Inference of Population History using Coalescent HMMs: Review and Outlook

Studying how diverse human populations are related is of historical and anthropological interest, in addition to providing a realistic null model for testing for signatures of natural selection or disease associations. Furthermore, understanding the demographic histories of other species is playing an increasingly important role in conservation genetics. A number of statistical methods have been developed to infer population demographic histories using whole-genome sequence data, with recent advances focusing on allowing for more flexible modeling choices, scaling to larger data sets, and increasing statistical power. Here we review coalescent hidden Markov models, a powerful class of population genetic inference methods that can effectively utilize linkage disequilibrium information. We highlight recent advances, give advice for practitioners, point out potential pitfalls, and present possible future research directions.Comment: 12 pages, 2 figure

How Many Subpopulations is Too Many? Exponential Lower Bounds for Inferring Population Histories

Reconstruction of population histories is a central problem in population genetics. Existing coalescent-based methods, like the seminal work of Li and Durbin (Nature, 2011), attempt to solve this problem using sequence data but have no rigorous guarantees. Determining the amount of data needed to correctly reconstruct population histories is a major challenge. Using a variety of tools from information theory, the theory of extremal polynomials, and approximation theory, we prove new sharp information-theoretic lower bounds on the problem of reconstructing population structure -- the history of multiple subpopulations that merge, split and change sizes over time. Our lower bounds are exponential in the number of subpopulations, even when reconstructing recent histories. We demonstrate the sharpness of our lower bounds by providing algorithms for distinguishing and learning population histories with matching dependence on the number of subpopulations. Along the way and of independent interest, we essentially determine the optimal number of samples needed to learn an exponential mixture distribution information-theoretically, proving the upper bound by analyzing natural (and efficient) algorithms for this problem.Comment: 38 pages, Appeared in RECOMB 201

GENOMICS OF ENDOGLIN PATHWAY IN PREECLAMPSIA

THE GENOMICS OF ENDOGLIN PATHWAY IN PREECLAMPSIA Mandy J. Bell, PhD, RN University of Pittsburgh, 2012 Preeclampsia is a pregnancy disorder that greatly impacts maternal and fetal/neonatal health and wellbeing. This case-control candidate gene association study investigated endoglin pathway genetic variation and its association with preeclampsia. Tagging single nucleotide polymorphisms (tSNPs) in ENG, TGFβ1, TGFβR1, ALK1, and TGFβR2 were genotyped with iPLEX® and TaqMan® in maternal/fetal dyads. The Prenatal Exposures and Preeclampsia Prevention study provided maternal DNA extracted from peripherally collected white blood cell pellets, along with umbilical cord serum we used for fetal DNA extraction. Data on 355 white (181 cases/174 controls) and 60 black (30 cases/30 controls) women matched on ancestry, age, and parity were analyzed. Separate subgroup allele/genotype/haplotype tests were conducted with Chi-square or Fisher’s exact tests. Binary logistic regression provided odds ratios for tSNPs with significant genotype tests. Analysis of maternal/fetal dyads was not conducted, because unlike the maternal samples, the fetal samples did not provide a quality template suitable for iPLEX® data collection. In white women, variation in ENG (rs11792480, rs10121110) and TGFβR2 (rs6550005) was associated with preeclampsia. Allelic frequency distributions in rs11792480, rs10121110, and rs6550005 were significantly different among cases and controls while genotype distributions of rs10121110 and rs6550005 were further associated with preeclampsia (p-values < .05). For rs10121110, women with the AA genotype were 2.290 times more likely to develop preeclampsia compared to the GG genotype (99% CI [1.022, 5.133], p = .008). ENG haplotype TACGA, which contains rs11792480 and rs10121110 risk alleles, was also over-represented in cases (p = .022). In black women, variation in TGFβ1 (rs4803455, rs4803457), TGFβR1 (rs10739778), and TGFβR2 (rs6550005, rs1346907, rs877572) was associated with preeclampsia. Allelic frequency distributions in rs10739778, rs6550005, rs1346907, and rs877572 were significantly different among cases and controls while genotype distributions of rs10739778, rs4803455, and rs4803457 were further associated with preeclampsia (p-values < .05). For rs4803457, women with the CT genotype were 7.437 more times likely to develop preeclampsia compared to the CC genotype (99% CI [1.192, 46.408], p = .005). These results demonstrate that variation in ENG pathway genes is associated with preeclampsia, with different genes from the same pathway contributing to preeclampsia in white compared to black women

The effect of an invasive bryozoan on community diversity and structure varies across two locations

Abstract Foundation species and invasive species strongly influence community diversity and structure, but typically in different ways. However, when widespread invasive species provide novel habitat within a community, their net effect may depend on both the environment and community composition. Fouling communities in northern and southern California harbors were surveyed to determine whether there was variation between two locations in the percent cover of an invasive bryozoan, Watersipora subtorquata (d'Orbigny, 1852), and its relationship to community diversity and composition in these two environments. Diversity significantly differed between locations and had a location-dependent association with W. subtorquata abundance. Communities were significantly dissimilar between locations, and W. subtorquata abundance had the highest percent contribution to community dissimilarity when compared to other species in the community. These results suggest that invasive species may have both facilitative and inhibitive relationships with species in a community, but that the net balance of these interactions depends on both the environmental and community context

Immune Responses to Viral Gene Therapy Vectors

Several viral vector-based gene therapy drugs have now received marketing approval. A much larger number of additional viral vectors are in various stages of clinical trials for the treatment of genetic and acquired diseases, with many more in pre-clinical testing. Efficiency of gene transfer and ability to provide long-term therapy make these vector systems very attractive. In fact, viral vector gene therapy has been able to treat or even cure diseases for which there had been no or only suboptimal treatments. However, innate and adaptive immune responses to these vectors and their transgene products constitute substantial hurdles to clinical development and wider use in patients. This review provides an overview of the type of immune responses that have been documented in animal models and in humans who received gene transfer with one of three widely tested vector systems, namely adenoviral, lentiviral, or adeno-associated viral vectors. Particular emphasis is given to mechanisms leading to immune responses, efforts to reduce vector immunogenicity, and potential solutions to the problems. At the same time, we point out gaps in our knowledge that should to be filled and problems that need to be addressed going forward

Three Decades of Internet- and Computer-Based Interventions for the Treatment of Depression: Protocol for a Systematic Review and Meta-Analysis

Background: Depression is one of the leading causes of disability worldwide. Internet- and computer-based interventions (IBIs) have been shown to provide effective, scalable forms of treatment. More than 100 controlled trials and a growing number of meta-analyses published over the past 30 years have demonstrated the efficacy of IBIs in reducing symptoms in the short and long term. Despite the large body of research, no comprehensive review or meta-analysis has been conducted to date that evaluates how the effectiveness of IBIs has evolved over time.Objective: This systematic review and meta-analysis aims to evaluate whether there has been a change in the effectiveness of IBIs on the treatment of depression over the past 30 years and to identify potential variables moderating the effect size.Methods: A sensitive search strategy will be executed across the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, EMBASE, and PsycINFO. Data extraction and evaluation will be conducted by two independent researchers. Risk of bias will be assessed. A multilevel meta-regression model will be used to analyze the data and estimate effect size.Results: The search was completed in mid-2019. We expect the results to be submitted for publication in early 2020.Conclusions: The year 2020 will mark 30 years since the first paper was published on the use of IBIs for the treatment of depression. Despite the large and rapidly growing body of research in the field, evaluations of effectiveness to date are missing the temporal dimension. This review will address that gap and provide valuable analysis of how the effectiveness of interventions has evolved over the past three decades; which participant-, intervention-, and study-related variables moderate changes in effectiveness; and where research in the field may benefit from increased focus.</p

Re-municipalization of public services: trend or hype?

Re-municipalization is part of a broader set of reverse privatization reforms. We argue the term re-municipalization lacks conceptual clarity and often confuses municipal level reversals from national ones, new service delivery from reversals, and mixed market positions (such as corporatization) from full public control. This conceptual confusion makes measurement of re-municipalization difficult. While more case studies are being discovered, studies based on quantitative time series do not show re-municipalization as an increasing trend. Much case study based research argues re-municipalization is politically transformative, but quantitative research generally finds re-municipalization to be part of a pragmatic market management process, a position confirmed by the papers in this special issue

A novel isoform of the Ly108 gene ameliorates murine lupus

Studies of human systemic lupus erythematosus patients and of murine congenic mouse strains associate genes in a DNA segment on chromosome 1 with a genetic predisposition for this disease. The systematic analysis of lupus-prone congenic mouse strains suggests a role for two isoforms of the Ly108 receptor in the pathogenesis of the disease. In this study, we demonstrate that Ly108 is involved in the pathogenesis of lupus-related autoimmunity in mice. More importantly, we identified a third protein isoform, Ly108-H1, which is absent in two lupus-prone congenic animals. Introduction of an Ly108-H1–expressing transgene markedly diminishes T cell–dependent autoimmunity in congenic B6.Sle1b mice. Thus, an immune response–suppressing isoform of Ly108 can regulate the pathogenesis of lupus.Peer Reviewe