Pub Date : 2024-11-20DOI: 10.1038/s41576-024-00794-y
C. Scott Gallagher, Geoffrey S. Ginsburg, Anjené Musick
Precision medicine provides patients with access to personally tailored treatments based on individual-level data. However, developing personalized therapies requires analyses with substantial statistical power to map genetic and epidemiologic associations that ultimately create models informing clinical decisions. As one solution, biobanks have emerged as large-scale, longitudinal cohort studies with long-term storage of biological specimens and health information, including electronic health records and participant survey responses. By providing access to individual-level data for genotype–phenotype mapping efforts, pharmacogenomic studies, polygenic risk score assessments and rare variant analyses, biobanks support ongoing and future precision medicine research. Notably, due in part to the geographical enrichment of biobanks in Western Europe and North America, European ancestries have become disproportionately over-represented in precision medicine research. Herein, we provide a genetics-focused review of biobanks from around the world that are in pursuit of supporting precision medicine. We discuss the limitations of their designs, ongoing efforts to diversify genomics research and strategies to maximize the benefits of research leveraging biobanks for all.
{"title":"Biobanking with genetics shapes precision medicine and global health","authors":"C. Scott Gallagher, Geoffrey S. Ginsburg, Anjené Musick","doi":"10.1038/s41576-024-00794-y","DOIUrl":"https://doi.org/10.1038/s41576-024-00794-y","url":null,"abstract":"<p>Precision medicine provides patients with access to personally tailored treatments based on individual-level data. However, developing personalized therapies requires analyses with substantial statistical power to map genetic and epidemiologic associations that ultimately create models informing clinical decisions. As one solution, biobanks have emerged as large-scale, longitudinal cohort studies with long-term storage of biological specimens and health information, including electronic health records and participant survey responses. By providing access to individual-level data for genotype–phenotype mapping efforts, pharmacogenomic studies, polygenic risk score assessments and rare variant analyses, biobanks support ongoing and future precision medicine research. Notably, due in part to the geographical enrichment of biobanks in Western Europe and North America, European ancestries have become disproportionately over-represented in precision medicine research. Herein, we provide a genetics-focused review of biobanks from around the world that are in pursuit of supporting precision medicine. We discuss the limitations of their designs, ongoing efforts to diversify genomics research and strategies to maximize the benefits of research leveraging biobanks for all.</p>","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"99 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142673332","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}
Pub Date : 2024-11-11DOI: 10.1038/s41576-024-00793-z
Simon Snoeck, Oliver Johanndrees, Thorsten Nürnberger, Cyril Zipfel
The plant immune system relies on germline-encoded pattern recognition receptors (PRRs) that sense foreign and plant-derived molecular patterns, and signal health threats. Genomic and pangenomic data sets provide valuable insights into the evolution of PRRs and their molecular triggers, which is furthering our understanding of plant–pathogen co-evolution and convergent evolution. Moreover, in silico and in vivo methods of PRR identification have accelerated the characterization of receptor–ligand complexes, and advances in protein structure prediction algorithms are revealing novel PRR sensor functions. Harnessing these recent advances to engineer PRRs presents an opportunity to enhance plant disease resistance against a broad spectrum of pathogens, enabling more sustainable agricultural practices. This Review summarizes both established and innovative approaches to leverage genomic data and translate resulting evolutionary insights into engineering PRR recognition specificities.
{"title":"Plant pattern recognition receptors: from evolutionary insight to engineering","authors":"Simon Snoeck, Oliver Johanndrees, Thorsten Nürnberger, Cyril Zipfel","doi":"10.1038/s41576-024-00793-z","DOIUrl":"https://doi.org/10.1038/s41576-024-00793-z","url":null,"abstract":"<p>The plant immune system relies on germline-encoded pattern recognition receptors (PRRs) that sense foreign and plant-derived molecular patterns, and signal health threats. Genomic and pangenomic data sets provide valuable insights into the evolution of PRRs and their molecular triggers, which is furthering our understanding of plant–pathogen co-evolution and convergent evolution. Moreover, in silico and in vivo methods of PRR identification have accelerated the characterization of receptor–ligand complexes, and advances in protein structure prediction algorithms are revealing novel PRR sensor functions. Harnessing these recent advances to engineer PRRs presents an opportunity to enhance plant disease resistance against a broad spectrum of pathogens, enabling more sustainable agricultural practices. This Review summarizes both established and innovative approaches to leverage genomic data and translate resulting evolutionary insights into engineering PRR recognition specificities.</p>","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"10 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142598302","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}
Pub Date : 2024-11-06DOI: 10.1038/s41576-024-00802-1
Abderrahman Khila
Abderrahman Khila highlights an important 2015 paper by Barson et al. that demonstrated how sexual conflict in Atlantic salmon affects genetic evolution.
{"title":"Genetic conflict and its resolution between the sexes","authors":"Abderrahman Khila","doi":"10.1038/s41576-024-00802-1","DOIUrl":"https://doi.org/10.1038/s41576-024-00802-1","url":null,"abstract":"Abderrahman Khila highlights an important 2015 paper by Barson et al. that demonstrated how sexual conflict in Atlantic salmon affects genetic evolution.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"68 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142588683","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}
Pub Date : 2024-11-06DOI: 10.1038/s41576-024-00801-2
Charles C. Davis, Sandra Knapp
Natural history collections are unparalleled resources for studying biodiversity across multiple dimensions. As multi-omic tools are being applied to museum specimens, the emerging field of museomics is undergoing a rapid and exciting transformation, with new opportunities, challenges and confrontations with past legacies. In this Comment, the authors showcase how the emerging field of museomics — the application of multi-omic tools to natural history collections — is undergoing a rapid and exciting transformation, with new opportunities, challenges and confrontations with past legacies.
{"title":"Exploring biodiversity through museomics","authors":"Charles C. Davis, Sandra Knapp","doi":"10.1038/s41576-024-00801-2","DOIUrl":"https://doi.org/10.1038/s41576-024-00801-2","url":null,"abstract":"Natural history collections are unparalleled resources for studying biodiversity across multiple dimensions. As multi-omic tools are being applied to museum specimens, the emerging field of museomics is undergoing a rapid and exciting transformation, with new opportunities, challenges and confrontations with past legacies. In this Comment, the authors showcase how the emerging field of museomics — the application of multi-omic tools to natural history collections — is undergoing a rapid and exciting transformation, with new opportunities, challenges and confrontations with past legacies.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"110 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142588684","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}
Pub Date : 2024-11-06DOI: 10.1038/s41576-024-00786-y
Joshua S. James, Junbiao Dai, Wei Leong Chew, Yizhi Cai
Synthetic genomics seeks to design and construct entire genomes to mechanistically dissect fundamental questions of genome function and to engineer organisms for diverse applications, including bioproduction of high-value chemicals and biologics, advanced cell therapies, and stress-tolerant crops. Recent progress has been fuelled by advancements in DNA synthesis, assembly, delivery and editing. Computational innovations, such as the use of artificial intelligence to provide prediction of function, also provide increasing capabilities to guide synthetic genome design and construction. However, translating synthetic genome-scale projects from idea to implementation remains highly complex. Here, we aim to streamline this implementation process by comprehensively reviewing the strategies for design, construction, delivery, debugging and tailoring of synthetic genomes as well as their potential applications.
{"title":"The design and engineering of synthetic genomes","authors":"Joshua S. James, Junbiao Dai, Wei Leong Chew, Yizhi Cai","doi":"10.1038/s41576-024-00786-y","DOIUrl":"https://doi.org/10.1038/s41576-024-00786-y","url":null,"abstract":"<p>Synthetic genomics seeks to design and construct entire genomes to mechanistically dissect fundamental questions of genome function and to engineer organisms for diverse applications, including bioproduction of high-value chemicals and biologics, advanced cell therapies, and stress-tolerant crops. Recent progress has been fuelled by advancements in DNA synthesis, assembly, delivery and editing. Computational innovations, such as the use of artificial intelligence to provide prediction of function, also provide increasing capabilities to guide synthetic genome design and construction. However, translating synthetic genome-scale projects from idea to implementation remains highly complex. Here, we aim to streamline this implementation process by comprehensively reviewing the strategies for design, construction, delivery, debugging and tailoring of synthetic genomes as well as their potential applications.</p>","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"36 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142588685","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":"Slide-tags enables spatial single-nucleus sequencing","authors":"Andrew J. C. Russell","doi":"10.1038/s41576-024-00797-9","DOIUrl":"https://doi.org/10.1038/s41576-024-00797-9","url":null,"abstract":"In this Tools of the Trade article, Andrew Russell describes Slide-tags, a method for scalable, spatially resolved single-nucleus sequencing.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"69 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142574463","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}
Pub Date : 2024-10-29DOI: 10.1038/s41576-024-00800-3
Julie Jung, Thomas King
In this Journal Club, Julie Jung and Thomas King recount a paper by Chan et al. that identified the regulatory changes underlying recurrent phenotypic evolution in stickleback fish.
{"title":"The phenotypic consequences of enhancer evolution","authors":"Julie Jung, Thomas King","doi":"10.1038/s41576-024-00800-3","DOIUrl":"https://doi.org/10.1038/s41576-024-00800-3","url":null,"abstract":"In this Journal Club, Julie Jung and Thomas King recount a paper by Chan et al. that identified the regulatory changes underlying recurrent phenotypic evolution in stickleback fish.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"127 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142520169","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}
Pub Date : 2024-10-29DOI: 10.1038/s41576-024-00798-8
Lingzhao Fang
Lingzhao Fang recalls how a 2002 paper by Brem et al., which investigated the genetic basis of natural variation in gene expression in budding yeast, and the GTEx atlas of genetic regulatory effects across human tissues inspired the FarmGTEx project to accelerate precision agriculture.
{"title":"Context-specific regulatory variants in precision medicine and agriculture","authors":"Lingzhao Fang","doi":"10.1038/s41576-024-00798-8","DOIUrl":"https://doi.org/10.1038/s41576-024-00798-8","url":null,"abstract":"Lingzhao Fang recalls how a 2002 paper by Brem et al., which investigated the genetic basis of natural variation in gene expression in budding yeast, and the GTEx atlas of genetic regulatory effects across human tissues inspired the FarmGTEx project to accelerate precision agriculture.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"11 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142536895","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}
Pub Date : 2024-10-29DOI: 10.1038/s41576-024-00799-7
Kejun Ying
In this Tools of the Trade article, Kejun Ying describes epigenome-wide Mendelian randomization, which integrates Mendelian randomization into a DNA-methylation-based epigenetic clock to identify CpG sites with potential causal links to lifespan and healthspan.
在这篇 "贸易工具"(Tools of the Trade)文章中,Kejun Ying介绍了全表观基因组孟德尔随机化(epigenome-wide Mendelian randomization),该方法将孟德尔随机化与基于DNA甲基化的表观遗传时钟相结合,以鉴定与寿命和健康寿命有潜在因果关系的CpG位点。
{"title":"Causal inference for epigenetic ageing","authors":"Kejun Ying","doi":"10.1038/s41576-024-00799-7","DOIUrl":"https://doi.org/10.1038/s41576-024-00799-7","url":null,"abstract":"In this Tools of the Trade article, Kejun Ying describes epigenome-wide Mendelian randomization, which integrates Mendelian randomization into a DNA-methylation-based epigenetic clock to identify CpG sites with potential causal links to lifespan and healthspan.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142520168","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}
Pub Date : 2024-10-25DOI: 10.1038/s41576-024-00795-x
Julia Horsfield
In this Journal Club, Julia Horsfield recounts two papers that demonstrated how cohesin and CTCF together organize the genome and regulate gene expression.
{"title":"Cohesin and CTCF emerge as building blocks of 3D genome structure","authors":"Julia Horsfield","doi":"10.1038/s41576-024-00795-x","DOIUrl":"https://doi.org/10.1038/s41576-024-00795-x","url":null,"abstract":"In this Journal Club, Julia Horsfield recounts two papers that demonstrated how cohesin and CTCF together organize the genome and regulate gene expression.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"2 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142489503","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}