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  • Articles  (413)
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  • Articles  (413)
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  • 1
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    Threespine Stickleback: A Model System For Evolutionary Genomics (2021)
    Annual Reviews
    Details
    Publication Date: 2021-04-28
    Description: The repeated adaptation of oceanic threespine sticklebacks to fresh water has made it a premier organism to study parallel evolution. These small fish have multiple distinct ecotypes that display a wide range of diverse phenotypic traits. Ecotypes are easily crossed in the laboratory, and families are large and develop quickly enough for quantitative trait locus analyses, positioning the threespine stickleback as a versatile model organism to address a wide range of biological questions. Extensive genomic resources, including linkage maps, a high-quality reference genome, and developmental genetics tools have led to insights into the genomic basis of adaptation and the identification of genomic changes controlling traits in vertebrates. Recently, threespine sticklebacks have been used as a model system to identify the genomic basis of highly complex traits, such as behavior and host–microbiome and host–parasite interactions. We review the latest findings and new avenues of research that have led the threespine stickleback to be considered a supermodel of evolutionary genomics. Expected final online publication date for the Annual Review of Genomics and Human Genetics Volume 22 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1527-8204
    Electronic ISSN: 1545-293X
    Topics: Biology
    Published by Annual Reviews
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  • 2
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    The Science and Art of Clinical Genetic Variant Classification and Its Impact on Test Accuracy (2021)
    Annual Reviews
    Details
    Publication Date: 2021-04-26
    Description: Clinical genetic variant classification science is a growing subspecialty of clinical genetics and genomics. The field's continued improvement is essential for the success of precision medicine in both germline (hereditary) and somatic (oncology) contexts. This review focuses on variant classification for DNA next-generation sequencing tests. We first summarize current limitations in variant discovery and definition, and then describe the current five- and four-tier classification systems outlined in dominant standards and guideline publications for germline and somatic tests, respectively. We then discuss measures of variant classification discordance and the field's bias for positive results, as well as considerations for panel size and population screening in the context of estimates of positive predictive value that incorporate estimated variant classification imperfections. Finally, we share opinions on the current state of variant classification from some of the authors of the most widely used standards and guideline publications and from other domain experts. Expected final online publication date for the Annual Review of Genomics and Human Genetics Volume 22 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1527-8204
    Electronic ISSN: 1545-293X
    Topics: Biology
    Published by Annual Reviews
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  • 3
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    The Emergence and Global Spread of Noninvasive Prenatal Testing (2021)
    Annual Reviews
    Details
    Publication Date: 2021-04-13
    Description: Since its introduction in 2011, noninvasive prenatal testing (NIPT) has spread rapidly around the world. It carries numerous benefits but also raises challenges, often related to sociocultural, legal, and economic contexts. This article describes the implementation of NIPT in nine countries, each with its own unique characteristics: Australia, Canada, China and Hong Kong, India, Israel, Lebanon, the Netherlands, the United Kingdom, and the United States. Themes covered for each country include the structure of the healthcare system, how NIPT is offered, counseling needs and resources, and cultural and legal context regarding disability and pregnancy termination. Some common issues emerge, including cost as a barrier to equitable access, the complexity of decision-making about public funding, and a shortage of appropriate resources that promote informed choice. Conversely, sociocultural values that underlie the use of NIPT vary greatly among countries. The issues described will become even more challenging as NIPT evolves from a second-tier to a first-tier screening test with expanded use. Expected final online publication date for the Annual Review of Genomics and Human Genetics Volume 22 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1527-8204
    Electronic ISSN: 1545-293X
    Topics: Biology
    Published by Annual Reviews
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  • 4
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    Investigating the Potential Roles of SINEs in the Human Genome (2021)
    Annual Reviews
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    Publication Date: 2021-04-01
    Description: Short interspersed nuclear elements (SINEs) are nonautonomous retrotransposons that occupy approximately 13% of the human genome. They are transcribed by RNA polymerase III and can be retrotranscribed and inserted back into the genome with the help of other autonomous retroelements. Because they are preferentially located close to or within gene-rich regions, they can regulate gene expression by various mechanisms that act at both the DNA and the RNA levels. In this review, we summarize recent findings on the involvement of SINEs in different types of gene regulation and discuss the potential regulatory functions of SINEs that are in close proximity to genes, Pol III–transcribed SINE RNAs, and embedded SINE sequences within Pol II–transcribed genes in the human genome. These discoveries illustrate how the human genome has exapted some SINEs into functional regulatory elements. Expected final online publication date for the Annual Review of Genomics and Human Genetics Volume 22 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1527-8204
    Electronic ISSN: 1545-293X
    Topics: Biology
    Published by Annual Reviews
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  • 5
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    Utility and Diversity: Challenges for Genomic Medicine (2021)
    Annual Reviews
    Details
    Publication Date: 2021-04-01
    Description: Genomic information is poised to play an increasing role in clinical care, extending beyond highly penetrant genetic conditions to less penetrant genotypes and common disorders. But with this shift, the question of clinical utility becomes a major challenge. A collaborative effort is necessary to determine the information needed to evaluate different uses of genomic information and then acquire that information. Another challenge must also be addressed if that process is to provide equitable benefits: the lack of diversity of genomic data. Current genomic knowledge comes primarily from populations of European descent, which poses the risk that most of the human population will be shortchanged when health benefits of genomics emerge. These two challenges have defined my career as a geneticist and have taught me that solutions must start with dialogue across disciplinary and social divides. Expected final online publication date for the Annual Review of Genomics and Human Genetics Volume 22 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1527-8204
    Electronic ISSN: 1545-293X
    Topics: Biology
    Published by Annual Reviews
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  • 6
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    The Yin and Yang of Histone Marks in Transcription (2021)
    Annual Reviews
    Details
    Publication Date: 2021-03-29
    Description: Nucleosomes wrap DNA and impede access for the machinery of transcription. The core histones that constitute nucleosomes are subject to a diversity of posttranslational modifications, or marks, that impact the transcription of genes. Their functions have sometimes been difficult to infer because the enzymes that write and read them are complex, multifunctional proteins. Here, we examine the evidence for the functions of marks and argue that the major marks perform a fairly small number of roles in either promoting transcription or preventing it. Acetylations and phosphorylations on the histone core disrupt histone-DNA contacts and/or destabilize nucleosomes to promote transcription. Ubiquitylations stimulate methylations that provide a scaffold for either the formation of silencing complexes or resistance to those complexes, and carry a memory of the transcriptional state. Tail phosphorylations deconstruct silencing complexes in particular contexts. We speculate that these fairly simple roles form the basis of transcriptional regulation by histone marks. Expected final online publication date for the Annual Review of Genomics and Human Genetics Volume 22 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1527-8204
    Electronic ISSN: 1545-293X
    Topics: Biology
    Published by Annual Reviews
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  • 7
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    Scaling Genetic Counseling in the Genomics Era (2021)
    Annual Reviews
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    Publication Date: 2021-03-15
    Description: The development of massively parallel sequencing–based genomic sequencing tests has increased genetic test availability and access. The field and practice of genetic counseling have adapted in response to this paradigm-shifting technology and the subsequent transition to practicing genomic medicine. While the key elements defining genetic counseling remain relevant, genetic counseling service delivery models and practice settings have evolved. Genetic counselors are addressing the challenges of direct-to-consumer and consumer-driven genetic testing, and genetic counseling training programs are responding to the ongoing increased demand for genetic counseling services across a broadening range of contexts. The need to diversify both the patient and participant groups with access to genetic information, as well as the field of genetic counseling, is at the forefront of research and training program initiatives. Genetic counselors are key stakeholders in the genomics era, and their contributions are essential to effectively and equitably deliver precision medicine. Expected final online publication date for the Annual Review of Genomics and Human Genetics Volume 22 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1527-8204
    Electronic ISSN: 1545-293X
    Topics: Biology
    Published by Annual Reviews
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  • 8
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    Applications of Single-Cell DNA Sequencing (2021)
    Annual Reviews
    Details
    Publication Date: 2021-03-15
    Description: Over the past decade, genomic analyses of single cells—the fundamental units of life—have become possible. Single-cell DNA sequencing has shed light on biological questions that were previously inaccessible across diverse fields of research, including somatic mutagenesis, organismal development, genome function, and microbiology. Single-cell DNA sequencing also promises significant future biomedical and clinical impact, spanning oncology, fertility, and beyond. While single-cell approaches that profile RNA and protein have greatly expanded our understanding of cellular diversity, many fundamental questions in biology and important biomedical applications require analysis of the DNA of single cells. Here, we review the applications and biological questions for which single-cell DNA sequencing is uniquely suited or required. We include a discussion of the fields that will be impacted by single-cell DNA sequencing as the technology continues to advance. Expected final online publication date for the Annual Review of Genomics and Human Genetics Volume 22 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1527-8204
    Electronic ISSN: 1545-293X
    Topics: Biology
    Published by Annual Reviews
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  • 9
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    Global Governance of Human Genome Editing: What Are the Rules? (2021)
    Annual Reviews
    Details
    Publication Date: 2021-03-05
    Description: Human gene editing, particularly using the new CRISPR/Cas9 technology, will greatly increase the capability to make precise changes to human genomes. Human gene editing can be broken into four major categories: somatic therapy, heritable gene editing, genetic enhancement, and basic and applied research. Somatic therapy is generally well governed by national regulatory systems, so the need for global governance is less urgent. All nations are in agreement that heritable gene editing should not proceed at this time, but there is likely to be divergence if and when such procedures are shown to be safe and effective. Gene editing for enhancement purposes is not feasible today but is more controversial with the public, and many nations do not have well-developed regulatory systems for addressing genetic enhancement. Finally, different nations treat research with human embryos very differently based on deeply embedded social, cultural, ethical, and legal traditions. Several international governance mechanisms are currently in operation for human gene editing, and several other governance mechanisms have been proposed. It is unlikely that any single mechanism will alone be effective for governing human gene editing; rather, a polycentric or ecosystem approach that includes several overlapping and interacting components is likely to be necessary. Expected final online publication date for the Annual Review of Genomics and Human Genetics Volume 22 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1527-8204
    Electronic ISSN: 1545-293X
    Topics: Biology
    Published by Annual Reviews
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  • 10
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    Population Screening for Inherited Predisposition to Breast and Ovarian Cancer (2020)
    Annual Reviews
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    Publication Date: 2020-08-31
    Description: The discovery of genes underlying inherited predisposition to breast and ovarian cancer has revolutionized the ability to identify women at high risk for these diseases before they become affected. Women who are carriers of deleterious variants in these genes can undertake surveillance and prevention measures that have been shown to reduce morbidity and mortality. However, under current strategies, the vast majority of women carriers remain undetected until they become affected. In this review, we show that universal testing, particularly of the BRCA1 and BRCA2 genes, fulfills classical disease screening criteria. This is especially true for BRCA1 and BRCA2 in Ashkenazi Jews but is translatable to all populations and may include additional genes. Utilizing genetic information for large-scale precision prevention requires a paradigmatic shift in health-care delivery. To address this need, we propose a direct-to-patient model, which is increasingly pertinent for fulfilling the promise of utilizing personal genomic information for disease prevention.
    Print ISSN: 1527-8204
    Electronic ISSN: 1545-293X
    Topics: Biology
    Published by Annual Reviews
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