal":{"name":"American journal of human genetics","volume":"112 5","pages":"1117-1138"},"PeriodicalIF":8.1,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143965912","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Plasma DNA Profile Associated with DNASE1L3 Gene Mutations: Clinical Observations, Relationships to Nuclease Substrate Preference, and In Vivo Correction.","authors":"Rebecca W Y Chan, Lee Serpas, Meng Ni, Stefano Volpi, Linda T Hiraki, Lai-Shan Tam, Ali Rashidfarrokhi, Priscilla C H Wong, Lydia H P Tam, Yueyang Wang, Peiyong Jiang, Alice S H Cheng, Wenlei Peng, Diana S C Han, Patty P P Tse, Pik Ki Lau, Wing-Shan Lee, Alberto Magnasco, Elisa Buti, Vanja Sisirak, Nora AlMutairi, K C Allen Chan, Rossa W K Chiu, Boris Reizis, Y M Dennis Lo","doi":"10.1016/j.ajhg.2025.04.001","DOIUrl":"https://doi.org/10.1016/j.ajhg.2025.04.001","url":null,"abstract":"","PeriodicalId":7659,"journal":{"name":"American journal of human genetics","volume":"112 5","pages":"1247"},"PeriodicalIF":8.1,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143959643","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"FBXO22 deficiency defines a pleiotropic syndrome of growth restriction and multi-system anomalies associated with a unique epigenetic signature.","authors":"Navin B Ramakrishna, Umar Bin Mohamad Sahari, Yoshikazu Johmura, Nur Ain Ali, Malak Alghamdi, Peter Bauer, Suliman Khan, Natalia Ordoñez, Mariana Ferreira, Jorge Pinto Basto, Fowzan S Alkuraya, Eissa Ali Faqeih, Mari Mori, Naif A M Almontashiri, Aisha Al Shamsi, Gehad ElGhazali, Hala Abu Subieh, Mode Al Ojaimi, Ayman W El-Hattab, Said Ahmed Said Al-Kindi, Nadia Alhashmi, Fahad Alhabshan, Abdulaziz Al Saman, Hala Tfayli, Mariam Arabi, Simone Khalifeh, Alan Taylor, Majid Alfadhel, Ruchi Jain, Shruti Sinha, Shruti Shenbagam, Revathy Ramachandran, Umut Altunoğlu, Anju Jacob, Nandu Thalange, Mireille El Bejjani, Arnaud Perrin, Jay W Shin, Almundher Al-Maawali, Azza Al-Shidhani, Amna Al-Futaisi, Fatma Rabea, Ikram Chekroun, Mohamed A Almarri, Tomohiko Ohta, Makoto Nakanishi, Alawi Alsheikh-Ali, Fahad R Ali, Aida M Bertoli-Avella, Bruno Reversade, Ahmad Abou Tayoun","doi":"10.1016/j.ajhg.2025.03.013","DOIUrl":"https://doi.org/10.1016/j.ajhg.2025.03.013","url":null,"abstract":"<p><p>FBXO22 encodes an F-box protein, which acts as a substrate-recognition component of the SKP1-CUL1-F-box (SCF) E3 ubiquitin ligase complex. Despite its known roles in the post-translational ubiquitination and degradation of specific substrates, including histone demethylases, the impact of FBXO22 on human development remains unknown. Here, we characterize a pleiotropic syndrome with prominent prenatal onset growth restriction and notable neurodevelopmental delay across 16 cases from 14 families. Through exome and genome sequencing, we identify four distinct homozygous FBXO22 variants with loss-of-function effects segregating with the disease: three predicted to lead to premature translation termination due to frameshift effects and a single-amino-acid-deletion variant, which, we show, impacts protein stability in vitro. We confirm that affected primary fibroblasts with a frameshift mutation are bereft of endogenous FBXO22 and show increased levels of the known substrate histone H3K9 demethylase KDM4B. Accordingly, we delineate a unique epigenetic signature for this disease in peripheral blood via long-read sequencing. Altogether, we identify and demonstrate that FBXO22 deficiency leads to a pleiotropic syndrome in humans, encompassing growth restriction and neurodevelopmental delay, the pathogenesis of which may be explained by broad chromatin alterations.</p>","PeriodicalId":7659,"journal":{"name":"American journal of human genetics","volume":"112 5","pages":"1233-1246"},"PeriodicalIF":8.1,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143959803","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rare predicted loss-of-function and damaging missense variants in CFHR5 associate with protection from age-related macular degeneration.","authors":"Aaron M Holleman, Aimee M Deaton, Rachel A Hoffing, Lynne Krohn, Philip LoGerfo, Paul Nioi, Mollie E Plekan, Sebastian Akle Serrano, Simina Ticau, Tony E Walshe, Anna Borodovsky, Lucas D Ward","doi":"10.1016/j.ajhg.2025.03.016","DOIUrl":"https://doi.org/10.1016/j.ajhg.2025.03.016","url":null,"abstract":"<p><p>Age-related macular degeneration (AMD) is a leading cause of blindness among older adults worldwide, but treatment options are limited. Genetics studies have implicated the CFH locus, containing CFH and five CFHR genes, CFHR1-5, in AMD. While CFH has been robustly linked with AMD risk, potential additional roles for the CFHR genes remain unclear, obscured by strong linkage disequilibrium across the locus. Investigating rare coding variants can help to identify causal genes in such regions. We used whole-exome sequencing data from 406,952 UK Biobank participants to examine AMD associations with genes at the CFH locus. For each gene, we used burden testing to examine associations of rare (minor-allele frequency [MAF] < 1%) predicted loss-of-function (pLoF) and predicted damaging missense variants with AMD. We considered \"broadly defined AMD\" (ICD-10 35.3; n_cases = 10,700) and \"strictly defined AMD\" (dry or wet AMD; n_cases = 346). Adjusting for CFH-region variants known to independently associate with AMD, we find that CFHR5 rare variant burden significantly associates with a decreased risk of broadly defined AMD (odds ratio [OR] = 0.75, p = 7 × 10^-4), with this association primarily driven by pLoF variants. Furthermore, the association of CFHR5 rare variants with AMD protection is estimated to be stronger for individuals with the CFH rs1061170 AMD risk allele (p.Tyr402His [p.Y402H]; interaction p = 0.04). Corresponding analyses of strict AMD were underpowered. However, we observe that thinning of the photoreceptor layer outer segment strongly predicts strict AMD and find that CFHR5 rare variant burden is significantly associated with increased thickness of this retinal layer (+0.34 SD, p = 4 × 10^-4, n = 45,365). These findings suggest CFHR5 inhibition as a potential therapeutic approach for AMD.</p>","PeriodicalId":7659,"journal":{"name":"American journal of human genetics","volume":"112 5","pages":"1062-1080"},"PeriodicalIF":8.1,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143958909","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Increasing the genomic workforce through research capacity building: Designing evaluation plans for maximum impact.","authors":"Karyn J Roberts, Weini Ogbagiorgis, Angela Sy, Sarah Williams-Blangero, LaMonica V Stewart, Eron Manusov, Sofia B Fernandez, Rachel D Clarke, Ebony B Madden","doi":"10.1016/j.ajhg.2025.03.002","DOIUrl":"10.1016/j.ajhg.2025.03.002","url":null,"abstract":"<p><p>More interventions are needed to address the need for workforce diversity and research capacity building (RCB) in genomics. In 2023, the National Human Genome Research Institute and the National Institute on Minority Health and Health Disparities of the National Institutes of Health funded the Diversity Centers for Genome Research Consortium to address this critical gap. The NIH program staff designed a prospective evaluation plan and developed common data elements (CDEs) that capture common evaluation outputs, synergize and streamline reporting, and facilitate continuous quality improvement. We created five CDEs: genomics programs and equipment, scientific productivity, scientific collaboration, community engagement, and workforce development. The prospective development of an evaluation plan based on CDEs facilitates the ongoing evaluation, reporting, and adjustment of RCB interventions to enhance the diversity of the genomics workforce.</p>","PeriodicalId":7659,"journal":{"name":"American journal of human genetics","volume":" ","pages":"967-974"},"PeriodicalIF":8.1,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143778743","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ACMG/AMP interpretation of BRCA1 missense variants: Structure-informed scores add evidence strength granularity to the PP3/BP4 computational evidence.","authors":"Lobna Ramadane-Morchadi, Nitsan Rotenberg, Ada Esteban-Sánchez, Cristina Fortuno, Alicia Gómez-Sanz, Matthew J Varga, Adam Chamberlin, Marcy E Richardson, Kyriaki Michailidou, Pedro Pérez-Segura, Amanda B Spurdle, Miguel de la Hoya","doi":"10.1016/j.ajhg.2024.12.011","DOIUrl":"https://doi.org/10.1016/j.ajhg.2024.12.011","url":null,"abstract":"<p><p>Classification of missense variants is challenging. Lacking compelling clinical and/or functional data, ACMG/AMP lines of evidence are restricted to PM2 (rarity code applied at supporting level) and PP3/BP4 (computational evidence based mostly on multiple-sequence-alignment conservation tools). Currently, the ClinGen ENIGMA BRCA1/2 Variant Curation Expert Panel uses BayesDel to apply PP3/BP4 to missense variants located in the BRCA1 RING/BRCT domains. The ACMG/AMP framework does not refer explicitly to protein structure as a putative source of pathogenic/benign evidence. Here, we tested the value of incorporating structure-based evidence such as relative solvent accessibility (RSA), folding stability (ΔΔG), and/or AlphaMissense pathogenicity to the classification of BRCA1 missense variants. We used MAVE functional scores as proxies for pathogenicity/benignity. We computed RSA and FoldX5.0 ΔΔG predictions using as alternative input templates for either PDB files or AlphaFold2 models, and we retrieved pre-computed AlphaMissense and BayesDel scores. We calculated likelihood ratios toward pathogenicity/benignity provided by the tools (individually or combined). We performed a clinical validation of major findings using the large-scale BRIDGES case-control dataset. AlphaMissense outperforms ΔΔG and BayesDel, providing similar PP3/BP4 evidence strengths with lower rate of variants in the uninformative score range. AlphaMissense combined with ΔΔG increases evidence strength granularity. AlphaFold2 models perform well as input templates for ΔΔG predictions. Regardless of the tool, BP4 (but not PP3) is highly dependent on RSA, with benignity evidence provided only to variants targeting buried or partially buried residues (RSA ≤ 60%). Stratification by functional domain did not reveal major differences. In brief, structure-based analysis improves PP3/BP4 assessment, uncovering a relevant role for RSA.</p>","PeriodicalId":7659,"journal":{"name":"American journal of human genetics","volume":"112 5","pages":"993-1002"},"PeriodicalIF":8.1,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143967546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural biology in variant interpretation: Perspectives and practices from two studies.","authors":"Matthew J Varga, Marcy E Richardson, Adam Chamberlin","doi":"10.1016/j.ajhg.2025.03.010","DOIUrl":"https://doi.org/10.1016/j.ajhg.2025.03.010","url":null,"abstract":"<p><p>Structural biology offers a powerful lens through which to assess genetic variants by providing insights into their impact on clinically relevant protein structure and function. Due to the availability of new, user-friendly, web-based tools, structural analyses by wider audiences have become more mainstream. These new tools, including AlphaMissense and AlphaFold, have recently been in the limelight due to their initial success and projected future promise; however, the intricacies and limitations of using these tools still need to be disseminated to the more general audience that is likely to use them in variant analysis. Here, we expound on frameworks applying structural biology to variant interpretation by examining two accompanying articles. To this end, we explore the nuances of choosing the correct protein model, compare and contrast various structural approaches, and highlight both the advantages and limitations of employing structural biology in variant interpretation. Using two articles published in this issue of The American Journal of Human Genetics as a baseline, we focus on case studies in TP53 and BRCA1 to illuminate gene-specific differences in the applications of structural information, which illustrate the complexities inherent in this field. Additionally, we discuss the implications of recent advancements, such as AlphaFold, and provide practical guidance for researchers navigating variant interpretation using structural biology.</p>","PeriodicalId":7659,"journal":{"name":"American journal of human genetics","volume":"112 5","pages":"984-992"},"PeriodicalIF":8.1,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143957579","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}