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Annual Review of Genomics and Human Genetics

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https://www.readbyqxmd.com/read/27362342/advancements-in-next-generation-sequencing
#1
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
#2
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
#3
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
#4
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
#5
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
https://www.readbyqxmd.com/read/27216776/crispr-cas9-for-human-genome-engineering-and-disease-research
#6
Xin Xiong, Meng Chen, Wendell A Lim, Dehua Zhao, Lei S Qi
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) system, a versatile RNA-guided DNA targeting platform, has been revolutionizing our ability to modify, manipulate, and visualize the human genome, which greatly advances both biological research and therapeutics development. Here, we review the current development of CRISPR/Cas9 technologies for gene editing, transcription regulation, genome imaging, and epigenetic modification. We discuss the broad application of this system to the study of functional genomics, especially genome-wide genetic screening, and to therapeutics development, including establishing disease models, correcting defective genetic mutations, and treating diseases...
August 31, 2016: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/27216775/recent-advances-in-defining-the-genetic-basis-of-rheumatoid-arthritis
#7
Chikashi Terao, Soumya Raychaudhuri, Peter K Gregersen
Rheumatoid arthritis (RA) is the most common inflammatory arthritis and exhibits genetic overlap with other autoimmune and inflammatory disorders. Although predominant associations with the HLA-DRB1 locus have been known for decades, recent data have revealed additional insight into the likely causative variants within HLA-DRB1 as well as within other HLA loci that contribute to disease risk. In addition, more than 100 common variants in non-HLA loci have been implicated in disease susceptibility. Genetic factors are involved not only in the development of RA, but also with various disease subphenotypes, including production and circulating levels of autoantibodies and joint destruction...
August 31, 2016: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/27147253/the-great-adventure-of-an-american-human-geneticist
#8
Arno G Motulsky, Mary-Claire King
It is my great pleasure to have been asked by the Editorial Committee of the Annual Review of Genomics and Human Genetics to write a short autobiography of my life in genetics over the past 70 years. It has been a great adventure. I came both to America and to human genetics by a circuitous and ultimately very fortunate route. I hope the next generation of geneticists will enjoy reading about it.
August 31, 2016: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/27147090/association-tests-for-rare-variants
#9
Dan L Nicolae
Over the past few years, interest in the identification of rare variants that influence human phenotype has led to the development of many statistical methods for testing for association between sets of rare variants and binary or quantitative traits. Here, I review some of the most important ideas that underlie these methods and the most relevant issues when choosing a method for analysis. In addition to the tests for association, I review crucial issues in performing a rare variant study, from experimental design to interpretation and validation...
August 31, 2016: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/27147089/evolution-of-gene-regulation-in-humans
#10
Steven K Reilly, James P Noonan
As a species, we possess unique biological features that distinguish us from other primates. Here, we review recent efforts to identify changes in gene regulation that drove the evolution of novel human phenotypes. We discuss genotype-directed comparisons of human and nonhuman primate genomes to identify human-specific genetic changes that may encode new regulatory functions. We also review phenotype-directed approaches, which use comparisons of gene expression or regulatory function in homologous human and nonhuman primate cells and tissues to identify changes in expression levels or regulatory activity that may be due to genetic changes in humans...
August 31, 2016: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/27147088/the-properties-of-long-noncoding-rnas-that-regulate-chromatin
#11
Michael Rutenberg-Schoenberg, Alec N Sexton, Matthew D Simon
Beyond coding for proteins, RNA molecules have well-established functions in the posttranscriptional regulation of gene expression. Less clear are the upstream roles of RNA in regulating transcription and chromatin-based processes in the nucleus. RNA is transcribed in the nucleus, so it is logical that RNA could play diverse and broad roles that would impact human physiology. Indeed, this idea is supported by well-established examples of noncoding RNAs that affect chromatin structure and function. There has been dramatic growth in studies focused on the nuclear roles of long noncoding RNAs (lncRNAs)...
August 31, 2016: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/27147087/phenome-wide-association-studies-as-a-tool-to-advance-precision-medicine
#12
Joshua C Denny, Lisa Bastarache, Dan M Roden
Beginning in the early 2000s, the accumulation of biospecimens linked to electronic health records (EHRs) made possible genome-phenome studies (i.e., comparative analyses of genetic variants and phenotypes) using only data collected as a by-product of typical health care. In addition to disease and trait genetics, EHRs proved a valuable resource for analyzing pharmacogenetic traits and developing reverse genetics approaches such as phenome-wide association studies (PheWASs). PheWASs are designed to survey which of many phenotypes may be associated with a given genetic variant...
August 31, 2016: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/27147086/host-factors-in-ebola-infection
#13
Angela L Rasmussen
Ebola virus (EBOV) emerged in West Africa in 2014 to devastating effect, and demonstrated that infection can cause a broad range of severe disease manifestations. As the virus itself was genetically similar to other Zaire ebolaviruses, the spectrum of pathology likely resulted from variable responses to infection in a large and genetically diverse population. This review comprehensively summarizes current knowledge of the host response to EBOV infection, including pathways hijacked by the virus to facilitate replication, host processes that contribute directly to pathogenesis, and host-pathogen interactions involved in subverting or antagonizing host antiviral immunity...
August 31, 2016: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/27089971/ctcf-and-cohesin-in-genome-folding-and-transcriptional-gene-regulation
#14
Matthias Merkenschlager, Elphège P Nora
Genome function, replication, integrity, and propagation rely on the dynamic structural organization of chromosomes during the cell cycle. Genome folding in interphase provides regulatory segmentation for appropriate transcriptional control, facilitates ordered genome replication, and contributes to genome integrity by limiting illegitimate recombination. Here, we review recent high-resolution chromosome conformation capture and functional studies that have informed models of the spatial and regulatory compartmentalization of mammalian genomes, and discuss mechanistic models for how CTCF and cohesin control the functional architecture of mammalian chromosomes...
August 31, 2016: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/27070266/germline-stem-cell-competition-mutation-hot-spots-genetic-disorders-and-older-fathers
#15
Norman Arnheim, Peter Calabrese
Some de novo human mutations arise at frequencies far exceeding the genome average mutation rate. Examples include the common mutations at one or a few sites in the genes that cause achondroplasia, Apert syndrome, multiple endocrine neoplasia type 2B, and Noonan syndrome. These mutations are recurrent, provide a gain of function, are paternally derived, and are more likely to be transmitted as the father ages. Recent experiments have tested whether the high mutation frequencies are due to an elevated mutation rate per cell division, as expected, or to an advantage of the mutant spermatogonial stem cells over wild-type stem cells...
August 31, 2016: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/26979405/lessons-from-hela-cells-the-ethics-and-policy-of-biospecimens
#16
Laura M Beskow
Human biospecimens have played a crucial role in scientific and medical advances. Although the ethical and policy issues associated with biospecimen research have long been the subject of scholarly debate, the story of Henrietta Lacks, her family, and the creation of HeLa cells captured the attention of a much broader audience. The story has been a catalyst for policy change, including major regulatory changes proposed in the United States surrounding informed consent. These proposals are premised in part on public opinion data, necessitating a closer look at what such data tell us...
August 31, 2016: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/26905785/cystic-fibrosis-and-its-management-through-established-and-emerging-therapies
#17
David R Spielberg, John P Clancy
Cystic fibrosis (CF) is the most common life-shortening autosomal recessive disorder in the Caucasian population and occurs in many other ethnicities worldwide. The daily treatment burden is substantial for CF patients even when they are well, with numerous pharmacologic and physical therapies targeting lung disease requiring the greatest time commitment. CF treatments continue to advance with greater understanding of factors influencing long-term morbidity and mortality. In recent years, in-depth understanding of genetic and protein structure-function relationships has led to the introduction of targeted therapies for patients with specific CF genotypes...
August 31, 2016: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/26905784/broad-consent-for-genomic-research-and-biobanking-perspectives-from-low-and-middle-income-countries
#18
Paulina Tindana, Jantina de Vries
Genomic research and biobanking are increasingly being conducted in the context of collaborations between researchers in high-income countries and those in low- and middle-income countries. Although these scientific advancements have presented unique opportunities for researchers to contribute to cutting-edge scientific projects and address important health problems, they have also challenged existing ethical and regulatory frameworks, particularly in sub-Saharan Africa. Broad consent is a model that allows the use of human biological samples and associated data in future research that may be unrelated to the original study...
August 31, 2016: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/26322648/noninvasive-prenatal-genetic-testing-current-and-emerging-ethical-legal-and-social-issues
#19
REVIEW
Mollie A Minear, Stephanie Alessi, Megan Allyse, Marsha Michie, Subhashini Chandrasekharan
Noninvasive prenatal genetic testing (NIPT) for chromosomal aneuploidy involving the analysis of cell-free fetal DNA became commercially available in 2011. The low false-positive rate of NIPT, which reduces unnecessary prenatal invasive diagnostic procedures, has led to broad clinician and patient adoption. We discuss the ethical, legal, and social issues raised by rapid and global dissemination of NIPT. The number of women using NIPT is anticipated to expand, and the number of conditions being tested for will continue to increase as well, raising concerns about the routinization of testing and negative impacts on informed decision making...
2015: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/26322647/eugenics-and-involuntary-sterilization-1907-2015
#20
REVIEW
Philip R Reilly
In England during the late nineteenth century, intellectuals, especially Francis Galton, called for a variety of eugenic policies aimed at ensuring the health of the human species. In the United States, members of the Progressive movement embraced eugenic ideas, especially immigration restriction and sterilization. Indiana enacted the first eugenic sterilization law in 1907, and the US Supreme Court upheld such laws in 1927. State programs targeted institutionalized, mentally disabled women. Beginning in the late 1930s, proponents rationalized involuntary sterilization as protecting vulnerable women from unwanted pregnancy...
2015: Annual Review of Genomics and Human Genetics
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