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Genome-wide association testing beyond SNPs 超越 SNP 的全基因组关联测试
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2024-10-07 DOI: 10.1038/s41576-024-00778-y
Laura Harris, Ellen M. McDonagh, Xiaolei Zhang, Katherine Fawcett, Amy Foreman, Petr Daneck, Panagiotis I. Sergouniotis, Helen Parkinson, Francesco Mazzarotto, Michael Inouye, Edward J. Hollox, Ewan Birney, Tomas Fitzgerald
{"title":"Genome-wide association testing beyond SNPs","authors":"Laura Harris, Ellen M. McDonagh, Xiaolei Zhang, Katherine Fawcett, Amy Foreman, Petr Daneck, Panagiotis I. Sergouniotis, Helen Parkinson, Francesco Mazzarotto, Michael Inouye, Edward J. Hollox, Ewan Birney, Tomas Fitzgerald","doi":"10.1038/s41576-024-00778-y","DOIUrl":"https://doi.org/10.1038/s41576-024-00778-y","url":null,"abstract":"<p>Decades of genetic association testing in human cohorts have provided important insights into the genetic architecture and biological underpinnings of complex traits and diseases. However, for certain traits, genome-wide association studies (GWAS) for common SNPs are approaching signal saturation, which underscores the need to explore other types of genetic variation to understand the genetic basis of traits and diseases. Copy number variation (CNV) is an important source of heritability that is well known to functionally affect human traits. Recent technological and computational advances enable the large-scale, genome-wide evaluation of CNVs, with implications for downstream applications such as polygenic risk scoring and drug target identification. Here, we review the current state of CNV-GWAS, discuss current limitations in resource infrastructure that need to be overcome to enable the wider uptake of CNV-GWAS results, highlight emerging opportunities and suggest guidelines and standards for future GWAS for genetic variation beyond SNPs at scale.</p>","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"10 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142383638","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}
引用次数: 0
A call to action to scale up research and clinical genomic data sharing 扩大研究与临床基因组数据共享的行动呼吁
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2024-10-07 DOI: 10.1038/s41576-024-00776-0
Zornitza Stark, David Glazer, Oliver Hofmann, Augusto Rendon, Christian R. Marshall, Geoffrey S. Ginsburg, Chris Lunt, Naomi Allen, Mark Effingham, Jillian Hastings Ward, Sue L. Hill, Raghib Ali, Peter Goodhand, Angela Page, Heidi L. Rehm, Kathryn N. North, Richard H. Scott
{"title":"A call to action to scale up research and clinical genomic data sharing","authors":"Zornitza Stark, David Glazer, Oliver Hofmann, Augusto Rendon, Christian R. Marshall, Geoffrey S. Ginsburg, Chris Lunt, Naomi Allen, Mark Effingham, Jillian Hastings Ward, Sue L. Hill, Raghib Ali, Peter Goodhand, Angela Page, Heidi L. Rehm, Kathryn N. North, Richard H. Scott","doi":"10.1038/s41576-024-00776-0","DOIUrl":"https://doi.org/10.1038/s41576-024-00776-0","url":null,"abstract":"<p>Genomic data from millions of individuals have been generated worldwide to drive discovery and clinical impact in precision medicine. Lowering the barriers to using these data collectively is needed to equitably realize the benefits of the diversity and scale of population data. We examine the current landscape of global genomic data sharing, including the evolution of data sharing models from data aggregation through to data visiting, and for certain use cases, cross-cohort analysis using federated approaches across multiple environments. We highlight emerging examples of best practice relating to participant, patient and community engagement; evolution of technical standards, tools and infrastructure; and impact of research and health-care policy. We outline 12 actions we can all take together to scale up efforts to enable safe global data sharing and move beyond projects demonstrating feasibility to routinely cross-analysing research and clinical data sets, optimizing benefit.</p>","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"5 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142383639","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}
引用次数: 0
Endogenous retroviruses: unveiling new targets for cancer immunotherapy 内源性逆转录病毒：揭示癌症免疫疗法的新目标
IF 39.1 1区 生物学
Nature Reviews Genetics Pub Date : 2024-10-03 DOI: 10.1038/s41576-024-00784-0
Shengbao Suo
{"title":"Endogenous retroviruses: unveiling new targets for cancer immunotherapy","authors":"Shengbao Suo","doi":"10.1038/s41576-024-00784-0","DOIUrl":"10.1038/s41576-024-00784-0","url":null,"abstract":"In this Journal Club, Shengbao Suo highlights two publications that underscore the importance of genetic regulation of endogenous retrovirus expression in tumours.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 12","pages":"827-827"},"PeriodicalIF":39.1,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142369081","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}
引用次数: 0
From computational models of the splicing code to regulatory mechanisms and therapeutic implications 从剪接代码的计算模型到调控机制和治疗意义
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2024-10-02 DOI: 10.1038/s41576-024-00774-2
Charlotte Capitanchik, Oscar G. Wilkins, Nils Wagner, Julien Gagneur, Jernej Ule
{"title":"From computational models of the splicing code to regulatory mechanisms and therapeutic implications","authors":"Charlotte Capitanchik, Oscar G. Wilkins, Nils Wagner, Julien Gagneur, Jernej Ule","doi":"10.1038/s41576-024-00774-2","DOIUrl":"https://doi.org/10.1038/s41576-024-00774-2","url":null,"abstract":"<p>Since the discovery of RNA splicing and its role in gene expression, researchers have sought a set of rules, an algorithm or a computational model that could predict the splice isoforms, and their frequencies, produced from any transcribed gene in a specific cellular context. Over the past 30 years, these models have evolved from simple position weight matrices to deep-learning models capable of integrating sequence data across vast genomic distances. Most recently, new model architectures are moving the field closer to context-specific alternative splicing predictions, and advances in sequencing technologies are expanding the type of data that can be used to inform and interpret such models. Together, these developments are driving improved understanding of splicing regulatory mechanisms and emerging applications of the splicing code to the rational design of RNA- and splicing-based therapeutics.</p>","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"46 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142362739","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}
引用次数: 0
Inference and applications of ancestral recombination graphs 祖先重组图的推断与应用
IF 39.1 1区 生物学
Nature Reviews Genetics Pub Date : 2024-09-30 DOI: 10.1038/s41576-024-00772-4
Rasmus Nielsen, Andrew H. Vaughn, Yun Deng
{"title":"Inference and applications of ancestral recombination graphs","authors":"Rasmus Nielsen,&nbsp;Andrew H. Vaughn,&nbsp;Yun Deng","doi":"10.1038/s41576-024-00772-4","DOIUrl":"10.1038/s41576-024-00772-4","url":null,"abstract":"Ancestral recombination graphs (ARGs) summarize the complex genealogical relationships between individuals represented in a sample of DNA sequences. Their use is currently revolutionizing the field of population genetics and is leading to the development of powerful new methods to elucidate individual and population genetic processes, including population size history, migration, admixture, recombination, mutation and selection. In this Review, we introduce the readers to the structure of ARGs and discuss how they relate to processes such as recombination and genetic drift. We explore differences and similarities between methods of estimating ARGs and provide concrete illustrative examples of how ARGs can be used to elucidate population-level processes. Ancestral recombination graphs (ARGs) are revolutionizing population genetics by elucidating genetic processes such as demography, migration and selection. This Review introduces ARG structure, compares estimation methods and illustrates their application to understanding population dynamics.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 1","pages":"47-58"},"PeriodicalIF":39.1,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142329578","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}
引用次数: 0
Selection on structural variation in the amylase locus 对淀粉酶基因座结构变异的选择
IF 39.1 1区 生物学
Nature Reviews Genetics Pub Date : 2024-09-27 DOI: 10.1038/s41576-024-00782-2
Kirsty Minton
{"title":"Selection on structural variation in the amylase locus","authors":"Kirsty Minton","doi":"10.1038/s41576-024-00782-2","DOIUrl":"10.1038/s41576-024-00782-2","url":null,"abstract":"Bolognini et al. report evidence of positive selection for human amylase gene duplications associated with the agricultural revolution.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 11","pages":"748-748"},"PeriodicalIF":39.1,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142321963","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}
引用次数: 0
The evolution of DNA sequencing with microfluidics 利用微流体技术进行 DNA 测序的发展历程
IF 39.1 1区 生物学
Nature Reviews Genetics Pub Date : 2024-09-27 DOI: 10.1038/s41576-024-00783-1
Camille L. G. Lambert, Guido van Mierlo, Johannes J. Bues, Orane J. Guillaume-Gentil, Bart Deplancke
{"title":"The evolution of DNA sequencing with microfluidics","authors":"Camille L. G. Lambert,&nbsp;Guido van Mierlo,&nbsp;Johannes J. Bues,&nbsp;Orane J. Guillaume-Gentil,&nbsp;Bart Deplancke","doi":"10.1038/s41576-024-00783-1","DOIUrl":"10.1038/s41576-024-00783-1","url":null,"abstract":"The adoption of microfluidics was fundamental to the development of cost-effective, high-throughput DNA sequencing. As the field progresses towards multi-omics, we reflect on the key concepts underlying microfluidics and how resulting engineering advances at the microscale drove the evolution of genomic sequencing. The adoption of microfluidics was fundamental to the development of cost-effective, high-throughput DNA sequencing. As the field progresses towards multi-omics, Lambert et al. reflect on the key concepts underlying microfluidics and how resulting engineering advances at the microscale drove the evolution of genomic sequencing.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 1","pages":"1-2"},"PeriodicalIF":39.1,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142321966","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}
引用次数: 0
Genome-scale models in human metabologenomics 人类代谢组学中的基因组尺度模型
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2024-09-19 DOI: 10.1038/s41576-024-00768-0
Adil Mardinoglu, Bernhard Ø. Palsson
{"title":"Genome-scale models in human metabologenomics","authors":"Adil Mardinoglu, Bernhard Ø. Palsson","doi":"10.1038/s41576-024-00768-0","DOIUrl":"https://doi.org/10.1038/s41576-024-00768-0","url":null,"abstract":"<p>Metabologenomics integrates metabolomics with other omics data types to comprehensively study the genetic and environmental factors that influence metabolism. These multi-omics data can be incorporated into genome-scale metabolic models (GEMs), which are highly curated knowledge bases that explicitly account for genes, transcripts, proteins and metabolites. By including all known biochemical reactions catalysed by enzymes and transporters encoded in the human genome, GEMs analyse and predict the behaviour of complex metabolic networks. Continued advancements to the scale and scope of GEMs — from cells and tissues to microbiomes and the whole body — have helped to design effective treatments and develop better diagnostic tools for metabolic diseases. Furthermore, increasing amounts of multi-omics data are incorporated into GEMs to better identify the underlying mechanisms, biomarkers and potential drug targets of metabolic diseases.</p>","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"4 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142245261","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}
引用次数: 0
Gene synthesis from a non-coding RNA 非编码 RNA 的基因合成
IF 39.1 1区 生物学
Nature Reviews Genetics Pub Date : 2024-09-18 DOI: 10.1038/s41576-024-00781-3
Linda Koch
{"title":"Gene synthesis from a non-coding RNA","authors":"Linda Koch","doi":"10.1038/s41576-024-00781-3","DOIUrl":"10.1038/s41576-024-00781-3","url":null,"abstract":"A study in Science investigating bacterial defence mechanisms against phages reports a novel mode of gene regulation through reverse transcription of a non-coding RNA template, leading to the formation of a toxic repetitive gene.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 11","pages":"747-747"},"PeriodicalIF":39.1,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142236231","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}
引用次数: 0
Tumbling bacteria and non-genetic individuality 翻滚细菌和非遗传个体性
IF 39.1 1区 生物学
Nature Reviews Genetics Pub Date : 2024-09-18 DOI: 10.1038/s41576-024-00779-x
Alejo E. Rodriguez-Fraticelli
{"title":"Tumbling bacteria and non-genetic individuality","authors":"Alejo E. Rodriguez-Fraticelli","doi":"10.1038/s41576-024-00779-x","DOIUrl":"10.1038/s41576-024-00779-x","url":null,"abstract":"In this Journal Club, Alejo Rodriguez-Fratelli discusses a paper by Spudich and Koshland Jr that characterized non-genetic cell individuality in bacteria, a concept with emerging relevance to cancer progression.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 12","pages":"826-826"},"PeriodicalIF":39.1,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142236227","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}
引用次数: 0
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