Localization of adaptive variants in human genomes using averaged one-dependence estimation.

Statistical methods for identifying adaptive mutations from population genetic data face several obstacles: assessing the significance of genomic outliers, integrating correlated measures of selection into one analytic framework, and distinguishing adaptive variants from hitchhiking neutral variants. Here, we introduce SWIF(r), a probabilistic method that detects selective sweeps by learning the distributions of multiple selection statistics under different evolutionary scenarios and calculating the posterior probability of a sweep at each genomic site. SWIF(r) is trained using simulations from a user-specified demographic model and explicitly models the joint distributions of selection statistics, thereby increasing its power to both identify regions undergoing sweeps and localize adaptive mutations. Using array and exome data from 45 ‡Khomani San hunter-gatherers of southern Africa, we identify an enrichment of adaptive signals in genes associated with metabolism and obesity. SWIF(r) provides a transparent probabilistic framework for localizing beneficial mutations that is extensible to a variety of evolutionary scenarios

Depression, Anxiety, Post-traumatic Stress Disorder and a History of Pervasive Gender-Based Violence Among Women Asylum Seekers Who Have Undergone Female Genital Mutilation/Cutting: A Retrospective Case Review

We sought to evaluate the frequency of anxiety, depression, PTSD, and any experiences of violence in women who had undergone Female Genital Mutilation/Cutting (FGM/C) and were seeking asylum in the United States. We undertook a retrospective qualitative descriptive study of FGM/C cases seen in an asylum clinic over a 2-year period. Standardized questionnaires provided quantitative scores for anxiety, depression and PTSD. Clients’ personal and physician medical affidavits were analyzed for experiences of violence. Of the 13 cases, anxiety and depression were exhibited by 92 and 100% of women, while all seven women screened for PTSD had symptoms. Qualitative analysis revealed extensive violence perpetrated against these women, demonstrating that FGM/C is only part of the trauma experienced. The high level of mental health disorders and endured violence has implications for providers working with FGM/C survivors and indicates the need for accessible mental health services and trauma-informed care

Reply to : On powerful GWAS in admixed populations

Non peer reviewe

Identification of genes involved in alcohol consumption and cigarettes smoking

We compared the results of quantitative linkage analysis using single-nucleotide polymorphisms and microsatellite markers and introduced a new screening test for multivariate quantitative linkage analysis using the Collaborative Study on the Genetics of Alcoholism data. We analyzed 115 extended non-Hispanic White families and tested for linkage using two phenotypes: the maximum number of drinks in a 24-hour period and the number of packs smoked per day for one year. Our results showed that the linkage signal increased using single-nucleotide polymorphisms compared with microsatellite markers and that the screening test gave similar results to that of the bivariate analysis, suggesting its potential use in reducing overall analysis time

Latin American Trans-ancestry INitiative for OCD genomics (LATINO): Study protocol

Obsessive-compulsive disorder (OCD) is a debilitating psychiatric disorder. Worldwide, its prevalence is ~2% and its etiology is mostly unknown. Identifying biological factors contributing to OCD will elucidate underlying mechanisms and might contribute to improved treatment outcomes. Genomic studies of OCD are beginning to reveal long-sought risk loci, but \u3e95% of the cases currently in analysis are of homogenous European ancestry. If not addressed, this Eurocentric bias will result in OCD genomic findings being more accurate for individuals of European ancestry than other ancestries, thereby contributing to health disparities in potential future applications of genomics. In this study protocol paper, we describe the Latin American Trans-ancestry INitiative for OCD genomics (LATINO, https://www.latinostudy.org). LATINO is a new network of investigators from across Latin America, the United States, and Canada who have begun to collect DNA and clinical data from 5000 richly phenotyped OCD cases of Latin American ancestry in a culturally sensitive and ethical manner. In this project, we will utilize trans-ancestry genomic analyses to accelerate the identification of OCD risk loci, fine-map putative causal variants, and improve the performance of polygenic risk scores in diverse populations. We will also capitalize on rich clinical data to examine the genetics of treatment response, biologically plausible OCD subtypes, and symptom dimensions. Additionally, LATINO will help elucidate the diversity of the clinical presentations of OCD across cultures through various trainings developed and offered in collaboration with Latin American investigators. We believe this study will advance the important goal of global mental health discovery and equity

Impact of Forensic Medical Evaluations on Immigration Relief Grant Rates and Correlates of Outcomes in the United States.

The purpose of this study was to investigate the impact of forensic medical evaluations on grant rates for applicants seeking immigration relief in the United States (U.S.) and to identify significant correlates of grant success. We conducted a retrospective analysis of 2584 cases initiated by Physicians for Human Rights between 2008-2018 that included forensic medical evaluations, and found that 81.6% of applicants for various forms of immigration relief were granted relief, as compared to the national asylum grant rate of 42.4%. Among the study’s cohort, the majority (73.7%) of positive outcomes were grants of asylum. A multivariable regression analysis revealed that age, continent of origin, history of sexual or gender-based violence, gang violence, LGB sexual orientation, and being detained by the U.S. government at the time of evaluation request were statistically associated with case outcomes. Forensic physical evaluation was more strongly associated with a positive outcome than forensic psychological evaluation. Our findings strengthen and expand prior evidence that forensic medical evaluations can have a substantial positive impact on an applicant’s immigration relief claim. Given the growing applicant pool in the U.S., there is an urgent need for more trained clinicians to conduct forensic medical evaluations as well as to educate adjudicators, immigration lawyers, and policy makers about the nature of the life-altering events that applicants for immigration relief experience

Mississippi River Flood Waters That Reached The Gulf Stream

Distributions of physical, biological, and chemical parameters in Florida Keys coastal waters seaward of the reef track were surveyed on September 9 to 13, 1993, as part of a coordinated multidisciplinary study of surface transport processes. A band of low-salinity water was observed along the shoreward side of the Florida Current over the downstream extent of the survey from Miami to Key West. Biological and chemical indicators within the band, together with its large volume, satellite imagery, and a surface drifter trajectory suggested the recent Mississippi River flood as the source

JWST Pathfinder Telescope Integration

The James Webb Space Telescope (JWST) is a 6.5m, segmented, IR telescope that will explore the first light of the universe after the big bang. In 2014, a major risk reduction effort related to the Alignment, Integration, and Test (AI&T) of the segmented telescope was completed. The Pathfinder telescope includes two Primary Mirror Segment Assemblies (PMSA's) and the Secondary Mirror Assembly (SMA) onto a flight-like composite telescope backplane. This pathfinder allowed the JWST team to assess the alignment process and to better understand the various error sources that need to be accommodated in the flight build. The successful completion of the Pathfinder Telescope provides a final integration roadmap for the flight operations that will start in August 2015

International meta-analysis of PTSD genome-wide association studies identifies sex- and ancestry-specific genetic risk loci.

The risk of posttraumatic stress disorder (PTSD) following trauma is heritable, but robust common variants have yet to be identified. In a multi-ethnic cohort including over 30,000 PTSD cases and 170,000 controls we conduct a genome-wide association study of PTSD. We demonstrate SNP-based heritability estimates of 5-20%, varying by sex. Three genome-wide significant loci are identified, 2 in European and 1 in African-ancestry analyses. Analyses stratified by sex implicate 3 additional loci in men. Along with other novel genes and non-coding RNAs, a Parkinson's disease gene involved in dopamine regulation, PARK2, is associated with PTSD. Finally, we demonstrate that polygenic risk for PTSD is significantly predictive of re-experiencing symptoms in the Million Veteran Program dataset, although specific loci did not replicate. These results demonstrate the role of genetic variation in the biology of risk for PTSD and highlight the necessity of conducting sex-stratified analyses and expanding GWAS beyond European ancestry populations