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Annual review of genomics and human genetics最新文献

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A Personal Retrospective on the US Department of Energy Contribution to the Human Genome Project. 个人回顾美国能源部对人类基因组计划的贡献。
IF 8.3 2区 生物学
Annual review of genomics and human genetics Pub Date : 2026-08-01 Epub Date: 2026-01-13 DOI: 10.1146/annurev-genom-050725-011420
Aristides A N Patrinos
{"title":"A Personal Retrospective on the US Department of Energy Contribution to the Human Genome Project.","authors":"Aristides A N Patrinos","doi":"10.1146/annurev-genom-050725-011420","DOIUrl":"10.1146/annurev-genom-050725-011420","url":null,"abstract":"<p><p>In this article, I recount and reflect on the US Department of Energy's contributions to sequence the human genome as part of the Human Genome Project.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":" ","pages":"1-19"},"PeriodicalIF":8.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145965066","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}
引用次数: 0
Beyond TADs and Compartments: Mesoscale Chromatin Folding and Its Dynamics in Transcriptional Regulation. 超越tad和区室：中尺度染色质折叠及其转录调控动力学。
IF 8.3 2区 生物学
Annual review of genomics and human genetics Pub Date : 2026-08-01 Epub Date: 2026-06-02 DOI: 10.1146/annurev-genom-020525-015843
Wu Zuo, Viviana I Risca
{"title":"Beyond TADs and Compartments: Mesoscale Chromatin Folding and Its Dynamics in Transcriptional Regulation.","authors":"Wu Zuo, Viviana I Risca","doi":"10.1146/annurev-genom-020525-015843","DOIUrl":"10.1146/annurev-genom-020525-015843","url":null,"abstract":"<p><p>Below the scale of long-range compartments and topologically associating domains (TADs) lie a diverse set of local chromatin organization features. Recent maps and single-molecule assays reveal modular sub-TAD units, nucleosome clutches, micro- and nanodomains, packing domains, microcompartments, and stripes arising from an interplay of loop extrusion, epigenetic affinity and condensates, and polymerase motion. We highlight how cohesin regulation and its crosstalk with transcription shape local topology, how microcompartments and affinity-driven hubs guide enhancer-promoter communication, and how nucleosome positioning and spacing set the energetic landscape on which these forces act. We also outline how sub-TAD architecture is related to dynamics and single-molecule heterogeneity, describe additional looping mechanisms and several case studies of mesoscale structure regulation, and discuss perspectives on how technological advances can build a more mechanistic understanding of mesoscale chromatin organization. Overall, we argue that the submegabase structure of chromatin, though complex, is an essential length scale for understanding transcriptional regulation.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":" ","pages":"131-158"},"PeriodicalIF":8.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148147890","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}
引用次数: 0
Experimental and Computational Approaches to Identify Noncoding Pathogenic Variation in Rare Disease. 鉴定罕见病非编码致病变异的实验与计算方法。
IF 8.3 2区 生物学
Annual review of genomics and human genetics Pub Date : 2026-08-01 Epub Date: 2026-05-21 DOI: 10.1146/annurev-genom-111124-024627
Laura E Covill, Lindsay Romo, Anne O'Donnell-Luria
{"title":"Experimental and Computational Approaches to Identify Noncoding Pathogenic Variation in Rare Disease.","authors":"Laura E Covill, Lindsay Romo, Anne O'Donnell-Luria","doi":"10.1146/annurev-genom-111124-024627","DOIUrl":"10.1146/annurev-genom-111124-024627","url":null,"abstract":"<p><p>Noncoding variants occur within noncoding genes as well as within the regulatory nontranslated regions of protein-coding genes. It is important to be aware that these variants have been increasingly implicated in developmental disease through a variety of mechanisms. However, they remain difficult to interpret clinically due to their unclear effect on transcript or protein abundance compared with coding variants. Here, we review methods to identify pathogenic noncoding variants in rare disease, which can present challenges due to the inaccessibility of disease-relevant tissue for many conditions. We explore experimental approaches such as high-throughput functional assays, omic data integration, and long-read sequencing. We also review computational methods for annotating and filtering variants, as well as machine learning methods for predicting variant effect and pathogenicity. We discuss the recent discovery of several developmental syndromes caused by noncoding variants and propose an integrated approach to identifying pathogenic noncoding variants within this patient cohort.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":" ","pages":"305-330"},"PeriodicalIF":8.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147986333","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}
引用次数: 0
Understanding the Role of Functional Noncoding Variation in Human Diseases with Lessons from Immunity. 了解功能性非编码变异在人类疾病中的作用与免疫的经验教训。
IF 8.3 2区 生物学
Annual review of genomics and human genetics Pub Date : 2026-08-01 Epub Date: 2026-04-01 DOI: 10.1146/annurev-genom-020625-084652
Xiao P Peng, John M Greally
{"title":"Understanding the Role of Functional Noncoding Variation in Human Diseases with Lessons from Immunity.","authors":"Xiao P Peng, John M Greally","doi":"10.1146/annurev-genom-020625-084652","DOIUrl":"10.1146/annurev-genom-020625-084652","url":null,"abstract":"<p><p>The advent of next-generation sequencing has expanded our understanding of the genotypic, pathobiological, and phenotypic spectrum of human disease, helping to inform more personalized patient care. Current clinical guidelines are prompting the generation of large volumes of clinical diagnostic genome sequencing data, but we remain unable to interpret variants found in the noncoding 98.5% of sequencing data. In this review, we discuss the known and emerging mechanisms by which noncoding variants cause human disease. Through the lens of immunity, we integrate insights from population genetics, evolutionary and functional genomics, and in silico strategies to propose a framework for identifying and characterizing potential disease-relevant noncoding variants with regulatory impact on gene expression. By tackling the assessment of this vast black box of missing genetic contributions to disease, we hope to improve diagnostic yields and clinical management for more unsolved patients.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":" ","pages":"331-353"},"PeriodicalIF":8.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147589522","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}
引用次数: 0
Community Engagement in Genomic Research: Where We Have Been and Where We Should Go. 基因组研究中的社区参与：我们已经做了什么，我们应该去哪里。
IF 8.3 2区 生物学
Annual review of genomics and human genetics Pub Date : 2026-08-01 Epub Date: 2026-05-08 DOI: 10.1146/annurev-genom-020525-034046
Mildred K Cho
{"title":"Community Engagement in Genomic Research: Where We Have Been and Where We Should Go.","authors":"Mildred K Cho","doi":"10.1146/annurev-genom-020525-034046","DOIUrl":"10.1146/annurev-genom-020525-034046","url":null,"abstract":"<p><p>Community engagement in science has a long history but is particularly important for genomics because of the legacy of eugenics and the importance of diversity and representation in population genetics. In this article, I describe the role of community engagement in the context of the evolving relationship between science and society. Specifically, modern genomics is occurring during a shift toward context-driven, interdisciplinary, and socially robust research that is driven less by traditional values of science and more by relational processes. I review different approaches to engagement, including community-based participatory research, research with patient advocacy organizations, and citizen science/DIY efforts. I then highlight the ethical justification for community engagement in genomic research, including the need to address the history of injustices in genetic science and lack of diversity of participants. Finally, I review some of the challenges of community engagement and where we can look for guidance on practices of knowledge co-production.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":" ","pages":"453-474"},"PeriodicalIF":8.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147855872","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}
引用次数: 0
Artificial Intelligence in Human Genetics. 人类遗传学中的人工智能。
IF 8.3 2区 生物学
Annual review of genomics and human genetics Pub Date : 2026-08-01 Epub Date: 2026-02-25 DOI: 10.1146/annurev-genom-111124-032550
Nadav Brandes
{"title":"Artificial Intelligence in Human Genetics.","authors":"Nadav Brandes","doi":"10.1146/annurev-genom-111124-032550","DOIUrl":"10.1146/annurev-genom-111124-032550","url":null,"abstract":"<p><p>Artificial intelligence (AI) technologies have recently undergone transformative growth in capabilities. In human genetics, AI is rapidly advancing our ability to reveal the effects of genetic variation. This review explores recent progress and remaining challenges across the diverse applications of AI in genotype-to-phenotype mapping, from predicting the functional and clinical consequences of mutations, to identifying causal genes, to estimating disease risk. Particular emphasis is placed on the growing utility of general-purpose foundation models trained on massive genomic data, including DNA and protein language models, alongside areas where narrower machine-learning approaches still dominate. The review concludes with key considerations for future progress and impact.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":" ","pages":"183-204"},"PeriodicalIF":8.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147288894","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}
引用次数: 0
Unraveling Non-B DNA Structures in the Era of Telomere-to-Telomere Genomes. 在端粒到端粒基因组时代揭示非b DNA结构。
IF 8.3 2区 生物学
Annual review of genomics and human genetics Pub Date : 2026-08-01 Epub Date: 2026-05-06 DOI: 10.1146/annurev-genom-120324-010100
Kateryna D Makova, Saswat Mohanty, Linnéa Smeds, Jacob Sieg, Angelika Lahnsteiner
{"title":"Unraveling Non-B DNA Structures in the Era of Telomere-to-Telomere Genomes.","authors":"Kateryna D Makova, Saswat Mohanty, Linnéa Smeds, Jacob Sieg, Angelika Lahnsteiner","doi":"10.1146/annurev-genom-120324-010100","DOIUrl":"10.1146/annurev-genom-120324-010100","url":null,"abstract":"<p><p>Telomere-to-telomere (T2T) genome assemblies now provide a complete representation of genomic sequences, enabling unprecedented exploration of non-B DNA structures-secondary conformations distinct from canonical B-DNA. These fully resolved genomes reveal the true abundance and chromosomal distribution of motifs capable of forming G-quadruplexes, Z-DNA, triplexes, and other noncanonical structures, including within previously inaccessible satellite and repetitive regions. T2T assemblies also illuminate how non-B DNA influences key biological processes such as replication, recombination, chromatin organization, and transcription. Moreover, emerging evidence links non-B DNA structures to genomic instability, mutation hotspots, and disease etiology. Comparative T2T analyses across species are beginning to uncover evolutionary patterns and selection pressures acting on these motifs. Integrating advanced prediction tools, AI-based analyses, and experimental validation promises to clarify the multifaceted roles of non-B DNA in genome function, regulation, and evolution.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":" ","pages":"73-101"},"PeriodicalIF":8.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147831754","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}
引用次数: 0
Transcriptional Regulatory Modulation as a Potential Therapeutic Modality. 转录调节作为一种潜在的治疗方式。
IF 8.3 2区 生物学
Annual review of genomics and human genetics Pub Date : 2026-08-01 Epub Date: 2026-04-01 DOI: 10.1146/annurev-genom-120324-124041
Navneet Matharu, Nadav Ahituv
{"title":"Transcriptional Regulatory Modulation as a Potential Therapeutic Modality.","authors":"Navneet Matharu, Nadav Ahituv","doi":"10.1146/annurev-genom-120324-124041","DOIUrl":"10.1146/annurev-genom-120324-124041","url":null,"abstract":"<p><p>Numerous human diseases are caused by changes in gene expression levels. In addition, changing the expression levels of specific genes can lead to therapeutic benefits for several diseases. Nuclease-deficient gene-editing proteins fused to transcriptional modulators that target gene regulatory elements have emerged as powerful, programmable, and customizable systems to modify gene expression for therapeutic benefits. Several of these systems have already been used in the clinic, and many more are under development. Here, we review these emerging technologies and assess their therapeutic potential, their delivery, and related challenges in the clinic.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":" ","pages":"407-426"},"PeriodicalIF":8.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147589517","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}
引用次数: 0
Pangenomic Initiatives in the Middle East. 中东的泛基因组计划。
IF 8.3 2区 生物学
Annual review of genomics and human genetics Pub Date : 2026-08-01 Epub Date: 2026-03-10 DOI: 10.1146/annurev-genom-020525-030036
Bassam Jamalalail, Mohammad Amiruddin Hashmi, Mohamed A Almarri, Nelson C Soares, Marc Haber, Omer S Alkhnbashi, Nasna Nassir, Stefan S Du Plessis, Alawi Alsheikh-Ali, Mohammed Uddin
{"title":"Pangenomic Initiatives in the Middle East.","authors":"Bassam Jamalalail, Mohammad Amiruddin Hashmi, Mohamed A Almarri, Nelson C Soares, Marc Haber, Omer S Alkhnbashi, Nasna Nassir, Stefan S Du Plessis, Alawi Alsheikh-Ali, Mohammed Uddin","doi":"10.1146/annurev-genom-020525-030036","DOIUrl":"10.1146/annurev-genom-020525-030036","url":null,"abstract":"<p><p>The pangenome initiative marks a major shift from reliance on a single human reference that undersamples global diversity. Building phased, diploid assemblies from specific regions reveals population haplotypes and structural variants. This review outlines core pangenome concepts and surveys initiatives across Middle Eastern countries, long underrepresented in genomic resources. We summarize advances in long-read sequencing and graph-based bioinformatics that now enable high-quality diploid assemblies and reference graphs. National genome programs exist in six countries, and some have launched pangenome efforts, revealing sequence and variant content absent from GRCh38 and CHM13. We examine how founder effects, consanguinity, and tribe-based endogamy shape the region's genetic architecture, producing runs of homozygosity and concentrated rare alleles that aid gene discovery yet challenge clinical interpretation. Finally, we argue for coordinated, region-wide pangenome initiatives, spanning ethnolinguistic and tribal groups, to create equitable genome references, improve mapping and variant calling for Middle Eastern haplotypes, and accelerate precision medicine across the region.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":" ","pages":"383-406"},"PeriodicalIF":8.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147430477","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}
引用次数: 0
Workforce Development in Genomic Data Science for Health: A Worldview. 健康基因组数据科学中的劳动力发展：世界观。
IF 7.9 2区 生物学
Annual review of genomics and human genetics Pub Date : 2025-08-01 Epub Date: 2025-04-09 DOI: 10.1146/annurev-genom-012224-122440
Sindiswa T Lukhele, Verena Ras, Nicola Mulder
{"title":"Workforce Development in Genomic Data Science for Health: A Worldview.","authors":"Sindiswa T Lukhele, Verena Ras, Nicola Mulder","doi":"10.1146/annurev-genom-012224-122440","DOIUrl":"10.1146/annurev-genom-012224-122440","url":null,"abstract":"<p><p>Genomics has the potential to transform human health, biomedical research, and life sciences by providing deep insights into genetic variation and disease mechanisms. However, fully realizing these benefits requires a well-trained workforce equipped to handle, analyze, and interpret increasingly complex genomic and linked datasets. The rapid evolution of sequencing technologies, machine learning, and data science tools has heightened the demand for professionals proficient in bioinformatics, high-performance computing, and genomic data governance. This review presents a global perspective on workforce development in genomic data science, detailing key competencies necessary for both research and clinical applications. We discuss some of the existing training programs, competency frameworks, and regional approaches to skills development while identifying gaps in education, infrastructure, and accessibility. Additionally, we explore the integration of genomic data science into healthcare, addressing challenges such as equitable access to training and the need for cross-disciplinary expertise. Tackling these challenges is essential for cultivating a diverse, skilled workforce capable of driving advancements in genomic research, precision medicine, and public health.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":" ","pages":"449-471"},"PeriodicalIF":7.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143967309","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}
引用次数: 0
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