Dataset Information

Improved imputation accuracy in Hispanic/Latino populations with larger and more diverse reference panels: applications in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL).

ABSTRACT: Imputation is commonly used in genome-wide association studies to expand the set of genetic variants available for analysis. Larger and more diverse reference panels, such as the final Phase 3 of the 1000 Genomes Project, hold promise for improving imputation accuracy in genetically diverse populations such as Hispanics/Latinos in the USA. Here, we sought to empirically evaluate imputation accuracy when imputing to a 1000 Genomes Phase 3 versus a Phase 1 reference, using participants from the Hispanic Community Health Study/Study of Latinos. Our assessments included calculating the correlation between imputed and observed allelic dosage in a subset of samples genotyped on a supplemental array. We observed that the Phase 3 reference yielded higher accuracy at rare variants, but that the two reference panels were comparable at common variants. At a sample level, the Phase 3 reference improved imputation accuracy in Hispanic/Latino samples from the Caribbean more than for Mainland samples, which we attribute primarily to the additional reference panel samples available in Phase 3. We conclude that a 1000 Genomes Project Phase 3 reference panel can yield improved imputation accuracy compared with Phase 1, particularly for rare variants and for samples of certain genetic ancestry compositions. Our findings can inform imputation design for other genome-wide association studies of participants with diverse ancestries, especially as larger and more diverse reference panels continue to become available.

SUBMITTER: Nelson SC

PROVIDER: S-EPMC5179925 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature

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Improved imputation accuracy in Hispanic/Latino populations with larger and more diverse reference panels: applications in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL).

Nelson Sarah C SC Stilp Adrienne M AM Papanicolaou George J GJ Taylor Kent D KD Rotter Jerome I JI Thornton Timothy A TA Laurie Cathy C CC

Human molecular genetics 20160626 15

Imputation is commonly used in genome-wide association studies to expand the set of genetic variants available for analysis. Larger and more diverse reference panels, such as the final Phase 3 of the 1000 Genomes Project, hold promise for improving imputation accuracy in genetically diverse populations such as Hispanics/Latinos in the USA. Here, we sought to empirically evaluate imputation accuracy when imputing to a 1000 Genomes Phase 3 versus a Phase 1 reference, using participants from the Hi ...[more]

PMID: 27346520

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Project description:BackgroundExcessive sedentary time is ubiquitous in developed nations and is associated with deleterious health outcomes. Few studies have examined whether the manner in which sedentary time is accrued (in short or long bouts) carries any clinical relevance. The purpose of this study was to examine the association of prolonged, uninterrupted sedentary behavior with glycemic biomarkers in a cohort of US Hispanic/Latino adults.MethodsWe studied 12 083 participants from the HCHS/SOL (Hispanic Community Health Study/Study of Latinos), a population-based study of Hispanic/Latino adults 18 to 74 years of age. Homeostatic model assessment of insulin resistance and glycosylated hemoglobin were measured from a fasting blood sample, and 2-hour glucose was measured after an oral glucose tolerance test. Sedentary time was objectively measured with a hip-mounted accelerometer. Prolonged, uninterrupted sedentariness was expressed as mean sedentary bout length.ResultsAfter adjustment for potential confounders and moderate to vigorous physical activity, longer sedentary bout duration was dose-dependently associated with increased homeostatic model assessment of insulin resistance (P for trend<0.001) and 2-hour glucose levels (P for trend=0.015). These associations were not independent of total sedentary time; however, a significant interaction between sedentary bout duration and total sedentary time was observed. Evaluation of the joint association of total sedentary time and sedentary bout duration showed that participants in the upper quartile for both sedentary characteristics (ie, high total sedentary time and high sedentary bout duration) had the highest levels of homeostatic model assessment of insulin resistance (P<0.001 versus low group for both sedentary characteristics) and 2-hour glucose (P=0.002 versus low group for both sedentary characteristics). High total sedentary time or high sedentary bout duration alone were not associated with differences in any glycemic biomarkers.ConclusionsAccruing sedentary time in prolonged, uninterrupted bouts may be deleteriously associated with biomarkers of glucose regulation.

Project description:BackgroundSedentary behavior is recognized as a distinct construct from lack of moderate-vigorous physical activity and is associated with deleterious health outcomes. Previous studies have primarily relied on self-reported data, whereas data on the relationship between objectively measured sedentary time and cardiometabolic biomarkers are sparse, especially among US Hispanics/Latinos.Methods and resultsWe examined associations of objectively measured sedentary time (via Actical accelerometers for 7 days) and multiple cardiometabolic biomarkers among 12 083 participants, aged 18 to 74 years, from the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). Hispanics/Latinos of diverse backgrounds (Central American, Cuban, Dominican, Mexican, Puerto Rican, and South American) were recruited from 4 US cities between 2008 and 2011. Sedentary time (<100 counts/min) was standardized to 16 hours/d of wear time. The mean sedentary time was 11.9 hours/d (74% of accelerometer wear time). After adjustment for moderate-vigorous physical activity and confounding variables, prolonged sedentary time was associated with decreased high-density lipoprotein cholesterol (P=0.04), and increased triglycerides, 2-hour glucose, fasting insulin, and homeostatic model assessment of insulin resistance (all P<0.0001). These associations were generally consistent across age, sex, Hispanic/Latino backgrounds, and physical activity levels. Even among individuals meeting physical activity guidelines, sedentary time was detrimentally associated with several cardiometabolic biomarkers (diastolic blood pressure, high-density lipoprotein cholesterol, fasting and 2-hour glucose, fasting insulin and homeostatic model assessment of insulin resistance; all P<0.05).ConclusionsOur large population-based, objectively derived data showed deleterious associations between sedentary time and cardiometabolic biomarkers, independent of physical activity, in US Hispanics/Latinos. Our findings emphasize the importance of reducing sedentary behavior for the prevention of cardiometabolic diseases, even in those who meet physical activity recommendations.

Project description:BackgroundPrevious diet findings in Hispanics/Latinos rarely reflect differences in commonly consumed and culturally relevant foods across heritage groups and by years lived in the United States.ObjectivesWe aimed to identify and compare a posteriori heritage-specific dietary patterns (DPs) and evaluate their associations with "healthfulness" [using the Alternative Healthy Eating Index-2010 (AHEI-2010)] and years living in the United States.MethodsWe used baseline data from a population-based cohort of 14,099 Hispanics/Latinos aged 18-74 y in the Hispanic Community Health Study/Study of Latinos. We performed principal factor analysis using two 24-h recalls to derive DPs, separately, in each heritage group (Cuban, Dominican, Mexican, Puerto Rican, Central American, and South American), and identified overarching DPs based on high-loading foods shared by ≥2 groups. We used multivariable linear regression to test associations of DPs with AHEI-2010 and years living in the United States.ResultsWe identified 5 overarching DPs (Burgers, Fries, & Soft Drinks; White Rice, Beans, & Red Meats; Fish; Egg & Cheese; and Alcohol). All Burgers, Fries, & Soft Drinks DPs were inversely associated with AHEI-2010, whereas all Fish DPs (except Dominican) were positively associated with this index (all P-trend < 0.001). White Rice, Beans, & Red Meats DPs showed inverse associations in Cuban and Central American groups and positive associations in Mexican-origin individuals (all P-trend < 0.001). Fewer years living in the United States was associated with higher scores for White Rice, Beans, & Red Meats DPs in Cuban and Mexican heritage groups and lower scores on Burgers, Fries, & Soft Drinks DPs in Cuban, Mexican, and Puerto Rican groups (all P-trend < 0.01).ConclusionsOur findings show substantial variation in DPs across Hispanics/Latinos and adherence to DPs by time in the United States, which could inform dietary interventions targeting this diverse US population. This trial was registered at clinicaltrials.gov as NCT02060344.

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Dataset Information

Improved imputation accuracy in Hispanic/Latino populations with larger and more diverse reference panels: applications in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL).

Publications

Improved imputation accuracy in Hispanic/Latino populations with larger and more diverse reference panels: applications in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL).

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