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Annual review of genomics and human genetics最新文献

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The UK Biobank: A Shining Example of Genome-Wide Association Study Science with the Power to Detect the Murky Complications of Real-World Epidemiology. 英国生物库：全基因组关联研究科学的光辉典范，有能力检测真实世界流行病学的复杂性。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2022-08-31 Epub Date: 2022-05-04 DOI: 10.1146/annurev-genom-121321-093606
Vanessa Y Tan, Nicholas J Timpson
{"title":"The UK Biobank: A Shining Example of Genome-Wide Association Study Science with the Power to Detect the Murky Complications of Real-World Epidemiology.","authors":"Vanessa Y Tan, Nicholas J Timpson","doi":"10.1146/annurev-genom-121321-093606","DOIUrl":"10.1146/annurev-genom-121321-093606","url":null,"abstract":"<p><p>Genome-wide association studies (GWASs) have successfully identified thousands of genetic variants that are reliably associated with human traits. Although GWASs are restricted to certain variant frequencies, they have improved our understanding of the genetic architecture of complex traits and diseases. The UK Biobank (UKBB) has brought substantial analytical opportunity and performance to association studies. The dramatic expansion of many GWAS sample sizes afforded by the inclusion of UKBB data has improved the power of estimation of effect sizes but, critically, has done so in a context where phenotypic depth and precision enable outcome dissection and the application of epidemiological approaches. However, at the same time, the availability of such a large, well-curated, and deeply measured population-based collection has the capacity to increase our exposure to the many complications and inferential complexities associated with GWASs and other analyses. In this review, we discuss the impact that UKBB has had in the GWAS era, some of the opportunities that it brings, and exemplar challenges that illustrate the reality of using data from this world-leading resource.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2022-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10271092","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
Natural and Experimental Rewiring of Gene Regulatory Regions. 基因调控区的自然和实验重配
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2022-08-31 Epub Date: 2022-04-26 DOI: 10.1146/annurev-genom-112921-010715
Damien J Downes, Jim R Hughes
{"title":"Natural and Experimental Rewiring of Gene Regulatory Regions.","authors":"Damien J Downes, Jim R Hughes","doi":"10.1146/annurev-genom-112921-010715","DOIUrl":"10.1146/annurev-genom-112921-010715","url":null,"abstract":"<p><p>The successful development and ongoing functioning of complex organisms depend on the faithful execution of the genetic code. A critical step in this process is the correct spatial and temporal expression of genes. The highly orchestrated transcription of genes is controlled primarily by <i>cis-</i>regulatory elements: promoters, enhancers, and insulators. The medical importance of this key biological process can be seen by the frequency with which mutations and inherited variants that alter <i>cis-</i>regulatory elements lead to monogenic and complex diseases and cancer. Here, we provide an overview of the methods available to characterize and perturb gene regulatory circuits. We then highlight mechanisms through which regulatory rewiring contributes to disease, and conclude with a perspective on how our understanding of gene regulation can be used to improve human health.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2022-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84218471","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
Decoding the Human Face: Progress and Challenges in Understanding the Genetics of Craniofacial Morphology. 解码人类面孔：了解颅面形态遗传学的进展与挑战》。
IF 7.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2022-08-31 Epub Date: 2022-04-28 DOI: 10.1146/annurev-genom-120121-102607
Sahin Naqvi, Hanne Hoskens, Franziska Wilke, Seth M Weinberg, John R Shaffer, Susan Walsh, Mark D Shriver, Joanna Wysocka, Peter Claes
{"title":"Decoding the Human Face: Progress and Challenges in Understanding the Genetics of Craniofacial Morphology.","authors":"Sahin Naqvi, Hanne Hoskens, Franziska Wilke, Seth M Weinberg, John R Shaffer, Susan Walsh, Mark D Shriver, Joanna Wysocka, Peter Claes","doi":"10.1146/annurev-genom-120121-102607","DOIUrl":"10.1146/annurev-genom-120121-102607","url":null,"abstract":"<p><p>Variations in the form of the human face, which plays a role in our individual identities and societal interactions, have fascinated scientists and artists alike. Here, we review our current understanding of the genetics underlying variation in craniofacial morphology and disease-associated dysmorphology, synthesizing decades of progress on Mendelian syndromes in addition to more recent results from genome-wide association studies of human facial shape and disease risk. We also discuss the various approaches used to phenotype and quantify facial shape, which are of particular importance due to the complex, multipartite nature of the craniofacial form. We close by discussing how experimental studies have contributed and will further contribute to our understanding of human genetic variation and then proposing future directions and applications for the field.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2022-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9482780/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87372734","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
Advancing Pharmacogenomics from Single-Gene to Preemptive Testing. 推进药物基因组学从单基因到抢先检测。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2022-08-31 DOI: 10.1146/annurev-genom-111621-102737
Cyrine E Haidar, Kristine R Crews, James M Hoffman, Mary V Relling, Kelly E Caudle
{"title":"Advancing Pharmacogenomics from Single-Gene to Preemptive Testing.","authors":"Cyrine E Haidar,&nbsp;Kristine R Crews,&nbsp;James M Hoffman,&nbsp;Mary V Relling,&nbsp;Kelly E Caudle","doi":"10.1146/annurev-genom-111621-102737","DOIUrl":"https://doi.org/10.1146/annurev-genom-111621-102737","url":null,"abstract":"<p><p>Pharmacogenomic testing can be an effective tool to enhance medication safety and efficacy. Pharmacogenomically actionable medications are widely used, and approximately 90-95% of individuals have an actionable genotype for at least one pharmacogene. For pharmacogenomic testing to have the greatest impact on medication safety and clinical care, genetic information should be made available at the time of prescribing (preemptive testing). However, the use of preemptive pharmacogenomic testing is associated with some logistical concerns, such as consistent reimbursement, processes for reporting preemptive results over an individual's lifetime, and result portability. Lessons can be learned from institutions that have implemented preemptive pharmacogenomic testing. In this review, we discuss the rationale and best practices for implementing pharmacogenomics preemptively.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2022-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9483991/pdf/nihms-1832645.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10114080","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: 7
Extrachromosomal DNA in Cancer. 癌症染色体外DNA。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2022-08-31 Epub Date: 2022-05-24 DOI: 10.1146/annurev-genom-120821-100535
Vineet Bafna, Paul S Mischel
{"title":"Extrachromosomal DNA in Cancer.","authors":"Vineet Bafna,&nbsp;Paul S Mischel","doi":"10.1146/annurev-genom-120821-100535","DOIUrl":"10.1146/annurev-genom-120821-100535","url":null,"abstract":"<p><p>In cancer, complex genome rearrangements and other structural alterations, including the amplification of oncogenes on circular extrachromosomal DNA (ecDNA) elements, drive the formation and progression of tumors. ecDNA is a particularly challenging structural alteration. By untethering oncogenes from chromosomal constraints, it elevates oncogene copy number, drives intratumoral genetic heterogeneity, promotes rapid tumor evolution, and results in treatment resistance. The profound changes in DNA shape and nuclear architecture generated by ecDNA alter the transcriptional landscape of tumors by catalyzing new types of regulatory interactions that do not occur on chromosomes. The current suite of tools for interrogating cancer genomes is well suited for deciphering sequence but has limited ability to resolve the complex changes in DNA structure and dynamics that ecDNA generates. Here, we review the challenges of resolving ecDNA form and function and discuss the emerging tool kit for deciphering ecDNA architecture and spatial organization, including what has been learned to date about how this dramatic change in shape alters tumor development, progression, and drug resistance.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2022-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10508221/pdf/nihms-1907774.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9701963","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: 10
Regulation of Molecular Diagnostics. 分子诊断学调控。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2022-08-31 DOI: 10.1146/annurev-genom-121521-010416
Gail H Javitt, Erik R Vollebregt
{"title":"Regulation of Molecular Diagnostics.","authors":"Gail H Javitt,&nbsp;Erik R Vollebregt","doi":"10.1146/annurev-genom-121521-010416","DOIUrl":"https://doi.org/10.1146/annurev-genom-121521-010416","url":null,"abstract":"<p><p>Molecular diagnostic tests enable rapid analysis of genomic and proteomic markers. These tests are subject to diverging premarket access and postmarket surveillance requirements and mechanisms in the United States and the European Union. Each of these jurisdictions has its own challenges in keeping the regulations up to date with technological developments. A specific area of attention is that of laboratory-developed tests in the United States and health institution in-house-produced tests in the European Union, for which the United States and the European Union have markedly different regulatory approaches. Both jurisdictions have specific but differing requirements for the use of test samples and test-related data under their rules regarding the protection of (personal) health data, which can cause complexity when moving samples or sample-related data from one jurisdiction to the other.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2022-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40333596","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: 2
The Next Frontier in Noninvasive Prenatal Diagnostics: Cell-Free Fetal DNA Analysis for Monogenic Disease Assessment. 无创产前诊断的下一个前沿:单基因疾病评估的无细胞胎儿DNA分析。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2022-08-31 Epub Date: 2022-03-22 DOI: 10.1146/annurev-genom-110821-113411
Lilian Pok Wa Zhong, Rossa W K Chiu
{"title":"The Next Frontier in Noninvasive Prenatal Diagnostics: Cell-Free Fetal DNA Analysis for Monogenic Disease Assessment.","authors":"Lilian Pok Wa Zhong,&nbsp;Rossa W K Chiu","doi":"10.1146/annurev-genom-110821-113411","DOIUrl":"https://doi.org/10.1146/annurev-genom-110821-113411","url":null,"abstract":"<p><p>With the widespread clinical adoption of noninvasive screening for fetal chromosomal aneuploidies based on cell-free DNA analysis from maternal plasma, more researchers are turning their attention to noninvasive prenatal assessment for single-gene disorders. The development of a spectrum of approaches to analyze cell-free DNA in maternal circulation, including relative mutation dosage, relative haplotype dosage, and size-based methods, has expanded the scope of noninvasive prenatal testing to sex-linked and autosomal recessive disorders. Cell-free fetal DNA analysis for several of the more prevalent single-gene disorders has recently been introduced into clinical service. This article reviews the analytical approaches currently available and discusses the extent of the clinical implementation of noninvasive prenatal testing for single-gene disorders.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2022-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40313135","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
Mosaicism in Tumor Suppressor Gene Syndromes: Prevalence, Diagnostic Strategies, and Transmission Risk. 肿瘤抑制基因综合征中的镶嵌现象:患病率、诊断策略和传播风险。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2022-08-31 DOI: 10.1146/annurev-genom-120121-105450
Jillian L Chen, David T Miller, Laura S Schmidt, David Malkin, Bruce R Korf, Charis Eng, David J Kwiatkowski, Krinio Giannikou
{"title":"Mosaicism in Tumor Suppressor Gene Syndromes: Prevalence, Diagnostic Strategies, and Transmission Risk.","authors":"Jillian L Chen,&nbsp;David T Miller,&nbsp;Laura S Schmidt,&nbsp;David Malkin,&nbsp;Bruce R Korf,&nbsp;Charis Eng,&nbsp;David J Kwiatkowski,&nbsp;Krinio Giannikou","doi":"10.1146/annurev-genom-120121-105450","DOIUrl":"https://doi.org/10.1146/annurev-genom-120121-105450","url":null,"abstract":"<p><p>A mosaic state arises when pathogenic variants are acquired in certain cell lineages during postzygotic development, and mosaic individuals may present with a generalized or localized phenotype. Here, we review the current state of knowledge regarding mosaicism for eight common tumor suppressor genes-<i>NF1</i>, <i>NF2</i>, <i>TSC1</i>, <i>TSC2</i>, <i>PTEN</i>, <i>VHL</i>, <i>RB1</i>, and <i>TP53</i>-and their related genetic syndromes/entities. We compare and discuss approaches for comprehensive diagnostic genetic testing, the spectrum of variant allele frequency, and disease severity. We also review affected individuals who have no mutation identified after conventional genetic analysis, as well as genotype-phenotype correlations and transmission risk for each tumor suppressor gene in full heterozygous and mosaic patients. This review provides new insight into similarities as well as marked differences regarding the appreciation of mosaicism in these tumor suppressor syndromes.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2022-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40333597","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
Maintaining Transcriptional Specificity Through Mitosis. 通过有丝分裂维持转录特异性。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2022-08-31 DOI: 10.1146/annurev-genom-121321-094603
Kenji Ito, Kenneth S Zaret
{"title":"Maintaining Transcriptional Specificity Through Mitosis.","authors":"Kenji Ito,&nbsp;Kenneth S Zaret","doi":"10.1146/annurev-genom-121321-094603","DOIUrl":"https://doi.org/10.1146/annurev-genom-121321-094603","url":null,"abstract":"<p><p>Virtually all cell types have the same DNA, yet each type exhibits its own cell-specific pattern of gene expression. During the brief period of mitosis, the chromosomes exhibit changes in protein composition and modifications, a marked condensation, and a consequent reduction in transcription. Yet as cells exit mitosis, they reactivate their cell-specific programs with high fidelity. Initially, the field focused on the subset of transcription factors that are selectively retained in, and hence bookmark, chromatin in mitosis. However, recent studies show that many transcription factors can be retained in mitotic chromatin and that, surprisingly, such retention can be due to nonspecific chromatin binding. Here, we review the latest studies focusing on low-level transcription via promoters, rather than enhancers, as contributing to mitotic memory, as well as new insights into chromosome structure dynamics, histone modifications, cell cycle signaling, and nuclear envelope proteins that together ensure the fidelity of gene expression through a round of mitosis.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2022-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9976632/pdf/nihms-1873036.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10813511","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: 10
The Genetics and Typical Traits of Thoracic Aortic Aneurysm and Dissection. 胸主动脉瘤及夹层的遗传学及典型特征。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2022-08-31 DOI: 10.1146/annurev-genom-111521-104455
Jotte Rodrigues Bento, Josephina Meester, Ilse Luyckx, Silke Peeters, Aline Verstraeten, Bart Loeys
{"title":"The Genetics and Typical Traits of Thoracic Aortic Aneurysm and Dissection.","authors":"Jotte Rodrigues Bento,&nbsp;Josephina Meester,&nbsp;Ilse Luyckx,&nbsp;Silke Peeters,&nbsp;Aline Verstraeten,&nbsp;Bart Loeys","doi":"10.1146/annurev-genom-111521-104455","DOIUrl":"https://doi.org/10.1146/annurev-genom-111521-104455","url":null,"abstract":"<p><p>Genetic predisposition and risk factors such as hypertension and smoking can instigate the development of thoracic aortic aneurysm (TAA), which can lead to highly lethal aortic wall dissection and/or rupture. Monogenic defects in multiple genes involved in the elastin-contractile unit and the TGFβ signaling pathway have been associated with TAA in recent years, along with several genetic modifiers and risk-conferring polymorphisms. Advances in omics technology have also provided significant insights into the processes behind aortic wall degeneration: inflammation, epigenetics, vascular smooth muscle phenotype change and depletion, reactive oxygen species generation, mitochondrial dysfunction, and angiotensin signaling dysregulation. These recent advances and findings might pave the way for a therapy that is capable of stopping and perhaps even reversing aneurysm progression.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2022-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40334755","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: 9
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