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RNA Sequencing in Disease Diagnosis. 疾病诊断中的 RNA 测序。
IF 7.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2024-08-01 Epub Date: 2024-08-06 DOI: 10.1146/annurev-genom-021623-121812
Craig Smail, Stephen B Montgomery
{"title":"RNA Sequencing in Disease Diagnosis.","authors":"Craig Smail, Stephen B Montgomery","doi":"10.1146/annurev-genom-021623-121812","DOIUrl":"10.1146/annurev-genom-021623-121812","url":null,"abstract":"<p><p>RNA sequencing (RNA-seq) enables the accurate measurement of multiple transcriptomic phenotypes for modeling the impacts of disease variants. Advances in technologies, experimental protocols, and analysis strategies are rapidly expanding the application of RNA-seq to identify disease biomarkers, tissue- and cell-type-specific impacts, and the spatial localization of disease-associated mechanisms. Ongoing international efforts to construct biobank-scale transcriptomic repositories with matched genomic data across diverse population groups are further increasing the utility of RNA-seq approaches by providing large-scale normative reference resources. The availability of these resources, combined with improved computational analysis pipelines, has enabled the detection of aberrant transcriptomic phenotypes underlying rare diseases. Further expansion of these resources, across both somatic and developmental tissues, is expected to soon provide unprecedented insights to resolve disease origin, mechanism of action, and causal gene contributions, suggesting the continued high utility of RNA-seq in disease diagnosis.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139740277","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 Myriad Decision at 10. Myriad 决定，第 10 页。
IF 7.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2024-08-01 Epub Date: 2024-08-06 DOI: 10.1146/annurev-genom-010323-011239
Jacob S Sherkow, Robert Cook-Deegan, Henry T Greely
{"title":"The <i>Myriad</i> Decision at 10.","authors":"Jacob S Sherkow, Robert Cook-Deegan, Henry T Greely","doi":"10.1146/annurev-genom-010323-011239","DOIUrl":"10.1146/annurev-genom-010323-011239","url":null,"abstract":"<p><p>A decade ago, the US Supreme Court decided <i>Association for Molecular Pathology v. Myriad Genetics, Inc.</i>, concluding that isolated genes were not patentable subject matter. Beyond being a mere patent dispute, the case was a political and cultural phenomenon, viewed as a harbinger for the health of the biotechnology industry. With a decade of perspective, though, <i>Myriad</i>'s impact seems much narrower. The law surrounding patentable subject matter-while greatly transformed-only centered on <i>Myriad</i> in small part. The case had only a modest impact on patenting practices both in and outside the United States. And persistent efforts to legislatively overturn the decision have not borne fruit. The significance of <i>Myriad</i> thus remains, even a decade later, hidden by larger developments in science and law that have occurred since the case was decided.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139995419","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
Somatic Gene Therapy: Ethics and Access. 体细胞基因疗法：伦理与获取。
IF 7.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2024-08-01 DOI: 10.1146/annurev-genom-021623-104458
Alison Bateman-House
{"title":"Somatic Gene Therapy: Ethics and Access.","authors":"Alison Bateman-House","doi":"10.1146/annurev-genom-021623-104458","DOIUrl":"https://doi.org/10.1146/annurev-genom-021623-104458","url":null,"abstract":"<p><p>Manipulation of a patient's genome for therapeutic ends is being attempted through numerous methods, some of which have resulted in disease-modifying interventions. The much anticipated promise of somatic gene therapy is starting to pay off; however, there remain many scientific unknowns, including concerns about safety and durability. A significant ethical concern is that of access to these novel interventions, an issue that is normally framed in terms of the high costs of approved products. I describe how access issues permeate gene therapy long before there is any commercial product and how even upstream decisions-such as choices of indication to pursue, viral vector, and where to site a trial-have significant implications for access to resultant products in both the developmental and commercial stages.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142078932","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
Clinical and Therapeutic Implications of Clonal Hematopoiesis. 克隆性造血的临床和治疗意义。
IF 7.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2024-08-01 DOI: 10.1146/annurev-genom-120722-100409
Giulia Petrone, Isik Turker, Pradeep Natarajan, Kelly L Bolton
{"title":"Clinical and Therapeutic Implications of Clonal Hematopoiesis.","authors":"Giulia Petrone, Isik Turker, Pradeep Natarajan, Kelly L Bolton","doi":"10.1146/annurev-genom-120722-100409","DOIUrl":"https://doi.org/10.1146/annurev-genom-120722-100409","url":null,"abstract":"<p><p>Clonal hematopoiesis (CH) is an age-related process whereby hematopoietic stem and progenitor cells (HSPCs) acquire mutations that lead to a proliferative advantage and clonal expansion. The most commonly mutated genes are epigenetic regulators, DNA damage response genes, and splicing factors, which are essential to maintain functional HSPCs and are frequently involved in the development of hematologic malignancies. Established risk factors for CH, including age, prior cytotoxic therapy, and smoking, increase the risk of acquiring CH and/or may increase CH fitness. CH has emerged as a novel risk factor in many age-related diseases, such as hematologic malignancies, cardiovascular disease, diabetes, and autoimmune disorders, among others. Future characterization of the mechanisms driving CH evolution will be critical to develop preventative and therapeutic approaches.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142078931","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 Role of Cilia and the Complex Genetics of Congenital Heart Disease. 纤毛的作用和先天性心脏病的复杂遗传学。
IF 7.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2024-08-01 Epub Date: 2024-08-06 DOI: 10.1146/annurev-genom-121222-105345
George C Gabriel, Madhavi Ganapathiraju, Cecilia W Lo
{"title":"The Role of Cilia and the Complex Genetics of Congenital Heart Disease.","authors":"George C Gabriel, Madhavi Ganapathiraju, Cecilia W Lo","doi":"10.1146/annurev-genom-121222-105345","DOIUrl":"10.1146/annurev-genom-121222-105345","url":null,"abstract":"<p><p>Congenital heart disease (CHD) can affect up to 1% of live births, and despite abundant evidence of a genetic etiology, the genetic landscape of CHD is still not well understood. A large-scale mouse chemical mutagenesis screen for mutations causing CHD yielded a preponderance of cilia-related genes, pointing to a central role for cilia in CHD pathogenesis. The genes uncovered by the screen included genes that regulate ciliogenesis and cilia-transduced cell signaling as well as many that mediate endocytic trafficking, a cell process critical for both ciliogenesis and cell signaling. The clinical relevance of these findings is supported by whole-exome sequencing analysis of CHD patients that showed enrichment for pathogenic variants in ciliome genes. Surprisingly, among the ciliome CHD genes recovered were many that encoded direct protein-protein interactors. Assembly of the CHD genes into a protein-protein interaction network yielded a tight interactome that suggested this protein-protein interaction may have functional importance and that its disruption could contribute to the pathogenesis of CHD. In light of these and other findings, we propose that an interactome enriched for ciliome genes may provide the genomic context for the complex genetics of CHD and its often-observed incomplete penetrance and variable expressivity.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140896903","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 Genetics and Functional Genomics of Osteoarthritis. 骨关节炎的遗传学和功能基因组学。
IF 7.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2024-08-01 DOI: 10.1146/annurev-genom-010423-095636
Ana Luiza Arruda, Georgia Katsoula, Shibo Chen, Ene Reimann, Peter Kreitmaier, Eleftheria Zeggini
{"title":"The Genetics and Functional Genomics of Osteoarthritis.","authors":"Ana Luiza Arruda, Georgia Katsoula, Shibo Chen, Ene Reimann, Peter Kreitmaier, Eleftheria Zeggini","doi":"10.1146/annurev-genom-010423-095636","DOIUrl":"https://doi.org/10.1146/annurev-genom-010423-095636","url":null,"abstract":"<p><p>Osteoarthritis is the most prevalent whole-joint degenerative disorder, and is characterized by the degradation of articular cartilage and the underlying bone structures. Almost 600 million people are affected by osteoarthritis worldwide. No curative treatments are available, and management strategies focus mostly on pain relief. Here, we provide a comprehensive overview of the available human genetic and functional genomics studies for osteoarthritis to date and delineate how these studies have helped shed light on disease etiopathology. We highlight genetic discoveries from genome-wide association studies and provide a detailed overview of molecular-level investigations in osteoarthritis tissues, including methylation-, transcriptomics-, and proteomics-level analyses. We review how functional genomics data from different molecular levels have helped to prioritize effector genes that can be used as drug targets or drug-repurposing opportunities. Finally, we discuss future directions with the potential to drive a step change in osteoarthritis research.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142078933","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
Toward Realizing the Promise of AI in Precision Health Across the Spectrum of Care. 实现人工智能在整个医疗领域精准医疗中的前景。
IF 7.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2024-08-01 Epub Date: 2024-08-06 DOI: 10.1146/annurev-genom-010323-010230
Jenna Wiens, Kayte Spector-Bagdady, Bhramar Mukherjee
{"title":"Toward Realizing the Promise of AI in Precision Health Across the Spectrum of Care.","authors":"Jenna Wiens, Kayte Spector-Bagdady, Bhramar Mukherjee","doi":"10.1146/annurev-genom-010323-010230","DOIUrl":"10.1146/annurev-genom-010323-010230","url":null,"abstract":"<p><p>Significant progress has been made in augmenting clinical decision-making using artificial intelligence (AI) in the context of secondary and tertiary care at large academic medical centers. For such innovations to have an impact across the spectrum of care, additional challenges must be addressed, including inconsistent use of preventative care and gaps in chronic care management. The integration of additional data, including genomics and data from wearables, could prove critical in addressing these gaps, but technical, legal, and ethical challenges arise. On the technical side, approaches for integrating complex and messy data are needed. Data and design imperfections like selection bias, missing data, and confounding must be addressed. In terms of legal and ethical challenges, while AI has the potential to aid in leveraging patient data to make clinical care decisions, we also risk exacerbating existing disparities. Organizations implementing AI solutions must carefully consider how they can improve care for all and reduce inequities.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140896966","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
PIK3CA-Related Disorders: From Disease Mechanism to Evidence-Based Treatments. PIK3CA 相关疾病：从疾病机制到循证治疗。
IF 7.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2024-08-01 Epub Date: 2024-08-06 DOI: 10.1146/annurev-genom-121222-114518
Gabriel M Morin, Lola Zerbib, Sophie Kaltenbach, Antoine Fraissenon, Estelle Balducci, Vahid Asnafi, Guillaume Canaud
{"title":"<i>PIK3CA</i>-Related Disorders: From Disease Mechanism to Evidence-Based Treatments.","authors":"Gabriel M Morin, Lola Zerbib, Sophie Kaltenbach, Antoine Fraissenon, Estelle Balducci, Vahid Asnafi, Guillaume Canaud","doi":"10.1146/annurev-genom-121222-114518","DOIUrl":"10.1146/annurev-genom-121222-114518","url":null,"abstract":"<p><p>Recent advances in genetic sequencing are transforming our approach to rare-disease care. Initially identified in cancer, gain-of-function mutations of the <i>PIK3CA</i> gene are also detected in malformation mosaic diseases categorized as <i>PIK3CA</i>-related disorders (PRDs). Over the past decade, new approaches have enabled researchers to elucidate the pathophysiology of PRDs and uncover novel therapeutic options. In just a few years, owing to vigorous global research efforts, PRDs have been transformed from incurable diseases to chronic disorders accessible to targeted therapy. However, new challenges for both medical practitioners and researchers have emerged. Areas of uncertainty remain in our comprehension of PRDs, especially regarding the relationship between genotype and phenotype, the mechanisms underlying mosaicism, and the processes involved in intercellular communication. As the clinical and biological landscape of PRDs is constantly evolving, this review aims to summarize current knowledge regarding <i>PIK3CA</i> and its role in nonmalignant human disease, from molecular mechanisms to evidence-based treatments.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139691072","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
Genome-Wide Screening Approaches for Biochemical Reactions Independent of Cell Growth 独立于细胞生长的生化反应的全基因组筛选方法
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2024-05-02 DOI: 10.1146/annurev-genom-121222-115958
Yuki Noguchi, Risa Matsui, Jaeyeon Suh, Yu Dou, Jun Suzuki
{"title":"Genome-Wide Screening Approaches for Biochemical Reactions Independent of Cell Growth","authors":"Yuki Noguchi, Risa Matsui, Jaeyeon Suh, Yu Dou, Jun Suzuki","doi":"10.1146/annurev-genom-121222-115958","DOIUrl":"https://doi.org/10.1146/annurev-genom-121222-115958","url":null,"abstract":"Genome-wide screening is a potent approach for comprehensively understanding the molecular mechanisms of biological phenomena. However, despite its widespread use in the past decades across various biological targets, its application to biochemical reactions with temporal and reversible biological outputs remains a formidable challenge. To uncover the molecular machinery underlying various biochemical reactions, we have recently developed the revival screening method, which combines flow cytometry–based cell sorting with library reconstruction from collected cells. Our refinements to the traditional genome-wide screening technique have proven successful in revealing the molecular machinery of biochemical reactions of interest. In this article, we elucidate the technical basis of revival screening, focusing on its application to CRISPR-Cas9 single guide RNA (sgRNA) library and complementary DNA (cDNA) library screening. Finally, we also discuss the future of genome-wide screening while describing recent achievements from in vitro and in vivo screening.","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2024-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140831318","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 Genetics of Human Sleep and Sleep Disorders 人类睡眠和睡眠障碍的遗传学
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2024-04-26 DOI: 10.1146/annurev-genom-121222-120306
Xianlin Zou, Louis J. Ptáček, Ying-Hui Fu
{"title":"The Genetics of Human Sleep and Sleep Disorders","authors":"Xianlin Zou, Louis J. Ptáček, Ying-Hui Fu","doi":"10.1146/annurev-genom-121222-120306","DOIUrl":"https://doi.org/10.1146/annurev-genom-121222-120306","url":null,"abstract":"Healthy sleep is vital for humans to achieve optimal health and longevity. Poor sleep and sleep disorders are strongly associated with increased morbidity and mortality. However, the importance of good sleep continues to be underrecognized. Mechanisms regulating sleep and its functions in humans remain mostly unclear even after decades of dedicated research. Advancements in gene sequencing techniques and computational methodologies have paved the way for various genetic analysis approaches, which have provided some insights into human sleep genetics. This review summarizes our current knowledge of the genetic basis underlying human sleep traits and sleep disorders. We also highlight the use of animal models to validate genetic findings from human sleep studies and discuss potential molecular mechanisms and signaling pathways involved in the regulation of human sleep.","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140800036","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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