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Annual review of genomics and human genetics最新文献

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Investigating the Potential Roles of SINEs in the Human Genome. 研究正弦函数在人类基因组中的潜在作用。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2021-08-31 Epub Date: 2021-04-01 DOI: 10.1146/annurev-genom-111620-100736
Xiao-Ou Zhang, Henry Pratt, Zhiping Weng
{"title":"Investigating the Potential Roles of SINEs in the Human Genome.","authors":"Xiao-Ou Zhang,&nbsp;Henry Pratt,&nbsp;Zhiping Weng","doi":"10.1146/annurev-genom-111620-100736","DOIUrl":"https://doi.org/10.1146/annurev-genom-111620-100736","url":null,"abstract":"<p><p>Short interspersed nuclear elements (SINEs) are nonautonomous retrotransposons that occupy approximately 13% of the human genome. They are transcribed by RNA polymerase III and can be retrotranscribed and inserted back into the genome with the help of other autonomous retroelements. Because they are preferentially located close to or within gene-rich regions, they can regulate gene expression by various mechanisms that act at both the DNA and the RNA levels. In this review, we summarize recent findings on the involvement of SINEs in different types of gene regulation and discuss the potential regulatory functions of SINEs that are in close proximity to genes, Pol III-transcribed SINE RNAs, and embedded SINE sequences within Pol II-transcribed genes in the human genome. These discoveries illustrate how the human genome has exapted some SINEs into functional regulatory elements.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":"22 ","pages":"199-218"},"PeriodicalIF":8.7,"publicationDate":"2021-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25552226","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: 14
Global Governance of Human Genome Editing: What Are the Rules? 人类基因组编辑的全球治理:规则是什么?
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2021-08-31 Epub Date: 2021-03-05 DOI: 10.1146/annurev-genom-111320-091930
Gary E Marchant
{"title":"Global Governance of Human Genome Editing: What Are the Rules?","authors":"Gary E Marchant","doi":"10.1146/annurev-genom-111320-091930","DOIUrl":"https://doi.org/10.1146/annurev-genom-111320-091930","url":null,"abstract":"<p><p>Human gene editing, particularly using the new CRISPR/Cas9 technology, will greatly increase the capability to make precise changes to human genomes. Human gene editing can be broken into four major categories: somatic therapy, heritable gene editing, genetic enhancement, and basic and applied research. Somatic therapy is generally well governed by national regulatory systems, so the need for global governance is less urgent. All nations are in agreement that heritable gene editing should not proceed at this time, but there is likely to be divergence if and when such procedures are shown to be safe and effective. Gene editing for enhancement purposes is not feasible today but is more controversial with the public, and many nations do not have well-developed regulatory systems for addressing genetic enhancement. Finally, different nations treat research with human embryos very differently based on deeply embedded social, cultural, ethical, and legal traditions. Several international governance mechanisms are currently in operation for human gene editing, and several other governance mechanisms have been proposed. It is unlikely that any single mechanism will alone be effective for governing human gene editing; rather, a polycentric or ecosystem approach that includes several overlapping and interacting components is likely to be necessary.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":"22 ","pages":"385-405"},"PeriodicalIF":8.7,"publicationDate":"2021-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25433231","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: 5
Brain Somatic Mutation in Aging and Alzheimer's Disease. 衰老和阿尔茨海默病中的大脑体细胞突变。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2021-08-31 Epub Date: 2021-05-12 DOI: 10.1146/annurev-genom-121520-081242
Michael B Miller, Hannah C Reed, Christopher A Walsh
{"title":"Brain Somatic Mutation in Aging and Alzheimer's Disease.","authors":"Michael B Miller,&nbsp;Hannah C Reed,&nbsp;Christopher A Walsh","doi":"10.1146/annurev-genom-121520-081242","DOIUrl":"https://doi.org/10.1146/annurev-genom-121520-081242","url":null,"abstract":"<p><p>Somatic mutations arise postzygotically, producing genetic differences between cells in an organism. Well established as a driver of cancer, somatic mutations also exist in nonneoplastic cells, including in the brain. Technological advances in nucleic acid sequencing have enabled recent breakthroughs that illuminate the roles of somatic mutations in aging and degenerative diseases of the brain. Somatic mutations accumulate during aging in human neurons, a process termed genosenium. A number of recent studies have examined somatic mutations in Alzheimer's disease (AD), primarily from the perspective of genes causing familial AD. We have also gained new information on genome-wide mutations, providing insights into the cellular events driving somatic mutation and cellular dysfunction. This review highlights recent concepts, methods, and findings in the progress to understand the role of brain somatic mutation in aging and AD.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":"22 ","pages":"239-256"},"PeriodicalIF":8.7,"publicationDate":"2021-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8612367/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38904747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 27
The Science and Art of Clinical Genetic Variant Classification and Its Impact on Test Accuracy. 临床遗传变异分类的科学与艺术及其对检测准确性的影响。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2021-08-31 Epub Date: 2021-04-26 DOI: 10.1146/annurev-genom-121620-082709
Hunter H Giles, Madhuri R Hegde, Elaine Lyon, Christine M Stanley, Iain D Kerr, Megan E Garlapow, Julie M Eggington
{"title":"The Science and Art of Clinical Genetic Variant Classification and Its Impact on Test Accuracy.","authors":"Hunter H Giles,&nbsp;Madhuri R Hegde,&nbsp;Elaine Lyon,&nbsp;Christine M Stanley,&nbsp;Iain D Kerr,&nbsp;Megan E Garlapow,&nbsp;Julie M Eggington","doi":"10.1146/annurev-genom-121620-082709","DOIUrl":"https://doi.org/10.1146/annurev-genom-121620-082709","url":null,"abstract":"<p><p>Clinical genetic variant classification science is a growing subspecialty of clinical genetics and genomics. The field's continued improvement is essential for the success of precision medicine in both germline (hereditary) and somatic (oncology) contexts. This review focuses on variant classification for DNA next-generation sequencing tests. We first summarize current limitations in variant discovery and definition, and then describe the current five- and four-tier classification systems outlined in dominant standards and guideline publications for germline and somatic tests, respectively. We then discuss measures of variant classification discordance and the field's bias for positive results, as well as considerations for panel size and population screening in the context of estimates of positive predictive value thatincorporate estimated variant classification imperfections. Finally, we share opinions on the current state of variant classification from some of the authors of the most widely used standards and guideline publications and from other domain experts.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":"22 ","pages":"285-307"},"PeriodicalIF":8.7,"publicationDate":"2021-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38908602","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: 1
Transcriptional Regulation by (Super)Enhancers: From Discovery to Mechanisms. (超级)增强子的转录调控:从发现到机制。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2021-08-31 Epub Date: 2021-05-05 DOI: 10.1146/annurev-genom-122220-093818
Frank Grosveld, Jente van Staalduinen, Ralph Stadhouders
{"title":"Transcriptional Regulation by (Super)Enhancers: From Discovery to Mechanisms.","authors":"Frank Grosveld,&nbsp;Jente van Staalduinen,&nbsp;Ralph Stadhouders","doi":"10.1146/annurev-genom-122220-093818","DOIUrl":"https://doi.org/10.1146/annurev-genom-122220-093818","url":null,"abstract":"<p><p>Accurate control of gene expression in the right cell at the right moment is of fundamental importance to animal development and homeostasis. At the heart of gene regulation lie the enhancers, a class of gene regulatory elements that ensures precise spatiotemporal activation of gene transcription. Mammalian genomes are littered with enhancers, which are frequently organized in cooperative clusters such as locus control regions and superenhancers. Here, we discuss our current knowledge of enhancer biology, including an overview of the discovery of the various enhancer subsets and the mechanistic models used to explain their gene regulatory function.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":"22 ","pages":"127-146"},"PeriodicalIF":8.7,"publicationDate":"2021-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38952321","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: 49
Heart Development and Congenital Structural Heart Defects. 心脏发育和先天性结构性心脏缺陷。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2021-08-31 Epub Date: 2021-06-01 DOI: 10.1146/annurev-genom-083118-015012
Lucile Houyel, Sigolène M Meilhac
{"title":"Heart Development and Congenital Structural Heart Defects.","authors":"Lucile Houyel,&nbsp;Sigolène M Meilhac","doi":"10.1146/annurev-genom-083118-015012","DOIUrl":"https://doi.org/10.1146/annurev-genom-083118-015012","url":null,"abstract":"<p><p>Congenital heart disease is the most frequent birth defect and the leading cause of death for the fetus and in the first year of life. The wide phenotypic diversity of congenital heart defects requires expert diagnosis and sophisticated repair surgery. Although these defects have been described since the seventeenth century, it was only in 2005 that a consensus international nomenclature was adopted, followed by an international classification in 2017 to help provide better management of patients. Advances in genetic engineering, imaging, and omics analyses have uncovered mechanisms of heart formation and malformation in animal models, but approximately 80% of congenital heart defects have an unknown genetic origin. Here, we summarize current knowledge of congenital structural heart defects, intertwining clinical and fundamental research perspectives, with the aim to foster interdisciplinary collaborations at the cutting edge of each field. We also discuss remaining challenges in better understanding congenital heart defects and providing benefits to patients.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":"22 ","pages":"257-284"},"PeriodicalIF":8.7,"publicationDate":"2021-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39039438","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: 17
Therapeutic Opportunities of Targeting Canonical and Noncanonical PcG/TrxG Functions in Acute Myeloid Leukemia. 针对急性髓性白血病中规范和非规范 PcG/TrxG 功能的治疗机会
IF 7.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2021-08-31 Epub Date: 2021-04-30 DOI: 10.1146/annurev-genom-111120-102443
Bernd B Zeisig, Chi Wai Eric So
{"title":"Therapeutic Opportunities of Targeting Canonical and Noncanonical PcG/TrxG Functions in Acute Myeloid Leukemia.","authors":"Bernd B Zeisig, Chi Wai Eric So","doi":"10.1146/annurev-genom-111120-102443","DOIUrl":"10.1146/annurev-genom-111120-102443","url":null,"abstract":"<p><p>Transcriptional deregulation is a key driver of acute myeloid leukemia (AML), a heterogeneous blood cancer with poor survival rates. Polycomb group (PcG) and Trithorax group (TrxG) genes, originally identified in <i>Drosophila melanogaster</i> several decades ago as master regulators of cellular identity and epigenetic memory, not only are important in mammalian development but also play a key role in AML disease biology. In addition to their classical canonical antagonistic transcriptional functions, noncanonical synergistic and nontranscriptional functions of PcG and TrxG are emerging. Here, we review the biochemical properties of major mammalian PcG and TrxG complexes and their roles in AML disease biology, including disease maintenance as well as drug resistance. We summarize current efforts on targeting PcG and TrxG for treatment of AML and propose rational synthetic lethality and drug-induced antagonistic pleiotropy options involving PcG and TrxG as potential new therapeutic avenues for treatment of AML.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":"22 ","pages":"103-125"},"PeriodicalIF":7.7,"publicationDate":"2021-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38935204","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 Need for a Human Pangenome Reference Sequence. 人类泛基因组参考序列的需求。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2021-08-31 Epub Date: 2021-04-30 DOI: 10.1146/annurev-genom-120120-081921
Karen H Miga, Ting Wang
{"title":"The Need for a Human Pangenome Reference Sequence.","authors":"Karen H Miga,&nbsp;Ting Wang","doi":"10.1146/annurev-genom-120120-081921","DOIUrl":"10.1146/annurev-genom-120120-081921","url":null,"abstract":"<p><p>The reference human genome sequence is inarguably the most important and widely used resource in the fields of human genetics and genomics. It has transformed the conduct of biomedical sciences and brought invaluable benefits to the understanding and improvement of human health. However, the commonly used reference sequence has profound limitations, because across much of its span, it represents the sequence of just one human haplotype. This single, monoploid reference structure presents a critical barrier to representing the broad genomic diversity in the human population. In this review, we discuss the modernization of the reference human genome sequence to a more complete reference of human genomic diversity, known as a human pangenome.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":"22 ","pages":"81-102"},"PeriodicalIF":8.7,"publicationDate":"2021-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8410644/pdf/nihms-1715955.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38935203","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 57
Threespine Stickleback: A Model System For Evolutionary Genomics. 三刺棒背鱼：进化基因组学的模型系统
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2021-08-31 Epub Date: 2021-04-28 DOI: 10.1146/annurev-genom-111720-081402
Kerry Reid, Michael A Bell, Krishna R Veeramah
{"title":"Threespine Stickleback: A Model System For Evolutionary Genomics.","authors":"Kerry Reid, Michael A Bell, Krishna R Veeramah","doi":"10.1146/annurev-genom-111720-081402","DOIUrl":"10.1146/annurev-genom-111720-081402","url":null,"abstract":"<p><p>The repeated adaptation of oceanic threespine sticklebacks to fresh water has made it a premier organism to study parallel evolution. These small fish have multiple distinct ecotypes that display a wide range of diverse phenotypic traits. Ecotypes are easily crossed in the laboratory, and families are large and develop quickly enough for quantitative trait locus analyses, positioning the threespine stickleback as a versatile model organism to address a wide range of biological questions. Extensive genomic resources, including linkage maps, a high-quality reference genome, and developmental genetics tools have led to insights into the genomic basis of adaptation and the identification of genomic changes controlling traits in vertebrates. Recently, threespine sticklebacks have been used as a model system to identify the genomic basis of highly complex traits, such as behavior and host-microbiome and host-parasite interactions. We review the latest findings and new avenues of research that have led the threespine stickleback to be considered a supermodel of evolutionary genomics.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":"22 ","pages":"357-383"},"PeriodicalIF":8.7,"publicationDate":"2021-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8415275/pdf/nihms-1730595.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38836885","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The Role of Electronic Health Records in Advancing Genomic Medicine. 电子健康记录在推进基因组医学中的作用。
IF 7.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2021-08-31 Epub Date: 2021-05-26 DOI: 10.1146/annurev-genom-121120-125204
Jodell E Linder, Lisa Bastarache, Jacob J Hughey, Josh F Peterson
{"title":"The Role of Electronic Health Records in Advancing Genomic Medicine.","authors":"Jodell E Linder, Lisa Bastarache, Jacob J Hughey, Josh F Peterson","doi":"10.1146/annurev-genom-121120-125204","DOIUrl":"10.1146/annurev-genom-121120-125204","url":null,"abstract":"<p><p>Recent advances in genomic technology and widespread adoption of electronic health records (EHRs) have accelerated the development of genomic medicine, bringing promising research findings from genome science into clinical practice. Genomic and phenomic data, accrued across large populations through biobanks linked to EHRs, have enabled the study of genetic variation at a phenome-wide scale. Through new quantitative techniques, pleiotropy can be explored with phenome-wide association studies, the occurrence of common complex diseases can be predicted using the cumulative influence of many genetic variants (polygenic risk scores), and undiagnosed Mendelian syndromes can be identified using EHR-based phenotypic signatures (phenotype risk scores). In this review, we trace the role of EHRs from the development of genome-wide analytic techniques to translational efforts to test these new interventions to the clinic. Throughout, we describe the challenges that remain when combining EHRs with genetics to improve clinical care.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":"22 ","pages":"219-238"},"PeriodicalIF":7.7,"publicationDate":"2021-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9297710/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39020313","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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