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Annual review of genomics and human genetics最新文献

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Massively Parallel Assays and Quantitative Sequence-Function Relationships. 大规模并行分析和定量序列-函数关系。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2019-08-31 Epub Date: 2019-05-15 DOI: 10.1146/annurev-genom-083118-014845
Justin B Kinney, David M McCandlish
{"title":"Massively Parallel Assays and Quantitative Sequence-Function Relationships.","authors":"Justin B Kinney,&nbsp;David M McCandlish","doi":"10.1146/annurev-genom-083118-014845","DOIUrl":"https://doi.org/10.1146/annurev-genom-083118-014845","url":null,"abstract":"<p><p>Over the last decade, a rich variety of massively parallel assays have revolutionized our understanding of how biological sequences encode quantitative molecular phenotypes. These assays include deep mutational scanning, high-throughput SELEX, and massively parallel reporter assays. Here, we review these experimental methods and how the data they produce can be used to quantitatively model sequence-function relationships. In doing so, we touch on a diverse range of topics, including the identification of clinically relevant genomic variants, the modeling of transcription factor binding to DNA, the functional and evolutionary landscapes of proteins, and <i>cis</i>-regulatory mechanisms in both transcription and mRNA splicing. We further describe a unified conceptual framework and a core set of mathematical modeling strategies that studies in these diverse areas can make use of. Finally, we highlight key aspects of experimental design and mathematical modeling that are important for the results of such studies to be interpretable and reproducible.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":"20 ","pages":"99-127"},"PeriodicalIF":8.7,"publicationDate":"2019-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genom-083118-014845","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37245779","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: 12
The Causes and Consequences of Genetic Interactions (Epistasis). 遗传相互作用的原因和结果(上位性)。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2019-08-31 Epub Date: 2019-05-13 DOI: 10.1146/annurev-genom-083118-014857
Júlia Domingo, Pablo Baeza-Centurion, Ben Lehner
{"title":"The Causes and Consequences of Genetic Interactions (Epistasis).","authors":"Júlia Domingo,&nbsp;Pablo Baeza-Centurion,&nbsp;Ben Lehner","doi":"10.1146/annurev-genom-083118-014857","DOIUrl":"https://doi.org/10.1146/annurev-genom-083118-014857","url":null,"abstract":"<p><p>The same mutation can have different effects in different individuals. One important reason for this is that the outcome of a mutation can depend on the genetic context in which it occurs. This dependency is known as epistasis. In recent years, there has been a concerted effort to quantify the extent of pairwise and higher-order genetic interactions between mutations through deep mutagenesis of proteins and RNAs. This research has revealed two major components of epistasis: nonspecific genetic interactions caused by nonlinearities in genotype-to-phenotype maps, and specific interactions between particular mutations. Here, we provide an overview of our current understanding of the mechanisms causing epistasis at the molecular level, the consequences of genetic interactions for evolution and genetic prediction, and the applications of epistasis for understanding biology and determining macromolecular structures.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":"20 ","pages":"433-460"},"PeriodicalIF":8.7,"publicationDate":"2019-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genom-083118-014857","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37235559","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: 138
The Status and Impact of Clinical Tumor Genome Sequencing. 临床肿瘤基因组测序的现状及影响
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2019-08-31 Epub Date: 2019-04-17 DOI: 10.1146/annurev-genom-083118-015034
Kenna R Mills Shaw, Anirban Maitra
{"title":"The Status and Impact of Clinical Tumor Genome Sequencing.","authors":"Kenna R Mills Shaw,&nbsp;Anirban Maitra","doi":"10.1146/annurev-genom-083118-015034","DOIUrl":"https://doi.org/10.1146/annurev-genom-083118-015034","url":null,"abstract":"<p><p>Since the discovery that DNA alterations initiate tumorigenesis, scientists and clinicians have been exploring ways to counter these changes with targeted therapeutics. The sequencing of tumor DNA was initially limited to highly actionable hot spots-areas of the genome that are frequently altered and have an approved matched therapy in a specific tumor type. Large-scale genome sequencing programs quickly developed technological improvements that enabled the deployment of whole-exome and whole-genome sequencing technologies at scale for pristine sample materials in research environments. However, the turning point for precision medicine in oncology was the innovations in clinical laboratories that improved turnaround time, depth of coverage, and the ability to reliably sequence archived, clinically available samples. Today, tumor genome sequencing no longer suffers from significant technical or financial hurdles, and the next opportunity for improvement lies in the optimal utilization of the technologies and data for many different tumor types.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":"20 ","pages":"413-432"},"PeriodicalIF":8.7,"publicationDate":"2019-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genom-083118-015034","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37324382","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: 18
Lynch Syndrome: From Screening to Diagnosis to Treatment in the Era of Modern Molecular Oncology. Lynch综合征:现代分子肿瘤学时代从筛查到诊断到治疗。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2019-08-31 Epub Date: 2019-03-08 DOI: 10.1146/annurev-genom-083118-015406
Stacey A Cohen, Colin C Pritchard, Gail P Jarvik
{"title":"Lynch Syndrome: From Screening to Diagnosis to Treatment in the Era of Modern Molecular Oncology.","authors":"Stacey A Cohen,&nbsp;Colin C Pritchard,&nbsp;Gail P Jarvik","doi":"10.1146/annurev-genom-083118-015406","DOIUrl":"https://doi.org/10.1146/annurev-genom-083118-015406","url":null,"abstract":"<p><p>Lynch syndrome is a hereditary cancer predisposition syndrome caused by germline alterations in the mismatch repair genes and is the most common etiology of hereditary colorectal cancer. While Lynch syndrome was initially defined by the clinical Amsterdam criteria, these criteria lack the sensitivity needed for clinical utility. This review covers the evolution of screening for Lynch syndrome from the use of tumor microsatellite instability and/or somatic alterations in mismatch repair protein expression by immunohistochemistry to the newest methods using next-generation sequencing. Additionally, it discusses the clinical implications of the diagnosis of Lynch syndrome as it affects cancer therapeutics and the role of screening in noncolorectal Lynch-associated cancers. As molecular oncology continues to evolve, it is crucial to remain current on the increasing complexity of Lynch syndrome diagnostics and treatment options.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":"20 ","pages":"293-307"},"PeriodicalIF":8.7,"publicationDate":"2019-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genom-083118-015406","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37037001","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: 45
Measuring Clonal Evolution in Cancer with Genomics. 用基因组学测量癌症克隆进化。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2019-08-31 Epub Date: 2019-05-05 DOI: 10.1146/annurev-genom-083117-021712
Marc J Williams, Andrea Sottoriva, Trevor A Graham
{"title":"Measuring Clonal Evolution in Cancer with Genomics.","authors":"Marc J Williams,&nbsp;Andrea Sottoriva,&nbsp;Trevor A Graham","doi":"10.1146/annurev-genom-083117-021712","DOIUrl":"https://doi.org/10.1146/annurev-genom-083117-021712","url":null,"abstract":"<p><p>Cancers originate from somatic cells in the human body that have accumulated genetic alterations. These mutations modify the phenotype of the cells, allowing them to escape the homeostatic regulation that maintains normal cell number. Viewed through the lens of evolutionary biology, the transformation of normal cells into malignant cells is evolution in action. Evolution continues throughout cancer growth, progression, treatment resistance, and disease relapse, driven by adaptation to changes in the cancer's environment, and intratumor heterogeneity is an inevitable consequence of this evolutionary process. Genomics provides a powerful means to characterize tumor evolution, enabling quantitative measurement of evolving clones across space and time. In this review, we discuss concepts and approaches to quantify and measure this evolutionary process in cancer using genomics.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":"20 ","pages":"309-329"},"PeriodicalIF":8.7,"publicationDate":"2019-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genom-083117-021712","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37213836","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: 47
The Development of Human Genetics at the National Research Centre, Cairo, Egypt: A Story of 50 Years. 埃及开罗国家研究中心人类遗传学的发展:一个50年的故事。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2019-08-31 Epub Date: 2019-03-08 DOI: 10.1146/annurev-genom-083118-015201
Samia A Temtamy
{"title":"The Development of Human Genetics at the National Research Centre, Cairo, Egypt: A Story of 50 Years.","authors":"Samia A Temtamy","doi":"10.1146/annurev-genom-083118-015201","DOIUrl":"https://doi.org/10.1146/annurev-genom-083118-015201","url":null,"abstract":"<p><p>This article describes my experiences over more than 50 years in initiating and maintaining research on human genetics and genomics at the National Research Centre in Cairo, Egypt, from its beginnings in a small unit of human genetics to the creation of the Center of Excellence for Human Genetics. This was also the subject of a lecture I gave at the 10th Conference of the African Society of Human Genetics, held in Cairo in November 2017, after which Professor Michèle Ramsay, president of the society, suggested that I write an autobiographical article for the <i>Annual Review of Genomics and Human Genetics</i>. I hope that I succeeded in the difficult assignment of summarizing the efforts of a researcher from a developing country to initiate and maintain the rapidly advancing science of human genetics and genomics in my own country and make contributions to the worldwide scientific community.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":"20 ","pages":"1-19"},"PeriodicalIF":8.7,"publicationDate":"2019-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genom-083118-015201","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37037003","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: 6
Consanguinity and Inbreeding in Health and Disease in North African Populations. 北非人群健康与疾病的血缘关系和近亲繁殖。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2019-08-31 Epub Date: 2019-04-30 DOI: 10.1146/annurev-genom-083118-014954
Lilia Romdhane, Nessrine Mezzi, Yosr Hamdi, Ghada El-Kamah, Abdelhamid Barakat, Sonia Abdelhak
{"title":"Consanguinity and Inbreeding in Health and Disease in North African Populations.","authors":"Lilia Romdhane,&nbsp;Nessrine Mezzi,&nbsp;Yosr Hamdi,&nbsp;Ghada El-Kamah,&nbsp;Abdelhamid Barakat,&nbsp;Sonia Abdelhak","doi":"10.1146/annurev-genom-083118-014954","DOIUrl":"https://doi.org/10.1146/annurev-genom-083118-014954","url":null,"abstract":"<p><p>North Africa is defined as the geographical region separated from the rest of the continent by the Sahara and from Europe by the Mediterranean Sea. The main demographic features of North African populations are their familial structure and high rates of familial and geographic endogamy, which have a proven impact on health, particularly the occurrence of genetic diseases, with a greater effect on the frequency and spectrum of the rarest forms of autosomal recessive genetic diseases. More than 500 different genetic diseases have been reported in this region, most of which are autosomal recessive. During the last few decades, there has been great interest in the molecular investigation of large consanguineous North African families. The development of local capacities has brought a substantial improvement in the molecular characterization of these diseases, but the genetic bases of half of them remain unknown. Diseases of known molecular etiology are characterized by their genetic and mutational heterogeneity, although some founder mutations are encountered relatively frequently. Some founder mutations are specific to a single country or a specific ethnic or geographic group, and others are shared by all North African countries or worldwide. The impact of consanguinity on common multifactorial diseases is less evident.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":"20 ","pages":"155-179"},"PeriodicalIF":8.7,"publicationDate":"2019-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genom-083118-014954","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37361681","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: 42
Pregnancy Immunogenetics and Genomics: Implications for Pregnancy-Related Complications and Autoimmune Disease. 妊娠免疫遗传学和基因组学:妊娠相关并发症和自身免疫性疾病的含义。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2019-08-31 Epub Date: 2019-03-08 DOI: 10.1146/annurev-genom-083118-014943
Hing-Yuen Yeung, Calliope A Dendrou
{"title":"Pregnancy Immunogenetics and Genomics: Implications for Pregnancy-Related Complications and Autoimmune Disease.","authors":"Hing-Yuen Yeung,&nbsp;Calliope A Dendrou","doi":"10.1146/annurev-genom-083118-014943","DOIUrl":"https://doi.org/10.1146/annurev-genom-083118-014943","url":null,"abstract":"<p><p>Pregnancy presents a singular physiological scenario during which the maternal immune system must accommodate the semiallogeneic fetus. Fluctuations between pro- and anti-inflammatory states are required throughout gestation to facilitate uterine tissue remodeling, fetal growth and development, and finally birth. Tolerance for the fetus must be established and maintained without fundamentally compromising the maternal immune system function, so that both the mother and fetus are protected from foreign insults. Here, we review our current understanding of how genetic variation at both maternal and fetal loci affects implantation and placenta formation, thereby determining the likelihood of a successful pregnancy outcome or the development of pregnancy-related complications. We also consider the impact of pregnancy on both the maternal and fetal systemic immune systems and the related implications for modulating ongoing autoimmune diseases and triggering their development.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":"20 ","pages":"73-97"},"PeriodicalIF":8.7,"publicationDate":"2019-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genom-083118-014943","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37037002","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
Advances in the Genetic Basis and Pathogenesis of Sarcomere Cardiomyopathies. 肌瘤性心肌病的遗传基础及发病机制研究进展。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2019-08-31 Epub Date: 2019-04-12 DOI: 10.1146/annurev-genom-083118-015306
Raquel Yotti, Christine E Seidman, Jonathan G Seidman
{"title":"Advances in the Genetic Basis and Pathogenesis of Sarcomere Cardiomyopathies.","authors":"Raquel Yotti,&nbsp;Christine E Seidman,&nbsp;Jonathan G Seidman","doi":"10.1146/annurev-genom-083118-015306","DOIUrl":"https://doi.org/10.1146/annurev-genom-083118-015306","url":null,"abstract":"<p><p>Hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy (DCM) are common heart muscle disorders that are caused by pathogenic variants in sarcomere protein genes. HCM is characterized by unexplained cardiac hypertrophy (increased chamber wall thickness) that is accompanied by enhanced cardiac contractility and impaired relaxation. DCM is defined as increased ventricular chamber volume with contractile impairment. In this review, we discuss recent analyses that provide new insights into the molecular mechanisms that cause these conditions. HCM studies have uncovered the critical importance of conformational changes that occur during relaxation and enable energy conservation, which are frequently disturbed by HCM mutations. DCM studies have demonstrated the considerable prevalence of truncating variants in titin and have discerned that these variants reduce contractile function by impairing sarcomerogenesis. These new pathophysiologic mechanisms open exciting opportunities to identify new pharmacological targets and develop future cardioprotective strategies.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":"20 ","pages":"129-153"},"PeriodicalIF":8.7,"publicationDate":"2019-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genom-083118-015306","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37322829","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: 105
Thinking About the Evolution of Complex Traits in the Era of Genome-Wide Association Studies. 全基因组关联研究时代对复杂性状进化的思考
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2019-08-31 Epub Date: 2019-07-05 DOI: 10.1146/annurev-genom-083115-022316
Guy Sella, Nicholas H Barton
{"title":"Thinking About the Evolution of Complex Traits in the Era of Genome-Wide Association Studies.","authors":"Guy Sella,&nbsp;Nicholas H Barton","doi":"10.1146/annurev-genom-083115-022316","DOIUrl":"https://doi.org/10.1146/annurev-genom-083115-022316","url":null,"abstract":"<p><p>Many traits of interest are highly heritable and genetically complex, meaning that much of the variation they exhibit arises from differences at numerous loci in the genome. Complex traits and their evolution have been studied for more than a century, but only in the last decade have genome-wide association studies (GWASs) in humans begun to reveal their genetic basis. Here, we bring these threads of research together to ask how findings from GWASs can further our understanding of the processes that give rise to heritable variation in complex traits and of the genetic basis of complex trait evolution in response to changing selection pressures (i.e., of polygenic adaptation). Conversely, we ask how evolutionary thinking helps us to interpret findings from GWASs and informs related efforts of practical importance.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":"20 ","pages":"461-493"},"PeriodicalIF":8.7,"publicationDate":"2019-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genom-083115-022316","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37404447","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: 143
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