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Annual review of genomics and human genetics最新文献

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Population Screening in Health Systems. 卫生系统中的人口筛查。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2022-08-31 Epub Date: 2022-02-17 DOI: 10.1146/annurev-genom-111221-115239
Marc S Williams
{"title":"Population Screening in Health Systems.","authors":"Marc S Williams","doi":"10.1146/annurev-genom-111221-115239","DOIUrl":"https://doi.org/10.1146/annurev-genom-111221-115239","url":null,"abstract":"<p><p>Applications of genomics to population screening are expanding in the United States and internationally. Many of these programs are being implemented in the context of healthcare systems, mostly in a clinical research setting, but there are some emerging examples of clinical models. This review examines these genomic population screening programs to identify common features and differences in screened conditions, genomic technology employed, approach to results disclosure, health outcomes, financial models, and sustainability. The diversity of approaches provides opportunities to learn and better understand the optimal approach to implementation based on the contextual setting.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":" ","pages":"549-567"},"PeriodicalIF":8.7,"publicationDate":"2022-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39628998","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: 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":"23 ","pages":"29-52"},"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
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":"23 ","pages":"449-473"},"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
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":" ","pages":"653-673"},"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":" ","pages":"413-425"},"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":" ","pages":"331-361"},"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":"23 ","pages":"53-71"},"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":" ","pages":"223-253"},"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
Predicting Archaic Hominin Phenotypes from Genomic Data. 从基因组数据预测古人类表型。
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-111521-121903
Colin M Brand, Laura L Colbran, John A Capra
{"title":"Predicting Archaic Hominin Phenotypes from Genomic Data.","authors":"Colin M Brand,&nbsp;Laura L Colbran,&nbsp;John A Capra","doi":"10.1146/annurev-genom-111521-121903","DOIUrl":"https://doi.org/10.1146/annurev-genom-111521-121903","url":null,"abstract":"<p><p>Ancient DNA provides a powerful window into the biology of extant and extinct species, including humans' closest relatives: Denisovans and Neanderthals. Here, we review what is known about archaic hominin phenotypes from genomic data and how those inferences have been made. We contend that understanding the influence of variants on lower-level molecular phenotypes-such as gene expression and protein function-is a promising approach to using ancient DNA to learn about archaic hominin traits. Molecular phenotypes have simpler genetic architectures than organism-level complex phenotypes, and this approach enables moving beyond association studies by proposing hypotheses about the effects of archaic variants that are testable in model systems. The major challenge to understanding archaic hominin phenotypes is broadening our ability to accurately map genotypes to phenotypes, but ongoing advances ensure that there will be much more to learn about archaic hominin phenotypes from their genomes.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":"23 ","pages":"591-612"},"PeriodicalIF":8.7,"publicationDate":"2022-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10250142/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9599993","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
The Role of Genome Sequencing in Neonatal Intensive Care Units. 基因组测序在新生儿重症监护病房中的作用。
IF 7.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2022-08-31 Epub Date: 2022-06-08 DOI: 10.1146/annurev-genom-120921-103442
Stephen F Kingsmore, F Sessions Cole
{"title":"The Role of Genome Sequencing in Neonatal Intensive Care Units.","authors":"Stephen F Kingsmore, F Sessions Cole","doi":"10.1146/annurev-genom-120921-103442","DOIUrl":"10.1146/annurev-genom-120921-103442","url":null,"abstract":"<p><p>Genetic diseases disrupt the functionality of an infant's genome during fetal-neonatal adaptation and represent a leading cause of neonatal and infant mortality in the United States. Due to disease acuity, gene locus and allelic heterogeneity, and overlapping and diverse clinical phenotypes, diagnostic genome sequencing in neonatal intensive care units has required the development of methods to shorten turnaround times and improve genomic interpretation. From 2012 to 2021, 31 clinical studies documented the diagnostic and clinical utility of first-tier rapid or ultrarapid whole-genome sequencing through cost-effective identification of pathogenic genomic variants that change medical management, suggest new therapeutic strategies, and refine prognoses. Genomic diagnosis also permits prediction of reproductive recurrence risk for parents and surviving probands. Using implementation science and quality improvement, deployment of a genomic learning healthcare system will contribute to a reduction of neonatal and infant mortality through the integration of genome sequencing into best-practice neonatal intensive care.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":"23 ","pages":"427-448"},"PeriodicalIF":7.7,"publicationDate":"2022-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9844117/pdf/nihms-1861578.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10528877","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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