Interpersonal Gut Microbiome Variation Drives Susceptibility and Resistance to Cholera Infection.

The gut microbiome is the resident microbial community of the gastrointestinal tract. This community is highly diverse, but how microbial diversity confers resistance or susceptibility to intestinal pathogens is poorly understood. Using transplantation of human microbiomes into several animal models of infection, we show that key microbiome species shape the chemical environment of the gut through the activity of the enzyme bile salt hydrolase. The activity of this enzyme reduced colonization by the major human diarrheal pathogen Vibrio cholerae by degrading the bile salt taurocholate that activates the expression of virulence genes. The absence of these functions and species permits increased infection loads on a personal microbiome-specific basis. These findings suggest new targets for individualized preventative strategies of V. cholerae infection through modulating the structure and function of the gut microbiome.

The genomic landscape of 2,023 colorectal cancers.

Colorectal carcinoma (CRC) is a common cause of mortality1, but a comprehensive description of its genomic landscape is lacking2-9. Here we perform whole-genome sequencing of 2,023 CRC samples from participants in the UK 100,000 Genomes Project, thereby providing a highly detailed somatic mutational landscape of this cancer. Integrated analyses identify more than 250 putative CRC driver genes, many not previously implicated in CRC or other cancers, including several recurrent changes outside the coding genome. We extend the molecular pathways involved in CRC development, define four new common subgroups of microsatellite-stable CRC based on genomic features and show that these groups have independent prognostic associations. We also characterize several rare molecular CRC subgroups, some with potential clinical relevance, including cancers with both microsatellite and chromosomal instability. We demonstrate a spectrum of mutational profiles across the colorectum, which reflect aetiological differences. These include the role of Escherichia colipks+ colibactin in rectal cancers10 and the importance of the SBS93 signature11-13, which suggests that diet or smoking is a risk factor. Immune-escape driver mutations14 are near-ubiquitous in hypermutant tumours and occur in about half of microsatellite-stable CRCs, often in the form of HLA copy number changes. Many driver mutations are actionable, including those associated with rare subgroups (for example, BRCA1 and IDH1), highlighting the role of whole-genome sequencing in optimizing patient care.

Rare variant associations with plasma protein levels in the UK Biobank.

Integrating human genomics and proteomics can help elucidate disease mechanisms, identify clinical biomarkers and discover drug targets1-4. Because previous proteogenomic studies have focused on common variation via genome-wide association studies, the contribution of rare variants to the plasma proteome remains largely unknown. Here we identify associations between rare protein-coding variants and 2,923 plasma protein abundances measured in 49,736 UK Biobank individuals. Our variant-level exome-wide association study identified 5,433 rare genotype-protein associations, of which 81% were undetected in a previous genome-wide association study of the same cohort5. We then looked at aggregate signals using gene-level collapsing analysis, which revealed 1,962 gene-protein associations. Of the 691 gene-level signals from protein-truncating variants, 99.4% were associated with decreased protein levels. STAB1 and STAB2, encoding scavenger receptors involved in plasma protein clearance, emerged as pleiotropic loci, with 77 and 41 protein associations, respectively. We demonstrate the utility of our publicly accessible resource through several applications. These include detailing an allelic series in NLRC4, identifying potential biomarkers for a fatty liver disease-associated variant in HSD17B13 and bolstering phenome-wide association studies by integrating protein quantitative trait loci with protein-truncating variants in collapsing analyses. Finally, we uncover distinct proteomic consequences of clonal haematopoiesis (CH), including an association between TET2-CH and increased FLT3 levels. Our results highlight a considerable role for rare variation in plasma protein abundance and the value of proteogenomics in therapeutic discovery.

Impact of the inaccessible genome on genotype imputation and genome-wide association studies.

Genotype imputation is widely used in genome-wide association studies (GWAS). However, both the genotyping chips and imputation reference panels are dependent on next-generation sequencing (NGS). Due to the nature of NGS, some regions of the genome are inaccessible to sequencing. To date, there has been no complete evaluation of these regions and their impact on the identification of associations in GWAS remains unclear. In this study, we systematically assess the extent to which variants in inaccessible regions are underrepresented on genotyping chips and imputation reference panels, in GWAS results and in variant databases. We also determine the proportion of genes located in inaccessible regions and compare the results across variant masks defined by the 1000 Genomes Project and the TOPMed program. Overall, fewer variants were observed in inaccessible regions in all categories analyzed. Depending on the mask used and normalized for region size, only 4%-17% of the genotyped variants are located in inaccessible regions and 52 to 581 genes were almost completely inaccessible. From the Cooperative Health Research in South Tyrol (CHRIS) study, we present a case study of an association located in an inaccessible region that is driven by genotyped variants and cannot be reproduced by imputation in GRCh37. We conclude that genotyping, NGS, genotype imputation and downstream analyses such as GWAS and fine mapping are systematically biased in inaccessible regions, due to missed variants and spurious associations. To help researchers assess gene and variant accessibility, we provide an online application (https://gab.gm.eurac.edu).

Indications and outcomes of transjugular intrahepatic portosystemic shunt insertion in two regional Australian hepatology centres.

BACKGROUND: Transjugular intrahepatic portosystemic shunt (TIPS) is an important therapy for complications of portal hypertension but remains underutilised in regional settings. AIMS: The aim of this study is to explore the demographics, indications, outcomes and complications in patients undergoing TIPS in two regional hepatology centres. METHODS: Retrospective analysis was undertaken of all patients undergoing TIPS at two regional centres between January 2017 and March 2023. The primary outcome measures were efficacy and complications of TIPS. Patient demographics (such as age, baseline liver severity scores and aetiology of liver disease) and indications for TIPS are detailed. RESULTS: Forty-eight patients underwent TIPS. Median age was 56 years (interquartile range (IQR): 46-65). The most common indications for TIPS were refractory ascites (n = 17) and failure of secondary prophylaxis of variceal bleeding (n = 13). Cumulative survival at 3 months and 1 year was 93% and 77% respectively. There was no significant difference in outcomes based on TIPS indication. The median number of paracenteses in patients undergoing TIPS for refractory ascites 1 year pre- and post-TIPS were 10 (IQR: 4.5-16) and 2 (IQR: 0-4) respectively (P < 0.001). There were no procedure-related deaths. Inpatient management of liver disease complications had a mean cost of $32 874.67 (SEM: 7779) in 1 year pre-TIPS compared with $12 304.70 (SEM: 3531.1) in 1 year post-TIPS (P < 0.001). CONCLUSIONS: TIPS is a safe and effective treatment to reduce complications of portal hypertension and can be performed successfully in the regional setting.

Gamification to Promote Physical Activity in Youth and Mothers With Obesity.

PURPOSE: Physical inactivity and sugar-sweetened beverage (SSB) consumption are associated with obesity. Gamification and self-monitoring to promote physical activity in youth is unknown, but evidence of effectiveness is present in adults. This study examined the effects of a gamification intervention on increased steps per day among parent-adolescent dyads with obesity compared with digital self-monitoring and if self-monitored SSB intake differed between these arms. METHODS: Youth ages 10-16 years and their mothers (N = 39 pairs), both with obesity, were randomized to a self-monitoring (N = 18) or a self-monitoring plus gamification arm (N = 21) for 9 weeks. The step goal was set and incrementally increased each week and was measured with Fitbit devices. Mixed effects linear regression examined changes in steps and SSB consumption per day, per week by study arm. RESULTS: During run-in, mothers averaged 8317 and youth 7508 steps per day. Compared with self-monitoring alone, gamification did not increase daily steps in mothers or youth beyond baseline levels. On average, SSB intake decreased in mothers by approximately 0.5 servings per day; occurred in both arms and persisted throughout the intervention. CONCLUSION: Gamification did not promote physical activity levels in mother-youth dyads with obesity. SSB intake declined in mothers with obesity in both study arms.

Enhancing patient safety: A national standard for cyber resiliency in healthcare.

With support from Public Safety Canada's Cyber Security Cooperation Program, HealthCareCAN and the Digital Governance Council developed a new standard to support cyber resiliency in Canada's healthcare system. With a clear framework and enhanced cybersecurity capabilities, healthcare organizations will be better protected from cybercrime, allowing them to respond more effectively to evolving threats and defend critical infrastructure. Health and information technology leaders can derive practical guidance and next steps from this three-year national project to enhance cyber resilience and improve safety within their organizations.

The impact of fear of hypoglycaemia on sleep in adolescents with type 1 diabetes.

AIMS: Fear of hypoglycaemia (FOH) can contribute to impaired sleep for adults with type 1 diabetes (T1D) and parents of children with T1D, although it is unknown how FOH may affect sleep for adolescents with T1D. This study examines the relationship between adolescent FOH and sleep and assessed the influences of continuous glucose monitor (CGM) and insulin pump use. METHODS: Adolescents ages 14-18 years with T1D completed questionnaires evaluating FOH (Child Hypoglycemia Fear Survey) and sleep (Pittsburgh Sleep Quality Index, PSQI). Analyses included linear and logistic regression, t-tests and Fisher's exact tests. RESULTS: Participants included 95 adolescents (52 female) with a median (IQR) age of 16.5 (15.3-17.7) years and a T1D duration of 5.7 (2.5-9.6) years. Analyses showed increased FOH-Worry subscale scores were associated with reduced sleep duration (ß = -0.03, p = 0.042, adjusting for BMI z-score, race and ethnicity) and increased sleep disturbances (OR = 1.1, p = 0.038, adjusting for race and ethnicity). Frequent CGM users had longer sleep duration (average 7.5 h) compared with infrequent or non-CGM users (average = 6.8 h; p = 0.029), and pump users had overall improved sleep health as determined by PSQI score (p = 0.019). Technology use did not have significant interactions in the relationships between FOH and sleep duration or sleep disturbances. CONCLUSIONS: Worrying about hypoglycaemia was associated with impaired sleep for adolescents with T1D. Diabetes technology users have some sleep improvements, but CGM and pump use do little to alter the relationship between FOH and sleep outcomes.

Gene Tree Discord, Simplex Plots, and Statistical Tests under the Coalescent.

A simple graphical device, the simplex plot of quartet concordance factors, is introduced to aid in the exploration of a collection of gene trees on a common set of taxa. A single plot summarizes all gene tree discord and allows for visual comparison to the expected discord from the multispecies coalescent model (MSC) of incomplete lineage sorting on a species tree. A formal statistical procedure is described that can quantify the deviation from expectation for each subset of four taxa, suggesting when the data are not in accord with the MSC, and thus that either gene tree inference error is substantial or a more complex model such as that on a network may be required. If the collection of gene trees is in accord with the MSC, the plots reveal when substantial incomplete lineage sorting is present. Applications to both simulated and empirical multilocus data sets illustrate the insights provided. [Gene tree discordance; hypothesis test; multispecies coalescent model; quartet concordance factor; simplex plot; species tree].

Surgical Training for Civilian Surgeons Interested in Humanitarian Surgery: A Scoping Review.

INTRODUCTION: Humanitarian surgery is essential to surgical care in limited resource settings. The difficulties associated with resource constraints necessitate special training for civilian surgeons to provide care in these situations. Specific training or curricula for humanitarian surgeons are not well described in the literature. This scoping review summarizes the existing literature and identifies areas for potential improvement. METHODS: A review of articles describing established courses for civilian surgeons interested in humanitarian surgery, as well as those describing training of civilian surgeons in conflict zones, was performed. A total of 4808 abstracts were screened by two independent reviewers, and 257 abstracts were selected for full-text review. Articles describing prehospital care and military experience were excluded from the full-text review. RESULTS: Of the eight relevant full texts, 10 established courses for civilian surgeons were identified. Cadaver-based teaching combined with didactics were the most common course themes. Courses provided technical education focused on the management of trauma and burns as well as emergencies in orthopedics, neurosurgery, obstetrics, and gynecology. Other courses were in specialty surgery, mainly orthopedics. Two fellowship programs were identified, and these provide a different model for training humanitarian surgeons. CONCLUSIONS: Humanitarian surgery is often practiced in austere environments, and civilian surgeons must be adequately trained to first do no harm. Current programs include cadaver-based courses focused on enhancing trauma surgery and surgical subspecialty skills, with adjunctive didactics covering resource allocation in austere environments. Fellowships programs may serve as an avenue to provide a more standardized education and a reliable pipeline of global surgeons.

Stimulator of interferon genes (STING) is an essential proviral host factor for human rhinovirus species A and C.

Human rhinoviruses (RVs) are positive-strand RNA viruses that cause respiratory tract disease in children and adults. Here we show that the innate immune signaling protein STING is required for efficient replication of members of two distinct RV species, RV-A and RV-C. The host factor activity of STING was identified in a genome-wide RNA interference (RNAi) screen and confirmed in primary human small airway epithelial cells. Replication of RV-A serotypes was strictly dependent on STING, whereas RV-B serotypes were notably less dependent. Subgenomic RV-A and RV-C RNA replicons failed to amplify in the absence of STING, revealing it to be required for a step in RNA replication. STING was expressed on phosphatidylinositol 4-phosphate (PI4P)-enriched membranes and was enriched in RV-A16 compared with RV-B14 replication organelles isolated in isopycnic gradients. The host factor activity of STING was species-specific, as murine STING (mSTING) did not rescue RV-A16 replication in STING-deficient cells. This species specificity mapped primarily to the cytoplasmic, ligand-binding domain of STING. Mouse-adaptive mutations in the RV-A16 2C protein allowed for robust replication in cells expressing mSTING, suggesting a role for 2C in recruiting STING to RV-A replication organelles. Palmitoylation of STING was not required for RV-A16 replication, nor was the C-terminal tail of STING that mediates IRF3 signaling. Despite co-opting STING to promote its replication, interferon signaling in response to STING agonists remained intact in RV-A16 infected cells. These data demonstrate a surprising requirement for a key host mediator of innate immunity to DNA viruses in the life cycle of a small pathogenic RNA virus.

Heterologous Ad.26.COV2.S versus homologous BNT162b2/mRNA-1273 as a third dose in solid organ transplant recipients seronegative after two-dose mRNA vaccination.

Heterologous vaccination ("mixing platforms") for the third (D3) dose of SARS-CoV-2 vaccine is a potential strategy to improve antibody responses in solid organ transplant recipients (SOTRs), but data are mixed regarding potential differential immunogenicity. We assessed for differences in immunogenicity and tolerability of homologous (BNT162b2 or mRNA-1273; D3-mRNA) versus heterologous (Ad.26.COV2.S; D3-JJ) D3 among 377 SARS-CoV-2-infection naïve SOTRs who remained seronegative after two mRNA vaccines. We measured anti-spike titers and used weighted Poisson regression to evaluate seroconversion and development of high-titers, comparing D3-JJ to D3-mRNA, at 1-, 3-, and 6 month post-D3. 1-month post-D3, seroconversion (63% vs. 52%, p = .3) and development of high-titers (29% vs. 25%, p = .7) were comparable between D3-JJ and D3-mRNA recipients. 3 month post-D3, D3-JJ recipients were 1.4-fold more likely to seroconvert (80% vs. 57%, weighted incidence-rate-ratio: wIRR = 1.10 1.401.77 , p = .006) but not more likely to develop high-titers (27% vs. 22%, wIRR = 0.44 0.921.93 , p = .8). 6 month post-D3, D3-JJ recipients were 1.41-fold more likely to seroconvert (88% vs. 59%, wIRR = 1.04 1.411.93 , p = .029) and 2.63-fold more likely to develop high-titers (59% vs. 21%, wIRR = 1.38 2.635.00 , p = .003). There was no differential signal in alloimmune events or reactogenicity between platforms. SOTRs without antibody response after two mRNA vaccines may derive benefit from heterologous Ad.26.COV2.S D3.

MSCquartets 1.0: quartet methods for species trees and networks under the multispecies coalescent model in R.

SUMMARY: MSCquartets is an R package for species tree hypothesis testing, inference of species trees and inference of species networks under the Multispecies Coalescent model of incomplete lineage sorting and its network analog. Input for these analyses are collections of metric or topological locus trees which are then summarized by the quartets displayed on them. Results of hypothesis tests at user-supplied levels are displayed in a simplex plot by color-coded points. The package implements the QDC and WQDC algorithms for topological and metric species tree inference, and the NANUQ algorithm for level-1 topological species network inference, all of which give statistically consistent estimators under the model. AVAILABILITY AND IMPLEMENTATION: MSCquartets is available through the Comprehensive R Archive Network: https://CRAN.R-project.org/package=MSCquartets.

The tree of blobs of a species network: identifiability under the coalescent.

Inference of species networks from genomic data under the Network Multispecies Coalescent Model is currently severely limited by heavy computational demands. It also remains unclear how complicated networks can be for consistent inference to be possible. As a step toward inferring a general species network, this work considers its tree of blobs, in which non-cut edges are contracted to nodes, so only tree-like relationships between the taxa are shown. An identifiability theorem, that most features of the unrooted tree of blobs can be determined from the distribution of gene quartet topologies, is established. This depends upon an analysis of gene quartet concordance factors under the model, together with a new combinatorial inference rule. The arguments for this theoretical result suggest a practical algorithm for tree of blobs inference, to be fully developed in a subsequent work.

Building a virtual community of practice: experience from the Canadian foundation for healthcare improvement's policy circle.

BACKGROUND: Communities of Practice are formed by people who interact regularly to engage in collective learning in a shared domain of human endeavor. Virtual Communities of Practice (VCoP) are online communities that use the internet to connect people who share a common concern or passion. VCoPs provide a platform to share and enhance knowledge. The Policy Circle is a VCoP that connects mid-career professionals from across Canada who are committed to improving healthcare policy and practice. We wanted to understand the perceived value of the VCoP. METHODS: We used qualitative and quantitative survey research to explore past and current Policy Circle members' thoughts, feelings, and behaviours related to the program. Our research was guided by the Value Creation Framework proposed by Wenger and colleagues. Three surveys were created in collaboration with stakeholders. Data were analyzed within cohort and in aggregate across cohorts. Qualitative data was analyzed thematically, and quantitative data was analyzed using descriptive statistics (means of ranked and scaled responses). RESULTS: Survey participation was high among members (Cohort 1: 67%, Cohort 2: 64%). Participants came from a variety of disciplines including medicine, health policy, allied health, and nursing, with most members having a direct role in health services research or practice. The program was successful in helping participants make connections (mean = 2.43 on a scale from 1 to 5: 1 = yes, significantly, 5 = not at all); variances in both qualitative and quantitative data indicated that levels of enthusiasm within the program varied among individuals. Members appreciated the access to resources; quarterly meetings (n = 11/11), and a curated reading list (n = 8/11) were the most valued resources. Participants reported the development of a sense of belonging (mean = 2.29) and facilitated knowledge exchange (mean = 2.43). At the time of this study, participants felt the program had minor impact on their work (mean = 3.5), however a majority of participants (50%) from Cohort 2 planned to acknowledge the program in their professional or academic endeavours. Through reflective responses, participants expressed a desire for continued and deeper professional network development. CONCLUSIONS: The Policy Circle was successful in facilitating knowledge exchange by creating a community that promoted trust, a sense of belonging and a supportive environment. Members were satisfied with the program; to promote further value, the Policy Circle should implement strategies that will continue member participation and networking after the program is finished.

Genetic potential and height velocity during childhood and adolescence do not fully account for shorter stature in cystic fibrosis.

BACKGROUND: Despite improved health, shorter stature is common in cystic fibrosis (CF). We aimed to describe height velocity (HV) and contribution of height-related genetic variants to height (HT) in CF. METHODS: HV cohort: standard deviation scores (-Z) for HT, mid-parental height-adjusted HT (MPAH), and HV were generated using our Pediatric Center's CF Foundation registry data. HV-Z was compared with population means at each age (5-17 y), the relationship of HV-Z with HT-Z assessed, and HT-Z compared with MPAH-Z. GRS cohort: HT genetic risk-Z (HT-GRS-Z) were determined for pancreatic exocrine sufficient (PS) and insufficient (PI) youth and adults from our CF center and their relationships with HT-Z assessed. RESULTS: HV cohort: average HV-Z was normal across ages in our cohort but was 1.5× lower (p < 0.01) for each SD decrease in HT-Z. MPAH-Z was lower than HT-Z (p < 0.001). GRS cohort: HT-GRS-Z more strongly correlated with HT-Z and better explained height variance in PS (rho = 0.42; R2= 0.25) vs. PI (rho = 0.27; R2 = 0.11). CONCLUSIONS: Despite shorter stature compared with peers and mid-parental height, youth with CF generally have normal linear growth in mid- and late childhood. PI tempered the heritability of height. These results suggest that, in CF, final height is determined early in life in CF and genetic potential is attenuated by other factors. IMPACT: Children with CF remain shorter than their healthy peers despite advances in care. Our study demonstrates that children with CF have persistent shorter stature from an early age and fail to reach their genetic potential despite height velocities comparable to those of average maturing healthy peers and similar enrichment in known height increasing single-nucleotide polymorphisms (SNPs). Genetic risk scores better explained variability in pancreatic sufficient than in pancreatic insufficient individuals, suggesting that other modifying factors are in play for pancreatic insufficient individuals with CF. Given the CF Foundation's recommendation to target not only normal body mass index, but normal height percentiles as well, this study adds valuable insight to this discussion.

Performance of simple serum-based tests to exclude cirrhosis prior to hepatitis C treatment in non-hospital settings in Australia.

BACKGROUND: Current guidelines suggest using transient elastography (TE) or aspartate aminotransferase to platelet ratio index (APRI) score <1 to exclude cirrhosis prior to commencing treatment for hepatitis C virus (HCV). Recently, fibrosis-4 (FIB-4) <0.93 has been shown to have a high negative predictive value (NPV) for the presence of cirrhosis. AIMS: To assess FIB-4 and APRI in a cohort of HCV patients and to validate FIB-4 <0.93 in populations of HCV-infected individuals with differing cirrhosis prevalence, including secondary care, primary care and prisons. METHODS: From our treatment database, we identified patients with complete data (n = 793). We calculated FIB-4 and APRI and correlated this with the presence of cirrhosis, determined by TE. We analysed the performance of FIB-4 and APRI using area under the receiver operating curve analysis. We calculated sensitivity, specificity, positive predictive value, NPV and number of patients misclassified using published cut-offs in populations with varying cirrhosis prevalence. RESULTS: FIB-4 was superior to APRI for the diagnosis of cirrhosis (area under the receiver operating curve 0.868 vs 0.802). In secondary care (cirrhosis prevalence 32%), APRI <1 had a NPV of 80% and misclassified 14% of patients. FIB-4 <0.93 had a NPV of 97% and misclassified 1%. In primary care and prison (cirrhosis prevalence 13% and 8%), the NPV for APRI <1 was 93% and 96%, respectively, but 5% of patients with cirrhosis were misclassified. FIB-4 <0.93 had excellent NPV in both primary care (97%) and prisoners (100%). CONCLUSIONS: FIB-4 <0.93 is highly efficient at ruling out cirrhosis in HCV patients and allows TE to be appropriately avoided, thereby streamlining treatment algorithms.

Sex differences in childhood sleep and health implications.

CONTEXT: Sleep is critical for optimal childhood metabolic health and neurodevelopment. However, there is limited knowledge regarding childhood sex differences in sleep, including children with neurodevelopmental disorders, and the impact of such differences on metabolic health. OBJECTIVE: To evaluate if sex differences in childhood sleep exist and if sleep associates with metabolic health outcomes equally by sex. Using autism spectrum disorder (ASD) as a case study, we also examine sleep sex differences in children with a neurodevelopmental disorder. METHODS: A narrative review explored the literature focussing on sex differences in childhood sleep. RESULTS: Sex differences in sleep were not detected among pre-adolescents. However, female adolescents were more likely to report impaired sleep than males. Childhood obesity is more common in males. Shorter sleep duration may be associated with obesity in male pre-adolescents/adolescents; although findings are mixed. ASD is male-predominant; yet, there was an indication that pre-adolescent female children with ASD had more impaired sleep. CONCLUSION: Sex differences in sleep appear to emerge in adolescence with more impaired sleep in females. This trend was also observed among pre-adolescent female children with ASD. Further research is needed on sex differences in childhood sleep and metabolic health and the underlying mechanisms driving these differences.

The Quality Mental Health Care Network: A roadmap to improving quality mental healthcare in Canada.

Although there are numerous quality of care frameworks, little attention has been given to the essential concepts that encompass quality mental healthcare. HealthCareCAN and the Mental Health Commission of Canada co-lead the Quality Mental Health Care Network (QMHCN), which has developed a quality mental healthcare framework, building on existing provincial, national, and international frameworks. HealthCareCAN conducted an environmental scan, key informant interviews, and focus groups with individuals with lived experiences to develop the framework. This article outlines the findings from this scan, interviews and focus groups.

Low-Frequency Synonymous Coding Variation in CYP2R1 Has Large Effects on Vitamin D Levels and Risk of Multiple Sclerosis.

Vitamin D insufficiency is common, correctable, and influenced by genetic factors, and it has been associated with risk of several diseases. We sought to identify low-frequency genetic variants that strongly increase the risk of vitamin D insufficiency and tested their effect on risk of multiple sclerosis, a disease influenced by low vitamin D concentrations. We used whole-genome sequencing data from 2,619 individuals through the UK10K program and deep-imputation data from 39,655 individuals genotyped genome-wide. Meta-analysis of the summary statistics from 19 cohorts identified in CYP2R1 the low-frequency (minor allele frequency = 2.5%) synonymous coding variant g.14900931G>A (p.Asp120Asp) (rs117913124[A]), which conferred a large effect on 25-hydroxyvitamin D (25OHD) levels (-0.43 SD of standardized natural log-transformed 25OHD per A allele; p value = 1.5 × 10-88). The effect on 25OHD was four times larger and independent of the effect of a previously described common variant near CYP2R1. By analyzing 8,711 individuals, we showed that heterozygote carriers of this low-frequency variant have an increased risk of vitamin D insufficiency (odds ratio [OR] = 2.2, 95% confidence interval [CI] = 1.78-2.78, p = 1.26 × 10-12). Individuals carrying one copy of this variant also had increased odds of multiple sclerosis (OR = 1.4, 95% CI = 1.19-1.64, p = 2.63 × 10-5) in a sample of 5,927 case and 5,599 control subjects. In conclusion, we describe a low-frequency CYP2R1 coding variant that exerts the largest effect upon 25OHD levels identified to date in the general European population and implicates vitamin D in the etiology of multiple sclerosis.