Annual review of genomics and human genetics最新文献

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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
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
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
The Joubert-Meckel-Nephronophthisis Spectrum of Ciliopathies. 纤毛病的joubert - meckel -肾病谱。
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-121321-093528
Julie C Van De Weghe, Arianna Gomez, Dan Doherty
{"title":"The Joubert-Meckel-Nephronophthisis Spectrum of Ciliopathies.","authors":"Julie C Van De Weghe,&nbsp;Arianna Gomez,&nbsp;Dan Doherty","doi":"10.1146/annurev-genom-121321-093528","DOIUrl":"https://doi.org/10.1146/annurev-genom-121321-093528","url":null,"abstract":"<p><p>The Joubert syndrome (JS), Meckel syndrome (MKS), and nephronophthisis (NPH) ciliopathy spectrum could be the poster child for advances and challenges in Mendelian human genetics over the past half century. Progress in understanding these conditions illustrates many core concepts of human genetics. The JS phenotype alone is caused by pathogenic variants in more than 40 genes; remarkably, all of the associated proteins function in and around the primary cilium. Primary cilia are near-ubiquitous, microtubule-based organelles that play crucial roles in development and homeostasis. Protruding from the cell, these cellular antennae sense diverse signals and mediate Hedgehog and other critical signaling pathways. Ciliary dysfunction causes many human conditions termed ciliopathies, which range from multiple congenital malformations to adult-onset single-organ failure. Research on the genetics of the JS-MKS-NPH spectrum has spurred extensive functional work exploring the broadly important role of primary cilia in health and disease. This functional work promises to illuminate the mechanisms underlying JS-MKS-NPH in humans, identify therapeutic targets across genetic causes, and generate future precision treatments.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":"23 ","pages":"301-329"},"PeriodicalIF":8.7,"publicationDate":"2022-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9437135/pdf/nihms-1816012.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9751888","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: 12
Establishing the Medical Actionability of Genomic Variants. 建立基因组变异的医学可操作性。
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-111021-032401
Katrina A B Goddard, Kristy Lee, Adam H Buchanan, Bradford C Powell, Jessica Ezzell Hunter
{"title":"Establishing the Medical Actionability of Genomic Variants.","authors":"Katrina A B Goddard,&nbsp;Kristy Lee,&nbsp;Adam H Buchanan,&nbsp;Bradford C Powell,&nbsp;Jessica Ezzell Hunter","doi":"10.1146/annurev-genom-111021-032401","DOIUrl":"https://doi.org/10.1146/annurev-genom-111021-032401","url":null,"abstract":"<p><p>Actionability is an important concept in medicine that does not have a well-accepted standard definition, nor is there a general consensus on how to establish it. Medical actionability is often conflated with clinical utility, a related but distinct concept. This lack of clarity contributes to practice variation and inconsistent coverage decisions in genomic medicine, leading to the potential for systematic bias in the use of evidence-based interventions. We clarify how medical actionability and clinical utility are distinct and then discuss the spectrum of actionability, including benefits for the person, the family, and society. We also describe applications across the life course, including prediction, diagnosis, and treatment. Current challenges in assessing the medical actionability of identified genomic variants include gaps in the evidence, limited contexts with practice guidelines, and subjective aspects of medical actionability. A standardized and authoritative assessment of medical actionability is critical to implementing genomic medicine in a fashion that improves population health outcomes and reduces health disparities.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":"23 ","pages":"173-192"},"PeriodicalIF":8.7,"publicationDate":"2022-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10184682/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9463891","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
Structural Variation in Cancer: Role, Prevalence, and Mechanisms. 癌症的结构变异:作用、流行和机制。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2022-06-02 DOI: 10.1146/annurev-genom-120121-101149
M. R. Cosenza, Bernardo Rodriguez-Martin, J. Korbel
{"title":"Structural Variation in Cancer: Role, Prevalence, and Mechanisms.","authors":"M. R. Cosenza, Bernardo Rodriguez-Martin, J. Korbel","doi":"10.1146/annurev-genom-120121-101149","DOIUrl":"https://doi.org/10.1146/annurev-genom-120121-101149","url":null,"abstract":"Somatic rearrangements resulting in genomic structural variation drive malignant phenotypes by altering the expression or function of cancer genes. Pan-cancer studies have revealed that structural variants (SVs) are the predominant class of driver mutation in most cancer types, but because they are difficult to discover, they remain understudied when compared with point mutations. This review provides an overview of the current knowledge of somatic SVs, discussing their primary roles, prevalence in different contexts, and mutational mechanisms. SVs arise throughout the life history of cancer, and 55% of driver mutations uncovered by the Pan-Cancer Analysis of Whole Genomes project represent SVs. Leveraging the convergence of cell biology and genomics, we propose a mechanistic classification of somatic SVs, from simple to highly complex DNA rearrangement classes. The actions of DNA repair and DNA replication processes together with mitotic errors result in a rich spectrum of SV formation processes, with cascading effects mediating extensive structural diversity after an initiating DNA lesion has formed. Thanks to new sequencing technologies, including the sequencing of single-cell genomes, open questions about the molecular triggers and the biomolecules involved in SV formation as well as their mutational rates can now be addressed. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":"2 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2022-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89511669","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: 19
Five Priorities of African Genomics Research: The Next Frontier. 非洲基因组学研究的五个优先事项:下一个前沿。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2022-05-16 DOI: 10.1146/annurev-genom-111521-102452
A. Wonkam, N. S. Munung, C. Dandara, K. Esoh, N. Hanchard, G. Landouré
{"title":"Five Priorities of African Genomics Research: The Next Frontier.","authors":"A. Wonkam, N. S. Munung, C. Dandara, K. Esoh, N. Hanchard, G. Landouré","doi":"10.1146/annurev-genom-111521-102452","DOIUrl":"https://doi.org/10.1146/annurev-genom-111521-102452","url":null,"abstract":"To embrace the prospects of accurately diagnosing thousands of monogenic conditions, predicting disease risks for complex traits or diseases, tailoring treatment to individuals' pharmacogenetic profiles, and potentially curing some diseases, research into African genomic variation is a scientific imperative. African genomes harbor millions of uncaptured variants accumulated over 300,000 years of modern humans' evolutionary history, with successive waves of admixture, migration, and natural selection combining with extensive ecological diversity to create a broad and exceptional genomic complexity. Harnessing African genomic complexity, therefore, will require sustained commitment and equitable collaboration from the scientific community and funding agencies. African governments must support academic public research and industrial partnerships that build the necessary genetic medicine workforce, utilize the emerging genomic big data to develop expertise in computer science and bioinformatics, and evolve national and global governance frameworks that recognize the ethical implications of data-driven genomic research and empower its application in African social, cultural, economic, and religious contexts. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":"1 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2022-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88635355","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
The Genetics of Brugada Syndrome. Brugada综合征的遗传学。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2022-05-13 DOI: 10.1146/annurev-genom-112921-011200
M. Cerrone, S. Costa, M. Delmar
{"title":"The Genetics of Brugada Syndrome.","authors":"M. Cerrone, S. Costa, M. Delmar","doi":"10.1146/annurev-genom-112921-011200","DOIUrl":"https://doi.org/10.1146/annurev-genom-112921-011200","url":null,"abstract":"Brugada syndrome is a heritable channelopathy characterized by a peculiar electrocardiogram (ECG) pattern and increased risk of cardiac arrhythmias and sudden death. The arrhythmias originate because of an imbalance between the repolarizing and depolarizing currents that modulate the cardiac action potential. Even if an overt structural cardiomyopathy is not typical of Brugada syndrome, fibrosis and structural changes in the right ventricle contribute to a conduction slowing, which ultimately facilitates ventricular arrhythmias. Currently, Mendelian autosomal dominant transmission is detected in less than 25% of all clinical confirmed cases. Although 23 genes have been associated with the condition, only SCN5A, encoding the cardiac sodium channel, is considered clinically actionable and disease causing. The limited monogenic inheritance has pointed toward new perspectives on the possible complex genetic architecture of the disease, involving polygenic inheritance and a polygenic risk score that can influence penetrance and risk stratification. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":"465 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2022-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75845215","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
A Journey Through Genetics to Biology. 从遗传学到生物学之旅
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2022-05-13 DOI: 10.1146/annurev-genom-010622-095109
V. van Heyningen
{"title":"A Journey Through Genetics to Biology.","authors":"V. van Heyningen","doi":"10.1146/annurev-genom-010622-095109","DOIUrl":"https://doi.org/10.1146/annurev-genom-010622-095109","url":null,"abstract":"Although my engagement with human genetics emerged gradually, and sometimes serendipitously, it has held me spellbound for decades. Without my teachers, students, postdocs, colleagues, and collaborators, I would not be writing this review of my scientific adventures. Early gene and disease mapping was a satisfying puzzle-solving exercise, but building biological insight was my main goal. The project trajectory was hugely influenced by the evolutionarily conserved nature of the implicated genes and by the pace of progress in genetic technologies. The rich detail of clinical observations, particularly in eye disease, makes humans an excellent model, especially when complemented by the use of multiple other animal species for experimental validation. The contributions of collaborators and rivals also influenced our approach. We are very fortunate to work in this era of unprecedented progress in genetics and genomics. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":"18 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2022-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81760346","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
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