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Annual Review of Genomics and Human Genetics

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https://www.readbyqxmd.com/read/28504904/application-of-panel-based-tests-for-inherited-risk-of-cancer
#1
Payal D Shah, Katherine L Nathanson
Next-generation or massively parallel sequencing has transformed the landscape of genetic testing for cancer susceptibility. Panel-based genetic tests evaluate multiple genes simultaneously and rapidly. Because these tests are frequently offered in clinical settings, understanding their clinical validity and utility is critical. When evaluating the inherited risk of breast and ovarian cancers, panel-based tests provide incremental benefit compared with BRCA1/2 genetic testing. For inherited risk of other cancers, such as colon cancer and pheochromocytoma-paraganglioma, the clinical utility and yield of panel-based testing are higher; in fact, simultaneous evaluation of multiple genes has been the historical standard for these diseases...
May 15, 2017: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/28498723/advances-in-preimplantation-genetic-testing-for-monogenic-disease-and-aneuploidy
#2
Nathan R Treff, Rebekah S Zimmerman
Genetic testing of preimplantation embryos promises to prevent monogenic disease in children born to at-risk couples, the transfer of unbalanced embryos to patients carrying a balanced translocation, and the use of aneuploid embryos created during in vitro fertilization. Technologies have evolved from fluorescence in situ hybridization to next-generation-sequencing-based aneuploidy screening and allow for simultaneous testing of multiple genetic abnormalities in a single biopsy. The field has also shifted away from polar body or blastomere biopsy and toward trophectoderm biopsy as the new standard...
May 12, 2017: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/28475368/tailoring-medulloblastoma-treatment-through-genomics-making-a-change-one-subgroup-at-a-time
#3
Borja L Holgado, Ana Guerreiro Stucklin, Livia Garzia, Craig Daniels, Michael D Taylor
After more than a decade of genomic studies in medulloblastoma, the time has come to capitalize on the knowledge gained and use it to directly improve patient care. Although metastatic and relapsed disease remain poorly understood, much has changed in how we define medulloblastoma, and it has become evident that with conventional therapies, specific groups of patients are currently under- or overtreated. In this review, we summarize the latest insights into medulloblastoma biology, focusing on how genomics is affecting patient stratification, informing preclinical studies of targeted therapies, and shaping the new generation of clinical trials...
May 5, 2017: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/28460196/a-robust-framework-for-microbial-archaeology
#4
Christina Warinner, Alexander Herbig, Allison Mann, James A Fellows Yates, Clemens L Weiß, Hernán A Burbano, Ludovic Orlando, Johannes Krause
Microbial archaeology is flourishing in the era of high-throughput sequencing, revealing the agents behind devastating historical plagues, identifying the cryptic movements of pathogens in prehistory, and reconstructing the ancestral microbiota of humans. Here, we introduce the fundamental concepts and theoretical framework of the discipline, then discuss applied methodologies for pathogen identification and microbiome characterization from archaeological samples. We give special attention to the process of identifying, validating, and authenticating ancient microbes using high-throughput DNAsequencing data...
April 26, 2017: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/28441061/precisely-where-are-we-going-charting-the-new-terrain-of-precision-prevention
#5
Karen M Meagher, Michelle L McGowan, Richard A Settersten, Jennifer R Fishman, Eric T Juengst
In addition to genetic data, precision medicine research gathers information about three factors that modulate gene expression: lifestyles, environments, and communities. The relevant research tools-epidemiology, environmental assessment, and socioeconomic analysis-are those of public health sciences rather than molecular biology. Because these methods are designed to support inferences and interventions addressing population health, the aspirations of this research are expanding from individualized treatment toward precision prevention in public health...
April 24, 2017: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/28426286/on-the-evolution-of-lactase-persistence-in-humans
#6
Laure Ségurel, Céline Bon
Lactase persistence-the ability of adults to digest the lactose in milk-varies widely in frequency across human populations. This trait represents an adaptation to the domestication of dairying animals and the subsequent consumption of their milk. Five variants are currently known to underlie this phenotype, which is monogenic in Eurasia but mostly polygenic in Africa. Despite being a textbook example of regulatory convergent evolution and gene-culture coevolution, the story of lactase persistence is far from clear: Why are lactase persistence frequencies low in Central Asian herders but high in some African hunter-gatherers?Whywas lactase persistence strongly selected for even though milk processing can reduce the amount of lactose? Are there other factors, outside of an advantage of caloric intake, that contributed to the selective pressure for lactase persistence? It is time to revisit what we know and still do not know about lactase persistence in humans...
April 19, 2017: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/28426285/the-yin-and-yang-of-autism-genetics-how-rare-de-novo-and-common-variations-affect-liability
#7
Pauline Chaste, Kathryn Roeder, Bernie Devlin
The etiology of autism spectrum disorder (ASD) is complex, involving both genetic and environmental contributions to individual and population-level liability. Early researchers hypothesized that ASD arises from polygenic inheritance, but later results, such as the identification of mutations in certain genes that are responsible for syndromes associated with ASD, led others to propose that de novo mutations of major effect would account for most cases. This yin and yang of monogenic causes and polygenic inheritance continues to this day...
April 19, 2017: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/28426284/participatory-genomic-research-ethical-issues-from-the-bottom-up-to-the-top-down
#8
Heide Aungst, Michelle L McGowan, Jennifer R Fishman
Participatory approaches to genomic research manifest along a continuum from bottom-up citizen-science initiatives designed to liberate scientific inquiry from the constraints of traditional research institutional contexts and professional practices to top-down investigator-initiated studies designed to expose the public to scientific research processes and build their support and enthusiasm for genomic research. With foundations as varied as open science, crowdsourcing, patient advocacy, social media, the digitization of health, and the neoliberalization of academic research, a range of ethical frameworks inform the modes of participatory genomic research...
April 19, 2017: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/28415858/recent-advances-in-mitochondrial-disease
#9
Lyndsey Craven, Charlotte L Alston, Robert W Taylor, Doug M Turnbull
Mitochondrial disease is a challenging area of genetics because two distinct genomes can contribute to disease pathogenesis. It is also challenging clinically because of the myriad of different symptoms and, until recently, a lack of a genetic diagnosis in many patients. The last five years has brought remarkable progress in this area.Weprovide a brief overview of mitochondrial origin, function, and biology, which are key to understanding the genetic basis of mitochondrial disease. However, the primary purpose of this review is to describe the recent advances related to the diagnosis, genetic basis, and prevention of mitochondrial disease, highlighting the newly described disease genes and the evolving methodologies aimed at preventing mitochondrial DNA disease transmission...
April 17, 2017: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/28415857/sharing-data-to-build-a-medical-information-commons-from-bermuda-to-the-global-alliance
#10
Robert Cook-Deegan, Rachel A Ankeny, Kathryn Maxson Jones
The Human Genome Project modeled its open science ethos on nematode biology, most famously through daily release of DNA sequence data based on the 1996 Bermuda Principles. That open science philosophy persists, but daily, unfettered release of data has had to adapt to constraints occasioned by the use of data from individual people, broader use of data not only by scientists but also by clinicians and individuals, the global reach of genomic applications and diverse national privacy and research ethics laws, and the rising prominence of a diverse commercial genomics sector...
April 17, 2017: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/28415856/gene-and-variant-annotation-for-mendelian-disorders-in-the-era-of-advanced-sequencing-technologies
#11
Samya Chakravorty, Madhuri Hegde
Comprehensive annotations of genetic and noncoding regions and corresponding accurate variant classification for Mendelian diseases are the next big challenge in the new genomic era of personalized medicine. Progress in the development of faster and more accurate pipelines for genome annotation and variant classification will lead to the discovery of more novel disease associations and candidate therapeutic targets. This ultimately will facilitate better patient recruitment in clinical trials. In this review, we describe the trends in research at the intersection of basic and clinical genomics that aims to increase understanding of overall genomic complexity, complex inheritance patterns of disease, and patient-phenotype-specific genomic associations...
April 17, 2017: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/28399667/gene-regulatory-elements-major-drivers-of-human-disease
#12
Sumantra Chatterjee, Nadav Ahituv
Gene expression changes, the driving forces for cellular diversity in multicellular organisms, are regulated by a diverse set of gene regulatory elements that direct transcription in specific cells. Mutations in these elements, ranging from chromosomal aberrations to single-nucleotide polymorphisms, are a major cause of human disease. However, we currently have a very limited understanding of how regulatory element genotypes lead to specific phenotypes. In this review, we discuss the various methods of regulatory element identification, the different types of mutations they harbor, and their impact on human disease...
April 7, 2017: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/28375652/the-microbiome-and-human-biology
#13
Rob Knight, Chris Callewaert, Clarisse Marotz, Embriette R Hyde, Justine W Debelius, Daniel McDonald, Mitchell L Sogin
Over the past few years, microbiome research has dramatically reshaped our understanding of human biology. New insights range from an enhanced understanding of how microbes mediate digestion and disease processes (e.g., in inflammatory bowel disease) to surprising associations with Parkinson's disease, autism, and depression. In this review, we describe how new generations of sequencing technology, analytical advances coupled to new software capabilities, and the integration of animal model data have led to these new discoveries...
March 20, 2017: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/28301737/the-clinic-is-my-laboratory-life-as-a-clinical-geneticist
#14
Judith G Hall
Clinical genetics is the application of advances in genetics and medicine to real human families. It involves diagnosis, care, and counseling concerning options available to affected individuals and their family members. Advances in medicine and genetics have led to dramatic changes in the scope and responsibilities of clinical genetics. This reflection on the last 50+ years of clinical genetics comes from personal experience, with an emphasis on the important contributions that clinical geneticists have made to the understanding of disease/disorder processes and mechanisms...
March 6, 2017: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/28142260/a-conversation-with-kurt-and-rochelle-hirschhorn
#15
Kurt Hirschhorn, Rochelle Hirschhorn, Joel N Hirschhorn
In this interview, Kurt and Rochelle Hirschhorn talk with their son, Joel, about their research and collaborations, the early years of medical genetics, the development of genetic counseling, the challenges of being a woman in science, and new challenges and directions for the study of human genetics. Expected final online publication date for the Annual Review of Genomics and Human Genetics Volume 18 is August 31, 2017. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
January 26, 2017: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/27362342/advancements-in-next-generation-sequencing
#16
Shawn E Levy, Richard M Myers
The term next-generation sequencing is almost a decade old, but it remains the colloquial way to describe highly parallel or high-output sequencing methods that produce data at or beyond the genome scale. Since the introduction of these technologies, the number of applications and methods that leverage the power of genome-scale sequencing has increased at an exponential pace. This review highlights recent concepts, technologies, and methods from next-generation sequencing to illustrate the breadth and depth of the applications and research areas that are driving progress in genomics...
August 31, 2016: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/27362341/defining-the-clinical-value-of-a-genomic-diagnosis-in-the-era-of-next-generation-sequencing
#17
Natasha T Strande, Jonathan S Berg
As with all fields of medicine, the first step toward medical management of genetic disorders is obtaining an accurate diagnosis, which often requires testing at the molecular level. Unfortunately, given the large number of genetic conditions without a specific intervention, only rarely does a genetic diagnosis alter patient management-which raises the question, what is the added value of obtaining a molecular diagnosis? Given the fast-paced advancement of genomic technologies, this is an important question to address in the context of genome-scale testing...
August 31, 2016: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/27362340/old-dogs-new-tricks-monogenic-autoinflammatory-disease-unleashed
#18
Monique Stoffels, Daniel L Kastner
Autoinflammatory diseases are inborn disorders of the innate immune system characterized by episodes of systemic inflammation that are mediated largely by myeloid cells. The field of autoinflammatory diseases has been established since 1999, following the identification of the first genes underlying periodic fever syndromes. This review focuses on developments that have transformed the field in the last two years. We discuss three newly described monogenic autoinflammatory diseases [deficiency of adenosine deaminase 2 (DADA2), a subtype of macrophage activation syndrome (MAS), and stimulator of interferon genes (STING)-associated vasculopathy with onset in infancy (SAVI)], discuss the possibilities of somatic mosaicism and digenic inheritance, and give an update on new concepts in pathways involved in familial Mediterranean fever (FMF)...
August 31, 2016: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/27216778/developmental-origins-of-common-disease-epigenetic-contributions-to-obesity
#19
Maya Kappil, Robert O Wright, Alison P Sanders
The perinatal period is a window of susceptibility for later life disease. Recent epigenetic findings are beginning to increase our understanding of the molecular mechanisms that may contribute to the programming of obesity. This review summarizes recent evidence that supports the role of epigenetically mediated early life programming in the later onset of obesity. Establishing such links between environmental exposures and modifiable molecular changes ultimately holds promise to inform interventional efforts toward alleviating the environmentally mediated onset of obesity...
August 31, 2016: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/27216777/genomic-analysis-of-the-emergence-evolution-and-spread-of-human-respiratory-rna-viruses
#20
Tommy T-Y Lam, Huachen Zhu, Yi Guan, Edward C Holmes
The emergence and reemergence of rapidly evolving RNA viruses-particularly those responsible for respiratory diseases, such as influenza viruses and coronaviruses-pose a significant threat to global health, including the potential of major pandemics. Importantly, recent advances in high-throughput genome sequencing enable researchers to reveal the genomic diversity of these viral pathogens at much lower cost and with much greater precision than they could before. In particular, the genome sequence data generated allow inferences to be made on the molecular basis of viral emergence, evolution, and spread in human populations in real time...
August 31, 2016: Annual Review of Genomics and Human Genetics
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