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Annual review of genomics and human genetics最新文献

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Revisiting Founder Populations in an Age of Global Biobanks. 重新审视全球生物库时代的创始种群。
IF 7.9 2区 生物学
Annual review of genomics and human genetics Pub Date : 2026-05-08 DOI: 10.1146/annurev-genom-020525-034901
Christa Caggiano, Ruhollah Shemirani, Eimear E Kenny
{"title":"Revisiting Founder Populations in an Age of Global Biobanks.","authors":"Christa Caggiano, Ruhollah Shemirani, Eimear E Kenny","doi":"10.1146/annurev-genom-020525-034901","DOIUrl":"https://doi.org/10.1146/annurev-genom-020525-034901","url":null,"abstract":"<p><p>Founder populations have played a pivotal role in human genetics, enabling the discovery of causal variants for disease and providing insight into population history and dynamics. The rapid expansion of global genomic databases has revealed that founder populations are far more common than once recognized, as population-scale sequencing now allows for systematic detection of founder events and founder-like population structure across the world. Contemporary genomic methods facilitate the characterization of founder populations using genetic metrics such as identity by descent, runs of homozygosity, and haplotype-based clustering. As the field shifts from small, ascertained founder cohorts to biobank-scale datasets containing millions of participants, new opportunities and challenges have emerged, including analytical, interpretive, and ethical complexities in the study of founder populations. Here, we review the historical and ongoing contributions of founder populations to genetics, outline current approaches for biobanks, and highlight growing opportunities to integrate founder population research into genomic medicine.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147855841","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 7.9 2区 生物学
Annual review of genomics and human genetics Pub 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":"https://doi.org/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":""},"PeriodicalIF":7.9,"publicationDate":"2026-05-08","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
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 7.9 2区 生物学
Annual review of genomics and human genetics Pub 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":"https://doi.org/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":""},"PeriodicalIF":7.9,"publicationDate":"2026-05-06","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
Modeling Dynamics, Cell Type Specificity, and Perturbations in Gene Regulatory Networks. 模型动力学，细胞类型特异性，和基因调控网络的扰动。
IF 7.9 2区 生物学
Annual review of genomics and human genetics Pub Date : 2026-04-21 DOI: 10.1146/annurev-genom-120922-103729
Junha Shin, Spencer Halberg-Spencer, Yuda Liu, Suvojit Hazra, Erika Da-Inn Lee, Sushmita Roy
{"title":"Modeling Dynamics, Cell Type Specificity, and Perturbations in Gene Regulatory Networks.","authors":"Junha Shin, Spencer Halberg-Spencer, Yuda Liu, Suvojit Hazra, Erika Da-Inn Lee, Sushmita Roy","doi":"10.1146/annurev-genom-120922-103729","DOIUrl":"https://doi.org/10.1146/annurev-genom-120922-103729","url":null,"abstract":"<p><p>Gene regulatory networks (GRNs) define the regulatory relationships among molecules such as transcription factors, chromatin remodelers, and target genes. GRNs play a critical role in diverse biological processes, including development, disease manifestation, and evolution. However, fully characterizing these networks across multiple cell types and states remains a significant challenge. Recent advances in single-cell omics have dramatically enhanced our ability to measure biological systems at unprecedented resolution. These technologies have opened new avenues for computational methods to infer GRNs, offering deeper insights into cell type-specific mechanisms, causality, and dynamic regulatory processes. This review summarizes the current state of GRN inference from single-cell omic datasets, with a particular focus on dynamics and perturbations, and outlines key open challenges that must be addressed to advance the field.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2026-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147760571","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
Cryptic Splicing in ALS: From Driving Disease Progression to Unlocking Novel Therapeutics. ALS中的隐剪接：从驱动疾病进展到解锁新疗法。
IF 7.9 2区 生物学
Annual review of genomics and human genetics Pub Date : 2026-04-21 DOI: 10.1146/annurev-genom-022024-011307
Sara Emad El-Agamy, Francesca Mattedi, Pietro Fratta
{"title":"Cryptic Splicing in ALS: From Driving Disease Progression to Unlocking Novel Therapeutics.","authors":"Sara Emad El-Agamy, Francesca Mattedi, Pietro Fratta","doi":"10.1146/annurev-genom-022024-011307","DOIUrl":"https://doi.org/10.1146/annurev-genom-022024-011307","url":null,"abstract":"<p><p>TDP-43 is an RNA-binding protein that regulates multiple aspects of RNA processing, and its mislocalization from the nucleus to the cytoplasm is a defining feature of amyotrophic lateral sclerosis (ALS). While both loss- and gain-of-function mechanisms contribute to disease, the discovery of cryptic splicing has shed light on the downstream consequences of TDP-43 nuclear clearance for neuronal health. Here, we highlight how loss of nuclear TDP-43 can drive a cascade of events that lead to the impairment of cellular proteostasis and result in a positive feedback loop that perpetuates neuronal dysfunction. This sustains the appearance of cryptic splicing events in genes that are involved in key pathways for the maintenance of axonal homeostasis and synaptic transmission. In contrast to their detrimental effects on neuronal health, cryptic splicing mechanisms may be harnessed to develop novel therapeutic strategies, unprecedentedly expanding the availability of therapeutic avenues for TDP-43 proteinopathies.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2026-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147760587","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 7.9 2区 生物学
Annual review of genomics and human genetics Pub 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":"https://doi.org/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":""},"PeriodicalIF":7.9,"publicationDate":"2026-04-01","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
Transcriptional Regulatory Modulation as a Potential Therapeutic Modality. 转录调节作为一种潜在的治疗方式。
IF 7.9 2区 生物学
Annual review of genomics and human genetics Pub 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":"https://doi.org/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. Systems using 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":""},"PeriodicalIF":7.9,"publicationDate":"2026-04-01","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
Organoid Perturbations as Tools to Explore Cellular Function and Plasticity. 类器官扰动作为探索细胞功能和可塑性的工具。
IF 7.9 2区 生物学
Annual review of genomics and human genetics Pub Date : 2026-03-20 DOI: 10.1146/annurev-genom-120324-024252
Katharina E Kohl, Georg A Busslinger
{"title":"Organoid Perturbations as Tools to Explore Cellular Function and Plasticity.","authors":"Katharina E Kohl, Georg A Busslinger","doi":"10.1146/annurev-genom-120324-024252","DOIUrl":"https://doi.org/10.1146/annurev-genom-120324-024252","url":null,"abstract":"<p><p>Organoids have reshaped biomedical research by providing stem cell-derived model systems that capture key aspects of tissue organization, homeostasis, and disease. Their physiological relevance and adaptability have made them indispensable tools for studying development, regeneration, and tumor biology under controlled experimental conditions. This is particularly powerful in the human setting, where organoids offer an experimentally accessible alternative to in vivo studies that are ethically and practically unfeasible. Central to their success is the ability to apply diverse perturbation strategies, ranging from targeted genetic edits and pharmacological interventions to microenvironmental and biomechanical manipulations, that reveal the molecular logic of cellular and tissue function. In this review, we discuss the current landscape of organoid perturbation studies, highlighting methodological advances, representative applications, and what these efforts have taught us about cellular behavior in complex systems. By outlining methodological innovations and conceptual insights, we aim to establish a framework for using organoids not only as descriptive models but as predictive systems for probing and engineering human tissue behavior.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2026-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147490515","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 7.9 2区 生物学
Annual review of genomics and human genetics Pub 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":"https://doi.org/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":""},"PeriodicalIF":7.9,"publicationDate":"2026-03-10","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
The Genomics and Genetics of Rare Disease Illuminate Human Biology. 罕见疾病的基因组学和遗传学阐明了人类生物学。
IF 7.9 2区 生物学
Annual review of genomics and human genetics Pub Date : 2026-03-04 DOI: 10.1146/annurev-genom-020525-014546
James R Lupski, Richard A Gibbs
{"title":"The Genomics and Genetics of Rare Disease Illuminate Human Biology.","authors":"James R Lupski, Richard A Gibbs","doi":"10.1146/annurev-genom-020525-014546","DOIUrl":"https://doi.org/10.1146/annurev-genom-020525-014546","url":null,"abstract":"<p><p>Richard Gibbs interviews James (Jim) Lupski about his training in New York and work in Houston to elucidate the role of complex genomic rearrangements in human genetic diseases. The challenges and excitement of developing human personalized genomics and the advantages of clinical translation of genome methods for both patients and researchers are discussed.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2026-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147353511","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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