Nature Reviews Genetics最新文献_第10页

The expanding diagnostic toolbox for rare genetic diseases 罕见遗传病诊断工具箱不断扩大

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2024-01-18 DOI: 10.1038/s41576-023-00683-w

Kristin D. Kernohan, Kym M. Boycott

{"title":"The expanding diagnostic toolbox for rare genetic diseases","authors":"Kristin D. Kernohan, Kym M. Boycott","doi":"10.1038/s41576-023-00683-w","DOIUrl":"10.1038/s41576-023-00683-w","url":null,"abstract":"Genomic technologies, such as targeted, exome and short-read genome sequencing approaches, have revolutionized the care of patients with rare genetic diseases. However, more than half of patients remain without a diagnosis. Emerging approaches from research-based settings such as long-read genome sequencing and optical genome mapping hold promise for improving the identification of disease-causal genetic variants. In addition, new omic technologies that measure the transcriptome, epigenome, proteome or metabolome are showing great potential for variant interpretation. As genetic testing options rapidly expand, the clinical community needs to be mindful of their individual strengths and limitations, as well as remaining challenges, to select the appropriate diagnostic test, correctly interpret results and drive innovation to address insufficiencies. If used effectively — through truly integrative multi-omics approaches and data sharing — the resulting large quantities of data from these established and emerging technologies will greatly improve the interpretative power of genetic and genomic diagnostics for rare diseases. Genomic technologies have greatly improved the diagnosis of rare genetic diseases. Here, the authors review emerging approaches for the identification of disease-causal genetic variants as well as omic technologies that show great potential for variant interpretation.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":null,"pages":null},"PeriodicalIF":42.7,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139489740","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

Challenges and best practices in omics benchmarking omics 基准制定的挑战和最佳实践

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2024-01-12 DOI: 10.1038/s41576-023-00679-6

Thomas G. Brooks, Nicholas F. Lahens, Antonijo Mrčela, Gregory R. Grant

{"title":"Challenges and best practices in omics benchmarking","authors":"Thomas G. Brooks, Nicholas F. Lahens, Antonijo Mrčela, Gregory R. Grant","doi":"10.1038/s41576-023-00679-6","DOIUrl":"10.1038/s41576-023-00679-6","url":null,"abstract":"Technological advances enabling massively parallel measurement of biological features — such as microarrays, high-throughput sequencing and mass spectrometry — have ushered in the omics era, now in its third decade. The resulting complex landscape of analytical methods has naturally fostered the growth of an omics benchmarking industry. Benchmarking refers to the process of objectively comparing and evaluating the performance of different computational or analytical techniques when processing and analysing large-scale biological data sets, such as transcriptomics, proteomics and metabolomics. With thousands of omics benchmarking studies published over the past 25 years, the field has matured to the point where the foundations of benchmarking have been established and well described. However, generating meaningful benchmarking data and properly evaluating performance in this complex domain remains challenging. In this Review, we highlight some common oversights and pitfalls in omics benchmarking. We also establish a methodology to bring the issues that can be addressed into focus and to be transparent about those that cannot: this takes the form of a spreadsheet template of guidelines for comprehensive reporting, intended to accompany publications. In addition, a survey of recent developments in benchmarking is provided as well as specific guidance for commonly encountered difficulties. In this Review, the authors summarize and discuss guidelines for omics benchmarking. They highlight common oversights and difficulties, offer guidance for frequently encountered issues and provide a structured form that can be used for comprehensive reporting of benchmarking studies.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":null,"pages":null},"PeriodicalIF":42.7,"publicationDate":"2024-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139431347","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

Real-time single-molecule imaging of transcriptional regulatory networks in living cells 活细胞中转录调控网络的实时单分子成像。

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2024-01-09 DOI: 10.1038/s41576-023-00684-9

Dong-Woo Hwang, Anna Maekiniemi, Robert H. Singer, Hanae Sato

{"title":"Real-time single-molecule imaging of transcriptional regulatory networks in living cells","authors":"Dong-Woo Hwang, Anna Maekiniemi, Robert H. Singer, Hanae Sato","doi":"10.1038/s41576-023-00684-9","DOIUrl":"10.1038/s41576-023-00684-9","url":null,"abstract":"Gene regulatory networks drive the specific transcriptional programmes responsible for the diversification of cell types during the development of multicellular organisms. Although our knowledge of the genes involved in these dynamic networks has expanded rapidly, our understanding of how transcription is spatiotemporally regulated at the molecular level over a wide range of timescales in the small volume of the nucleus remains limited. Over the past few decades, advances in the field of single-molecule fluorescence imaging have enabled real-time behaviours of individual transcriptional components to be measured in living cells and organisms. These efforts are now shedding light on the dynamic mechanisms of transcription, revealing not only the temporal rules but also the spatial coordination of underlying molecular interactions during various biological events. In this Review, Hwang and co-authors outline single-molecule fluorescence imaging techniques that can be used in living cells to visualize individual molecules involved in the spatiotemporal regulation of gene expression. This Review also delves into the biological insights gained through these methodologies.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":null,"pages":null},"PeriodicalIF":42.7,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139403776","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

Swapping genes within and beyond our bodies 在我们身体内外交换基因。

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2023-12-20 DOI: 10.1038/s41576-023-00689-4

Mashaal Sohail

引用次数: 0

Efficient computation reveals rare CRISPR–Cas systems 高效计算揭示了罕见的 CRISPR-Cas 系统。

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2023-12-19 DOI: 10.1038/s41576-023-00690-x

Henry Ertl

引用次数: 0

Spatial resolution of host–microbiome interactions 宿主-微生物组相互作用的空间分辨率

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2023-12-15 DOI: 10.1038/s41576-023-00687-6

Kirsty Minton

引用次数: 0

The transition from genomics to phenomics in personalized population health 个性化人群健康从基因组学向表型组学过渡

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2023-12-13 DOI: 10.1038/s41576-023-00674-x

James T. Yurkovich, Simon J. Evans, Noa Rappaport, Jeffrey L. Boore, Jennifer C. Lovejoy, Nathan D. Price, Leroy E. Hood

{"title":"The transition from genomics to phenomics in personalized population health","authors":"James T. Yurkovich, Simon J. Evans, Noa Rappaport, Jeffrey L. Boore, Jennifer C. Lovejoy, Nathan D. Price, Leroy E. Hood","doi":"10.1038/s41576-023-00674-x","DOIUrl":"10.1038/s41576-023-00674-x","url":null,"abstract":"Modern health care faces several serious challenges, including an ageing population and its inherent burden of chronic diseases, rising costs and marginal quality metrics. By assessing and optimizing the health trajectory of each individual using a data-driven personalized approach that reflects their genetics, behaviour and environment, we can start to address these challenges. This assessment includes longitudinal phenome measures, such as the blood proteome and metabolome, gut microbiome composition and function, and lifestyle and behaviour through wearables and questionnaires. Here, we review ongoing large-scale genomics and longitudinal phenomics efforts and the powerful insights they provide into wellness. We describe our vision for the transformation of the current health care from disease-oriented to data-driven, wellness-oriented and personalized population health. This Perspective reviews large-scale genomics and longitudinal phenomics efforts and the insights they can provide into wellness. The authors describe their vision for the transformation of the current health care from disease-oriented to data-driven, wellness-oriented and personalized population health.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":null,"pages":null},"PeriodicalIF":42.7,"publicationDate":"2023-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138657527","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

Decoding human genetic variation using a synthetic paradigm 使用合成范式解码人类基因变异

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2023-12-06 DOI: 10.1038/s41576-023-00682-x

Aashiq H. Kachroo

引用次数: 0

Divergence and conservation of the meiotic recombination machinery 减数分裂重组机制的分化与保存。

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2023-11-30 DOI: 10.1038/s41576-023-00669-8

Meret Arter, Scott Keeney

{"title":"Divergence and conservation of the meiotic recombination machinery","authors":"Meret Arter, Scott Keeney","doi":"10.1038/s41576-023-00669-8","DOIUrl":"10.1038/s41576-023-00669-8","url":null,"abstract":"Sexually reproducing eukaryotes use recombination between homologous chromosomes to promote chromosome segregation during meiosis. Meiotic recombination is almost universally conserved in its broad strokes, but specific molecular details often differ considerably between taxa, and the proteins that constitute the recombination machinery show substantial sequence variability. The extent of this variation is becoming increasingly clear because of recent increases in genomic resources and advances in protein structure prediction. We discuss the tension between functional conservation and rapid evolutionary change with a focus on the proteins that are required for the formation and repair of meiotic DNA double-strand breaks. We highlight phylogenetic relationships on different time scales and propose that this remarkable evolutionary plasticity is a fundamental property of meiotic recombination that shapes our understanding of molecular mechanisms in reproductive biology. In this Review, the authors describe the evolutionary conservation and divergence of the meiotic recombination machinery, focusing on proteins that are required for meiotic double-strand break formation, double-strand break repair via homologous recombination and the formation of crossover and non-crossover recombinant DNA molecules.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":null,"pages":null},"PeriodicalIF":42.7,"publicationDate":"2023-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138461215","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

SWI/SNF function compensated by another chromatin remodeller SWI/SNF功能由另一种染色质重塑剂补偿

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2023-11-27 DOI: 10.1038/s41576-023-00680-z

Henry Ertl

引用次数: 0