Exome sequencing and analysis of 454,787 UK Biobank participants.
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SUBMITTER: Backman JD
PROVIDER: S-EPMC8596853 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The UK Biobank is a prospective study of 502,543 individuals, combining extensive phenotypic and genotypic data with streamlined access for researchers around the world1. Here we describe the release of exome-sequence data for the first 49,960 study participants, revealing approximately 4 million coding variants (of which around 98.6% have a frequency of less than 1%). The data include 198,269 autosomal predicted loss-of-function (LOF) variants, a more than 14-fold increase compared to the imputed sequence. Nearly all genes (more than 97%) had at least one carrier with a LOF variant, and most genes (more than 69%) had at least ten carriers with a LOF variant. We illustrate the power of characterizing LOF variants in this population through association analyses across 1,730 phenotypes. In addition to replicating established associations, we found novel LOF variants with large effects on disease traits, including PIEZO1 on varicose veins, COL6A1 on corneal resistance, MEPE on bone density, and IQGAP2 and GMPR on blood cell traits. We further demonstrate the value of exome sequencing by surveying the prevalence of pathogenic variants of clinical importance, and show that 2% of this population has a medically actionable variant. Furthermore, we characterize the penetrance of cancer in carriers of pathogenic BRCA1 and BRCA2 variants. Exome sequences from the first 49,960 participants highlight the promise of genome sequencing in large population-based studies and are now accessible to the scientific community.
| S-EPMC7759458 | biostudies-literature
Project description:IntroductionA previous study of 200,000 exome-sequenced UK Biobank participants to test for association of rare coding variants with hypertension implicated two genes at exome-wide significance, DNMT3A and FES. A total of 42 genes had an uncorrected p value <0.001. These results were followed up in a larger sample of 470,000 exome-sequenced participants.MethodsWeighted burden analysis of rare coding variants in a new sample of 97,050 cases and 172,263 controls was carried out for these 42 genes. Those showing evidence for association were then analysed in the combined sample of 167,127 cases and 302,691 controls.ResultsThe association of DNMT3A and FES with hypertension was replicated in the new sample and they and the previously implicated gene NPR1, which codes for a membrane-bound guanylate cyclase, were all exome-wide significant in the combined sample. Also exome-wide significant as risk genes for hypertension were GUCY1A1, ASXL1, and SMAD6, while GUCY1B1 had a nominal p value of <0.0001. GUCY1A1 and GUCY1B1 code for subunits of a soluble guanylate cyclase. For two genes, DBH, which codes for dopamine beta hydroxylase, and INPPL1, rare coding variants predicted to impair gene function were protective against hypertension, again with exome-wide significance.ConclusionThe findings offer new insights into biological risk factors for hypertension which could be the subject of further investigation. In particular, genetic variants predicted to impair the function of either membrane-bound guanylate cyclase, activated by natriuretic peptides, or soluble guanylate cyclase, activated by nitric oxide, increase risk of hypertension. Conversely, variants impairing the function of dopamine beta hydroxylase, responsible for the synthesis of norepinephrine, reduce hypertension risk.
| S-EPMC10712968 | biostudies-literature
Project description:ImportanceDetection of disease-associated variants in the BRCA1 and BRCA2 (BRCA1/2) genes allows for cancer prevention and early diagnosis in high-risk individuals.ObjectivesTo identify pathogenic and likely pathogenic (P/LP) BRCA1/2 variants in an unselected research cohort, and to characterize the features associated with P/LP variants.Design, setting, and participantsThis is a cross-sectional study of adult volunteers (n = 50 726) who underwent exome sequencing at a single health care system (Geisinger Health System, Danville, Pennsylvania) from January 1, 2014, to March 1, 2016. Participants are part of the DiscovEHR cohort and were identified through the Geisinger MyCode Community Health Initiative. They consented to a research protocol that included sequencing and return of actionable test results. Clinical data from electronic health records and clinical visits were correlated with variants. Comparisons were made between those with (cases) and those without (controls) P/LP variants in BRCA1/2.Main outcomesPrevalence of P/LP BRCA1/2 variants in cohort, proportion of variant carriers not previously ascertained through clinical testing, and personal and family history of relevant cancers among BRCA1/2 variant carriers and noncarriers.ResultsOf the 50 726 health system patients who underwent exome sequencing, 50 459 (99.5%) had no expected pathogenic BRCA1/2 variants and 267 (0.5%) were BRCA1/2 carriers. Of the 267 cases (148 [55.4%] were women and 119 [44.6%] were men with a mean [range] age of 58.9 [23-90] years), 183 (68.5%) received clinically confirmed results in their electronic health record. Among the 267 participants with P/LP BRCA1/2 variants, 219 (82.0%) had no prior clinical testing, 95 (35.6%) had BRCA1 variants, and 172 (64.4%) had BRCA2 variants. Syndromic cancer diagnoses were present in 11 (47.8%) of the 23 deceased BRCA1/2 carriers and in 56 (20.9%) of all 267 BRCA1/2 carriers. Among women, 31 (20.9%) of 148 variant carriers had a personal history of breast cancer, compared with 1554 (5.2%) of 29 880 noncarriers (odds ratio [OR], 5.95; 95% CI, 3.88-9.13; P < .001). Ovarian cancer history was present in 15 (10.1%) of 148 variant carriers and in 195 (0.6%) of 29 880 variant noncarriers (OR, 18.30; 95% CI, 10.48-31.4; P < .001). Among 89 BRCA1/2 carriers without prior testing but with comprehensive personal and family history data, 44 (49.4%) did not meet published guidelines for clinical testing.Conclusions and relevanceThis study found that compared with previous clinical care, exome sequencing-based screening identified 5 times as many individuals with P/LP BRCA1/2 variants. These findings suggest that genomic screening may identify BRCA1/2-associated cancer risk that might otherwise remain undetected within health care systems and may provide opportunities to reduce morbidity and mortality in patients.
| S-EPMC6324494 | biostudies-literature
Project description:BackgroundFrailty indices (FIs) measure variation in health between aging individuals. Researching FIs in resources with large-scale genetic and phenotypic data will provide insights into the causes and consequences of frailty. Thus, we aimed to develop an FI using UK Biobank data, a cohort study of 500,000 middle-aged and older adults.MethodsAn FI was calculated using 49 self-reported questionnaire items on traits covering health, presence of diseases and disabilities, and mental well-being, according to standard protocol. We used multiple imputation to derive FI values for the entire eligible sample in the presence of missing item data (N = 500,336). To validate the measure, we assessed associations of the FI with age, sex, and risk of all-cause mortality (follow-up ≤ 9.7 years) using linear and Cox proportional hazards regression models.ResultsMean FI in the cohort was 0.125 (SD = 0.075), and there was a curvilinear trend toward higher values in older participants. FI values were also marginally higher on average in women than in men. In survival models, 10% higher baseline frailty (ie, a 0.1 FI increment) was associated with higher risk of death (hazard ratio = 1.65; 95% confidence interval: 1.62-1.68). Associations were stronger in younger participants than in older participants, and in men than in women (hazard ratios: 1.72 vs. 1.56, respectively).ConclusionsThe FI is a valid measure of frailty in UK Biobank. The cohort's data are open access for researchers to use, and we provide script for deriving this tool to facilitate future studies on frailty.
| S-EPMC6417451 | biostudies-literature
Project description:Pharmacogenetics studies how genetic variation leads to variability in drug response. Guidelines for selecting the right drug and right dose for patients based on their genetics are clinically effective, but are widely unused. For some drugs, the normal clinical decision making process may lead to the optimal dose of a drug that minimizes side effects and maximizes effectiveness. Without measurements of genotype, physicians and patients may adjust dosage in a manner that reflects the underlying genetics. The emergence of genetic data linked to longitudinal clinical data in large biobanks offers an opportunity to confirm known pharmacogenetic interactions as well as discover novel associations by investigating outcomes from normal clinical practice. Here we use the UK Biobank to search for pharmacogenetic interactions among 200 drugs and 9 genes among 200,000 participants. We identify associations between pharmacogene phenotypes and drug maintenance dose as well as differential drug response phenotypes. We find support for several known drug-gene associations as well as novel pharmacogenetic interactions.
| S-EPMC7951365 | biostudies-literature
Project description:The evidence on the association between alcohol consumption and adiposity is inconsistent and fragmented. We investigated the longitudinal association between alcohol consumption pattern and four different adiposity markers with repeated measures of adiposity and obesity incidence. We categorized current drinkers based on the sex-specific quartiles of their weekly alcohol consumption and the UK alcohol drinking guidelines. We used multivariable adjusted generalised linear models. With the exception of a direct association between alcohol volume and body fat percentage (BF%) in women (B = 0.42%; 95%CI: 0.04, 0.80% for women in the top quartile), we found no associations between alcohol consumption and adiposity markers for either sex. Red wine and champagne/white wine consumption were inversely associated with waist circumference (WC) for both sexes (B = -0.58 cm, 95%CI: -0.77, -0.38 cm and B= -0.49 cm, 95%CI: -0.68, -0.29 cm, respectively, for women; B = -0.28 cm, 95%CI: -0.47, -0.08 cm and B = -0.23 cm, 95%CI: -0.42, -0.04 cm, respectively, for men). Female and male spirit drinkers had higher WC than non-spirit drinkers. Alcohol consumption was associated with a lower risk of obesity incidence in women (OR:0.60, 95%CI:0.45, 0.80 for the 2nd quartile, OR:0.53, 95%CI: 0.40, 0.70 for the 3rd quartile and OR:0.61, 95%CI:0.46, 0.80 for the 4th quartile). We found limited evidence of longitudinal associations between alcohol intake and adiposity. The few statistically significant associations we observed are unlikely to be of clinical importance.
| S-EPMC9565835 | biostudies-literature
Project description:PurposeTo examine whether sociodemographic, and ocular factors relate to optical coherence tomography (OCT)-derived foveal curvature (FC) in healthy individuals.MethodsWe developed a deep learning model to quantify OCT-derived FC from 63,939 participants (age range, 39-70 years). Associations of FC with sociodemographic, and ocular factors were obtained using multilevel regression analysis (to allow for right and left eyes) adjusting for age, sex, ethnicity, height (model 1), visual acuity, spherical equivalent, corneal astigmatism, center point retinal thickness (CPRT), intraocular pressure (model 2), deprivation (Townsend index), higher education, annual income, and birth order (model 3). Fovea curvature was modeled as a z-score.ResultsMales had on average steeper FC (0.077; 95% confidence interval [CI] 0.077-0.078) than females (0.068; 95% CI 0.068-0.069). Compared with whites, non-white individuals showed flatter FC, particularly those of black ethnicity. In black males, -0.80 standard deviation (SD) change when compared with whites (95% CI -0.89, -0.71; P 5.2e10-68). In black females, -0.70 SD change when compared with whites (95% CI -0.77, -0.63; p 2.3e10-93). Ocular factors (visual acuity, refractive status, and CPRT) showed a graded inverse association with FC that persisted after adjustment. Macular curvature showed a positive association with FC. Income showed a linear trend increase in males (P for linear trend = 0.005).ConclusionsWe demonstrate marked differences in FC with ethnicity on the largest cohort studied for this purpose to date. Ocular factors showed a graded association with FC. Implementation of FC quantification in research and on the clinical setting can enhance the understanding of clinical macular phenotypes in health and disease.
| S-EPMC9344217 | biostudies-literature
Project description:AimsThe study aimed to identify specific genes and functional genetic variants affecting susceptibility to two alcohol-related phenotypes: heavy drinking and problem drinking.MethodsPhenotypic and exome sequence data were downloaded from the UK Biobank. Reported drinks in the last 24 hours were used to define heavy drinking, while responses to a mental health questionnaire defined problem drinking. Gene-wise weighted burden analysis was applied, with genetic variants which were rarer and/or had a more severe functional effect being weighted more highly. Additionally, previously reported variants of interest were analysed inidividually.ResultsOf exome sequenced subjects, for heavy drinking, there were 8166 cases and 84,461 controls, while for problem drinking, there were 7811 cases and 59,606 controls. No gene was formally significant after correction for multiple testing, but three genes possibly related to autism were significant at P < 0.001, FOXP1, ARHGAP33 and CDH9, along with VGF which may also be of psychiatric interest. Well established associations with rs1229984 in ADH1B and rs671 in ALDH2 were confirmed, but previously reported variants in ALDH1B1 and GRM3 were not associated with either phenotype.ConclusionsThis large study fails to conclusively implicate any novel genes or variants. It is possible that more definitive results will be obtained when sequence data for the remaining UK Biobank participants become available and/or if data can be obtained for a more extreme phenotype such as alcohol dependence disorder. This research has been conducted using the UK Biobank Resource.
| S-EPMC9270990 | biostudies-literature
Project description:BackgroundFrailty and multimorbidity have been suggested as risk factors for severe COVID-19 disease.AimsWe investigated, in the UK Biobank, whether frailty and multimorbidity were associated with risk of hospitalisation with COVID-19.Methods502,640 participants aged 40-69 years at baseline (54-79 years at COVID-19 testing) were recruited across UK during 2006-10. A modified assessment of frailty using Fried's classification was generated from baseline data. COVID-19 test results (England) were available for 16/03/2020-01/06/2020, mostly taken in hospital settings. Logistic regression was used to discern associations between frailty, multimorbidity and COVID-19 diagnoses, after adjusting for sex, age, BMI, ethnicity, education, smoking and number of comorbidity groupings, comparing COVID-19 positive, COVID-19 negative and non-tested groups.Results4510 participants were tested for COVID-19 (positive = 1326, negative = 3184). 497,996 participants were not tested. Compared to the non-tested group, after adjustment, COVID-19 positive participants were more likely to be frail (OR = 1.4 [95%CI = 1.1, 1.8]), report slow walking speed (OR = 1.3 [1.1, 1.6]), report two or more falls in the past year (OR = 1.3 [1.0, 1.5]) and be multimorbid (≥ 4 comorbidity groupings vs 0-1: OR = 1.9 [1.5, 2.3]). However, similar strength of associations were apparent when comparing COVID-19 negative and non-tested groups. However, frailty and multimorbidity were not associated with COVID-19 diagnoses, when comparing COVID-19 positive and COVID-19 negative participants.Discussion and conclusionsFrailty and multimorbidity do not appear to aid risk stratification, in terms of positive versus negative results of COVID-19 testing. Investigation of the prognostic value of these markers for adverse clinical sequelae following COVID-19 disease is urgently needed.
| S-EPMC7377312 | biostudies-literature
Project description:BackgroundFrailty and multimorbidity are common in type 2 diabetes (T2D), including people <65 years. Guidelines recommend adjustment of treatment targets in people with frailty or multimorbidity. It is unclear how recommendations to adjust treatment targets in people with frailty or multimorbidity should be applied to different ages. We assess implications of frailty/multimorbidity in middle/older-aged people with T2D.MethodsWe analysed UK Biobank participants (n = 20,566) with T2D aged 40-72 years comparing two frailty measures (Fried frailty phenotype and Rockwood frailty index) and two multimorbidity measures (Charlson Comorbidity index and count of long-term conditions (LTCs)). Outcomes were mortality, Major Adverse Cardiovascular Event (MACE), hospitalization with hypoglycaemia or fall/fracture.ResultsHere we show that choice of measure influences the population identified: 42% of participants are frail or multimorbid by at least one measure; 2.2% by all four measures. Each measure is associated with mortality, MACE, hypoglycaemia, and fall or fracture. The absolute 5-year mortality risk is higher in older versus younger participants with a given level of frailty (e.g. 1.9%, and 9.9% in men aged 45 and 65, respectively, using frailty phenotype) or multimorbidity (e.g. 1.3%, and 7.8% in men with 4 LTCs aged 45 and 65, respectively). Using frailty phenotype, the relationship between higher HbA1c and mortality is stronger in frail compared with pre-frail or robust participants.ConclusionsAssessment of frailty/multimorbidity should be embedded within routine management of middle-aged and older people with T2D. Method of identification as well as features such as age impact baseline risk and should influence clinical decisions (e.g. glycaemic control).
| S-EPMC9053176 | biostudies-literature