kalis: a modern implementation of the Li & Stephens model for local ancestry inference in R.

BACKGROUND: Approximating the recent phylogeny of N phased haplotypes at a set of variants along the genome is a core problem in modern population genomics and central to performing genome-wide screens for association, selection, introgression, and other signals. The Li & Stephens (LS) model provides a simple yet powerful hidden Markov model for inferring the recent ancestry at a given variant, represented as an N × N distance matrix based on posterior decodings. RESULTS: We provide a high-performance engine to make these posterior decodings readily accessible with minimal pre-processing via an easy to use package kalis, in the statistical programming language R. kalis enables investigators to rapidly resolve the ancestry at loci of interest and developers to build a range of variant-specific ancestral inference pipelines on top. kalis exploits both multi-core parallelism and modern CPU vector instruction sets to enable scaling to hundreds of thousands of genomes. CONCLUSIONS: The resulting distance matrices accessible via kalis enable local ancestry, selection, and association studies in modern large scale genomic datasets.

Association of structural variation with cardiometabolic traits in Finns.

The contribution of genome structural variation (SV) to quantitative traits associated with cardiometabolic diseases remains largely unknown. Here, we present the results of a study examining genetic association between SVs and cardiometabolic traits in the Finnish population. We used sensitive methods to identify and genotype 129,166 high-confidence SVs from deep whole-genome sequencing (WGS) data of 4,848 individuals. We tested the 64,572 common and low-frequency SVs for association with 116 quantitative traits and tested candidate associations using exome sequencing and array genotype data from an additional 15,205 individuals. We discovered 31 genome-wide significant associations at 15 loci, including 2 loci at which SVs have strong phenotypic effects: (1) a deletion of the ALB promoter that is greatly enriched in the Finnish population and causes decreased serum albumin level in carriers (p = 1.47 × 10-54) and is also associated with increased levels of total cholesterol (p = 1.22 × 10-28) and 14 additional cholesterol-related traits, and (2) a multi-allelic copy number variant (CNV) at PDPR that is strongly associated with pyruvate (p = 4.81 × 10-21) and alanine (p = 6.14 × 10-12) levels and resides within a structurally complex genomic region that has accumulated many rearrangements over evolutionary time. We also confirmed six previously reported associations, including five led by stronger signals in single nucleotide variants (SNVs) and one linking recurrent HP gene deletion and cholesterol levels (p = 6.24 × 10-10), which was also found to be strongly associated with increased glycoprotein level (p = 3.53 × 10-35). Our study confirms that integrating SVs in trait-mapping studies will expand our knowledge of genetic factors underlying disease risk.

Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences.

BACKGROUND: Mitochondrial genome copy number (MT-CN) varies among humans and across tissues and is highly heritable, but its causes and consequences are not well understood. When measured by bulk DNA sequencing in blood, MT-CN may reflect a combination of the number of mitochondria per cell and cell-type composition. Here, we studied MT-CN variation in blood-derived DNA from 19184 Finnish individuals using a combination of genome (N = 4163) and exome sequencing (N = 19034) data as well as imputed genotypes (N = 17718). RESULTS: We identified two loci significantly associated with MT-CN variation: a common variant at the MYB-HBS1L locus (P = 1.6 × 10-8), which has previously been associated with numerous hematological parameters; and a burden of rare variants in the TMBIM1 gene (P = 3.0 × 10-8), which has been reported to protect against non-alcoholic fatty liver disease. We also found that MT-CN is strongly associated with insulin levels (P = 2.0 × 10-21) and other metabolic syndrome (metS)-related traits. Using a Mendelian randomization framework, we show evidence that MT-CN measured in blood is causally related to insulin levels. We then applied an MT-CN polygenic risk score (PRS) derived from Finnish data to the UK Biobank, where the association between the PRS and metS traits was replicated. Adjusting for cell counts largely eliminated these signals, suggesting that MT-CN affects metS via cell-type composition. CONCLUSION: These results suggest that measurements of MT-CN in blood-derived DNA partially reflect differences in cell-type composition and that these differences are causally linked to insulin and related traits.

Evaluation of a pilot, community-led mental illness de-stigmatization theater intervention in rural uganda.

BACKGROUND: In rural areas of low- and middle- income countries, mental health care is often unavailable and inaccessible, and stigma is a major barrier to treatment. Destigmatization can increase treatment-seeking attitudes, community support, and acceptance of individuals suffering from mental illness. This study's primary objective was to evaluate the impact of a community-led, theater-based destigmatization campaign for mental illness conducted in the Busoga region of Eastern Uganda. METHODS: One hundred residents of the Busoga region were randomly selected via cluster sampling to complete a structured questionnaire assessing mental health stigma. Four focus groups were conducted for qualitative data on mental health stigma. Common misconceptions and specific points of stigma were identified from these responses, and local village health team personnel developed and performed a culturally-adapted theatrical performance addressing these points. Changes in perceptions of mental illness were measured among 57 attendees using two measures, the Broad Acceptance Scale (designed to reflect factors that contribute to structural stigma) and Personal Acceptance Scale (designed to reflect factors that contribute to interpersonal, or public stigma), before and after the performance. RESULTS: There was a significant increase in acceptance according to the Broad Acceptance Scale (p < .001) and Personal Acceptance Scale (p < .001). Qualitative responses from play attendees also indicated a decrease in stigma and an increased sense of the importance of seeking treatment for mentally ill patients. CONCLUSION: This study shows community-led, theater intervention may be an effective tool for the destigmatization of mental illness in rural areas of Uganda. Larger studies are needed to further test the efficacy of this approach and potential for longer-term scalabilityand sustainability.

An Epidemic Amidst a Pandemic: Musculoskeletal Firearm Injuries During the COVID-19 Pandemic.

BACKGROUND: The COVID-19 pandemic has substantially impacted the delivery of health care, both through direct care associated with COVID-19 and through more pervasive effects. Our goal was to evaluate whether the number of orthopaedic consultations for firearm injuries differed during the early months of the COVID-19 pandemic compared with the same period in prior years. We hypothesized that the initial months of the COVID-19 pandemic, compared with the same period in prior years, would have a higher number of orthopaedic consultations for firearm injuries and a lower rate of outpatient follow-up after consultations. METHODS: A prospectively collected database of orthopaedic trauma consultations at a level-I trauma center was queried for firearm injuries. We compared the number of orthopaedic consultations for firearm injury during the initial months of the COVID-19 pandemic (March 23, 2020, to September 30, 2020, referred to as the pandemic group) with identical dates from 2017 to 2019 (referred to as the pre-pandemic group). Outpatient follow-up rates, ZIP codes (and associated Area Deprivation Index), and demographic data were compared between the pandemic group and the pre-pandemic group. RESULTS: During the entire study period, 552 orthopaedic consultations for firearm injuries were identified. There was a 63% increase in the daily mean number of firearm injury consultations in the pandemic group, to 1.01, compared with the pre-pandemic group, 0.62 (p < 0.001). There was no difference in the rate of outpatient follow-up: 66% for the pandemic group and 72% for the pre-pandemic group. There was no difference in the percentage of patients from the most socially deprived decile: 45.3% in the pandemic group and 49.5% in the pre-pandemic group. Patients presenting during the pandemic were more often uninsured (75.8%) relative to the pre-pandemic group (67.9%), with a lack of health insurance significantly decreasing the likelihood of outpatient follow-up (p < 0.01). CONCLUSIONS: Compared with the same period in prior years, there was a significant increase in the number of orthopaedic consultations for firearm injuries during the early months of the COVID-19 pandemic in our community. Patient race, socioeconomic status, and outpatient follow-up were similar between the pandemic group and the pre-pandemic group. There was a higher proportion of uninsured patients within the pandemic group and a lower rate of follow-up among those without insurance.

Multicohort analysis of the maternal age effect on recombination.

Several studies have reported that the number of crossovers increases with maternal age in humans, but others have found the opposite. Resolving the true effect has implications for understanding the maternal age effect on aneuploidies. Here, we revisit this question in the largest sample to date using single nucleotide polymorphism (SNP)-chip data, comprising over 6,000 meioses from nine cohorts. We develop and fit a hierarchical model to allow for differences between cohorts and between mothers. We estimate that over 10 years, the expected number of maternal crossovers increases by 2.1% (95% credible interval (0.98%, 3.3%)). Our results are not consistent with the larger positive and negative effects previously reported in smaller cohorts. We see heterogeneity between cohorts that is likely due to chance effects in smaller samples, or possibly to confounders, emphasizing that care should be taken when interpreting results from any specific cohort about the effect of maternal age on recombination.