DNA methylation at the suppressor of cytokine signaling 3 (SOCS3) gene influences height in childhood

Human height is strongly influenced by genetics but the contribution of modifiable epigenetic factors is under-explored, particularly in low and middle-income countries (LMIC). We investigate links between blood DNA methylation and child height in four LMIC cohorts (n = 1927) and identify a robust association at three CpGs in the suppressor of cytokine signaling 3 (SOCS3) gene which replicates in a high-income country cohort (n = 879). SOCS3 methylation (SOCS3m)-height associations are independent of genetic effects. Mendelian randomization analysis confirms a causal effect of SOCS3m on height. In longitudinal analysis, SOCS3m explains a maximum 9.5% of height variance in mid-childhood while the variance explained by height polygenic risk score increases from birth to 21 years. Children's SOCS3m is associated with prenatal maternal folate and socio-economic status. In-vitro characterization confirms a regulatory effect of SOCS3m on gene expression. Our findings suggest epigenetic modifications may play an important role in driving child height in LMIC.

Model-assisted analyses of longitudinal, ordinal outcomes with absorbing states

Studies of critically ill, hospitalized patients often follow participants and characterize daily health status using an ordinal outcome variable. Statistically, longitudinal proportional odds models are a natural choice in these settings since such models can parsimoniously summarize differences across patient groups and over time. However, when one or more of the outcome states is absorbing, the proportional odds assumption for the follow-up time parameter will likely be violated, and more flexible longitudinal models are needed. Motivated by the VIOLET Study (Ginde et al), a parallel-arm, randomized clinical trial of Vitamin D 3 in critically ill patients, we discuss and contrast several treatment effect estimands based on time-dependent odds ratio parameters, and we detail contemporary modeling approaches. In VIOLET, the outcome is a four-level ordinal variable where the lowest "not alive" state is absorbing and the highest "at-home" state is nearly absorbing. We discuss flexible extensions of the proportional odds model for longitudinal data that can be used for either model-based inference, where the odds ratio estimator is taken directly from the model fit, or for model-assisted inferences, where heterogeneity across cumulative log odds dichotomizations is modeled and results are summarized to obtain an overall odds ratio estimator. We focus on direct estimation of cumulative probability model (CPM) parameters using likelihood-based analysis procedures that naturally handle absorbing states. We illustrate the modeling procedures, the relative precision of model-based and model-assisted estimators, and the possible differences in the values for which the estimators are consistent through simulations and analysis of the VIOLET Study data.

Babies of South Asian and European Ancestry Show Similar Associations With Genetic Risk Score for Birth Weight Despite the Smaller Size of South Asian Newborns

Size at birth is known to be influenced by various fetal and maternal factors, including genetic effects. South Asians have a high burden of low birth weight and cardiometabolic diseases, yet studies of common genetic variations underpinning these phenotypes are lacking. We generated independent, weighted fetal genetic scores (fGSs) and maternal genetic scores (mGSs) from 196 birth weight-associated variants identified in Europeans and conducted an association analysis with various fetal birth parameters and anthropometric and cardiometabolic traits measured at different follow-up stages (5-6-year intervals) from seven Indian and Bangladeshi cohorts of South Asian ancestry. The results from these cohorts were compared with South Asians in UK Biobank and the Exeter Family Study of Childhood Health, a European ancestry cohort. Birth weight increased by 50.7 g and 33.6 g per SD of fGS (P = 9.1 × 10-11) and mGS (P = 0.003), respectively, in South Asians. A relatively weaker mGS effect compared with Europeans indicates possible different intrauterine exposures between Europeans and South Asians. Birth weight was strongly associated with body size in both childhood and adolescence (P = 3 × 10-5 to 1.9 × 10-51); however, fGS was associated with body size in childhood only (P < 0.01) and with head circumference, fasting glucose, and triglycerides in adults (P < 0.01). The substantially smaller newborn size in South Asians with comparable fetal genetic effect to Europeans on birth weight suggests a significant role of factors related to fetal growth that were not captured by the present genetic scores. These factors may include different environmental exposures, maternal body size, health and nutritional status, etc. Persistent influence of genetic loci on size at birth and adult metabolic syndrome in our study supports a common genetic mechanism that partly explains associations between early development and later cardiometabolic health in various populations, despite marked differences in phenotypic and environmental factors in South Asians.

Design and analysis of two-phase studies with multivariate longitudinal data

Two-phase studies are crucial when outcome and covariate data are available in a first phase sample (e.g., a cohort study), but costs associated with retrospective ascertainment of a novel exposure limit the size of the second phase sample, in whom the exposure is collected. For longitudinal outcomes, one class of two-phase studies stratifies subjects based on an outcome vector summary (e.g., an average or a slope over time) and oversamples subjects in the extreme value strata while undersampling subjects in the medium value stratum. Based on the choice of the summary, two-phase studies for longitudinal data can increase efficiency of time-varying and/or time-fixed exposure parameter estimates. In this manuscript, we extend efficient, two-phase study designs to multivariate longitudinal continuous outcomes, and we detail two analysis approaches. The first approach is a multiple imputation analysis that combines complete data from subjects selected for phase two with the incomplete data from those not selected. The second approach is a conditional maximum likelihood analysis that is intended for applications where only data from subjects selected for phase two are available. Importantly, we show that both approaches can be applied to secondary analyses of previously conducted two-phase studies. We examine finite sample operating characteristics of the two approaches and use the Lung Health Study (Connett et al., 1993) to examine genetic associations with lung function decline over time. This article is protected by copyright. All rights reserved.

Characterizing multidimensional poverty in Migori County, Kenya and its association with depression

INTRODUCTION

Narrow, unidimensional measures of poverty often fail to measure true poverty and inadequately capture its drivers. Multidimensional indices of poverty more accurately capture the diversity of poverty. There is little research regarding the association between multidimensional poverty and depression.

METHODS

A cross-sectional survey was administered in five sub-locations in Migori County, Kenya. A total of 4,765 heads of household were surveyed. Multidimensional poverty indices were used to determine the association of poverty with depression using the Patient Health Questionnaire (PHQ-8) depression screening tool.

RESULTS

Across the geographic areas surveyed, the overall prevalence of household poverty (deprivation headcount) was 19.4%, ranging from a low of 13.6% in Central Kamagambo to a high of 24.6% in North Kamagambo. Overall multidimensional poverty index varied from 0.053 in Central Kamagambo to 0.098 in North Kamagambo. Of the 3,939 participants with depression data available, 481 (12.2%) met the criteria for depression based on a PHQ-8 depression score ≥10. Poverty showed a dose-response association with depression.

CONCLUSIONS

Multidimensional poverty indices can be used to accurately capture poverty in rural Kenya and to characterize differences in poverty across areas. There is a clear association between multidimensional poverty and depressive symptoms, including a dose effect with increasing poverty intensity. This supports the importance of multifaceted poverty policies and interventions to improve wellbeing and reduce depression.

Should We Implement Geographic or Patient-Reported Social Determinants of Health Measures In Cardiovascular Patients

Objectives

To compare patient-reported social determinants of health (SDOH) to the Brokamp Area Deprivation Index (ADI), and evaluate the association of patient-reported SDOH and ADI with mortality in patients with cardiovascular disease (CVD).

Design

Prospective cohort.

Setting

Academic medical center.

Participants

Adults with acute coronary syndrome (ACS) and/or acute exacerbation of heart failure (HF) hospitalized between 2011 and 2015.

Methods

Patient-reported SDOH included: income range, education, health insurance, and household size. ADI was calculated using census tract level variables of poverty, median income, high school completion, lack of health insurance, assisted income, and vacant housing.

Primary Outcome

All-cause mortality, up to 5 years follow-up.

Results

The sample was 60% male, 84% White, and 93% insured; mean patient-reported household income was $48,000 (SD $34,000). ADI components were significantly associated with corresponding patient-reported variables. In age, sex, and race adjusted Cox regression models, ADI was associated with mortality for ACS (HR 1.23, 95% CI 1.06, 1.42), but not HF (HR 1.09, 95% CI .99, 1.21). Mortality models for ACS improved with consideration of social determinants data (C-statistics: base demographic model=.612; ADI added=.644; patient-reported SDOH added=.675; both ADI and patient-reported SDOH added=.689). HF mortality models improved only slightly (C-statistics: .600, .602, .617, .620, respectively).

Conclusions

The Brokamp ADI is associated with mortality in hospitalized patients with CVD. In the absence of available patient-reported data, hospitals could implement the Brokamp ADI as an approximation for patient-reported data to enhance risk stratification of patients with CVD.

Do components of adult height predict body composition and cardiometabolic risk in a young adult South Asian Indian population? Findings from a hospital-based cohort study in Pune, India: Pune Children's Study

OBJECTIVES

We investigated whether the relationship between components of height and cardiovascular disease (CVD) risk may be explained by body composition. We also examined relationships between parental heights and offspring CVD risk.

DESIGN

A cohort study using cross-sectional data.

SETTING

A secondary care hospital setting in Pune, India.

PARTICIPANTS

We studied 357 young adults and their parents in the Pune Children's Study. Primary and secondary outcomes: we measured weight, total height, leg length, sitting height, plasma glucose, insulin and lipids, and blood pressure (BP). Total and regional lean and fat mass were measured by dual X-ray absorptiometry.

RESULTS

Leg length was inversely related, and sitting height was directly related to BMI. Total height and leg length were directly related to lean mass, while sitting height was directly related to both lean and fat mass. Leg length was inversely related to systolic BP and 120 min glucose, independent of lean and fat mass. Sitting height was directly related to systolic BP and triglycerides; these relationships were attenuated on adjustment for lean and fat mass. When examined simultaneously, greater leg length was protective and greater sitting height was associated with a more detrimental CVD risk profile.

CONCLUSIONS

Shorter adult leg length and greater sitting height are associated with a more adverse CVD risk factor profile. The mechanisms need further study, but our findings suggest a role for lean and fat mass.

The Association of Maternal Age With Fetal Growth and Newborn Measures: The Mumbai Maternal Nutrition Project (MMNP)

Background:

Young maternal age is associated with poorer birth outcomes, but the mechanisms are incompletely understood. Using data from a prospective cohort of pregnant women living in Mumbai slums, India, we tested whether lower maternal age was associated with adverse fetal growth.

Methods:

Fetal crown-rump length (CRL) was recorded at a median (interquartile range, IQR) of 10 weeks’ gestation (9-10 weeks). Head circumference (HC), biparietal diameter (BPD), femur length (FL), and abdominal circumference (AC) were recorded at 19 (19-20) and 29 (28-30) weeks. Newborns were measured at a median (IQR) of 2 days (1-3 days) from delivery. Gestation was assessed using prospectively collected menstrual period dates.

Results:

The sample comprised 1653 singleton fetuses without major congenital abnormalities, of whom 1360 had newborn measurements. Fetuses of younger mothers had smaller CRL (0.01 standard deviation [SD] per year of maternal age; 95% confidence interval CI: 0.00-0.02¹; P = .04), and smaller HC, FL, and AC at subsequent visits. Fetal growth of HC (0.04 cm; 95% CI: 0.02-0.05; P < .001), BPD (0.01 cm; 95% CI: 0.00-0.01; P = .009), FL (0.04 cm; 95% CI: 0.02-0.06; P < .001), and AC (0.01 cm; 95% CI: 0.00-0.01; P = .003) up to the third trimester increased with maternal age. Skinfolds, head, and mid-upper arm circumferences were smaller in newborns of younger mothers. Adjusting for maternal prepregnancy socioeconomic status, body mass index, height, and parity attenuated the associations between maternal age and newborn size but did not change those with fetal biometry.

Conclusion:

Fetuses of younger mothers were smaller from the first trimester onward and grew slower, independently of known confounding factors.

Comparing BMI with skinfolds to estimate age at adiposity rebound and its associations with cardio-metabolic risk markers in adolescence

Background

Body mass index (BMI) reaches a nadir in mid-childhood, known as the adiposity rebound (AR). Earlier AR is associated with a higher risk of cardio-vascular diseases in later life. Skinfolds, which are a more direct measure of adiposity, may give better insight into the relationship between childhood adiposity and later obesity and cardio-metabolic risk.

Objective

We aimed to assess whether AR corresponds to a rebound in skinfolds, and compare associations of BMI-derived AR and skinfold-derived AR with cardio-metabolic risk markers in adolescence.

Methods

We used penalised splines with random coefficients to estimate BMI and skinfold trajectories of 604 children from the Mysore Parthenon Birth Cohort. Age at AR was identified using differentiation of the BMI and skinfold growth curves between 2 and 10 years of age. At 13.5 years, we measured blood pressure, and glucose, insulin and lipid concentrations.

Results

BMI and skinfolds had different growth patterns. Boys reached BMI-derived AR earlier than skinfold-derived AR (estimated difference: 0.41 years; 95% CI:[0.23, 0.56]), whereas the opposite was observed in girls (estimated difference: −0.71 years; 95% CI:[−0.90, −0.54]). At 13.5 years, children with earlier BMI-derived AR had higher BMI (−0.58 SD per SD increase of AR; 95%CI:[−0.65, −0.52]), fat mass (−0.44; 95%CI:[−0.50, −0.37]), insulin resistance (HOMA-IR: −0.20; 95%CI:[−0.28, −0.12]) and systolic blood pressure (−0.20; 95%CI:[−0.28, −0.11]), and lower HDL-cholesterol (0.12; 95%CI:[0.04, 0.21]). The associations were independent of BMI at time of rebound, but were fully explained by fat mass at 13.5 years. Similar associations were found for skinfold-derived AR.

Conclusion

BMI-derived adiposity rebound predicts later cardio-metabolic risk markers similarly to that derived from skinfolds, a direct measure of adiposity.

Protocol for the EMPHASIS study; epigenetic mechanisms linking maternal pre-conceptional nutrition and children's health in India and Sub-Saharan Africa

Background

Animal studies have shown that nutritional exposures during pregnancy can modify epigenetic marks regulating fetal development and susceptibility to later disease, providing a plausible mechanism to explain the developmental origins of health and disease. Human observational studies have shown that maternal peri-conceptional diet predicts DNA methylation in offspring. However, a causal pathway from maternal diet, through changes in DNA methylation, to later health outcomes has yet to be established. The EMPHASIS study (Epigenetic Mechanisms linking Pre-conceptional nutrition and Health Assessed in India and Sub-Saharan Africa, ISRCTN14266771) will investigate epigenetically mediated links between peri-conceptional nutrition and health-related outcomes in children whose mothers participated in two randomized controlled trials of micronutrient supplementation before and during pregnancy.

Methods

The original trials were the Mumbai Maternal Nutrition Project (MMNP, ISRCTN62811278) in which Indian women were offered a daily snack made from micronutrient-rich foods or low-micronutrient foods (controls), and the Peri-conceptional Multiple Micronutrient Supplementation Trial (PMMST, ISRCTN13687662) in rural Gambia, in which women were offered a daily multiple micronutrient (UNIMMAP) tablet or placebo. In the EMPHASIS study, DNA methylation will be analysed in the children of these women (~1100 children aged 5–7 y in MMNP and 298 children aged 7–9 y in PMMST). Cohort-specific and cross-cohort effects will be explored. Differences in DNA methylation between allocation groups will be identified using the Illumina Infinium MethylationEPIC array, and by pyrosequencing top hits and selected candidate loci. Associations will be analysed between DNA methylation and health-related phenotypic outcomes, including size at birth, and children’s post-natal growth, body composition, skeletal development, cardio-metabolic risk markers (blood pressure, serum lipids, plasma glucose and insulin) and cognitive function. Pathways analysis will be used to test for enrichment of nutrition-sensitive loci in biological pathways. Causal mechanisms for nutrition-methylation-phenotype associations will be explored using Mendelian Randomization. Associations between methylation unrelated to supplementation and phenotypes will also be analysed.

Conclusion

The study will increase understanding of the epigenetic mechanisms underpinning the long-term impact of maternal nutrition on offspring health. It will potentially lead to better nutritional interventions for mothers preparing for pregnancy, and to identification of early life biomarkers of later disease risk.

Getting started with tables

Background

Tables are often overlooked by many readers of papers who tend to focus on the text. Good tables tell much of the story of a paper and give a richer insight into the details of the study participants and the main research findings. Being confident in reading tables and constructing clear tables are important skills for researchers to master.

Method

Common forms of tables were considered, along with the standard statistics used in them. Papers in the Archives of Public Health published during 2015 and 2016 were hand-searched for examples to illustrate the points being made. Presentation of graphs and figures were not considered as they are outside the scope of the paper.

Results

Basic statistical concepts are outlined to aid understanding of each of the tables presented. The first table in many papers gives an overview of the study population and its characteristics, usually giving numbers and percentages of the study population in different categories (e.g. by sex, educational attainment, smoking status) and summaries of measured characteristics (continuous variables) of the participants (e.g. age, height, body mass index). Tables giving the results of the analyses follow; these often include summaries of characteristics in different groups of participants, as well as relationships between the outcome under study and the exposure of interest. For continuous outcome data, results are often expressed as differences between means, or regression or correlation coefficients. Ratio/relative measures (e.g. relative risks, odds ratios) are usually used for binary outcome measures that take one of two values for each study participants (e.g. dead versus alive, obese versus non-obese). Tables come in many forms, but various standard types are described here.

Conclusion

Clear tables provide much of the important detail in a paper and researchers are encouraged to read and construct them with care.

Effect of a micronutrient-rich snack taken preconceptionally and throughout pregnancy on ultrasound measures of fetal growth: The Mumbai Maternal Nutrition Project (MMNP)

Improving micronutrient intakes of under‐nourished mothers in low‐ and middle‐income countries increases birth weight, but there is little data on the nature and timing during gestation of any effects on fetal growth. Ultrasound measures of fetal size were used to determine whether and when a food‐based supplement affected fetal growth. Non‐pregnant women living in Mumbai slums, India (N = 6,513), were randomly assigned to receive either a daily micronutrient‐rich snack containing green leafy vegetables, fruit, and milk (treatment) or a snack made from lower‐micronutrient vegetables (control) in addition to their usual diet from before pregnancy until delivery. From 2,291 pregnancies, the analysis sample comprised 1,677 fetuses (1,335 fetuses of women supplemented for ≥3 months before conception). First‐trimester (median: 10 weeks, interquartile range: 9–12 weeks) fetal crown‐rump length was measured. Fetal head circumference, biparietal diameter, femur length, and abdominal circumference were measured during the second (19, 19–20 weeks) and third trimesters (29, 28–30 weeks). The intervention had no effect on fetal size or growth at any stage of pregnancy. In the second trimester, there were interactions between parity and allocation group for biparietal diameter (p = .02) and femur length (p = .04) with both being smaller among fetuses of primiparous women and larger among those of multiparous women, in the treatment group compared with the controls. Overall, a micronutrient‐rich supplement did not increase standard ultrasound measures of fetal size and growth at any stage of pregnancy. Additional ultrasound measures of fetal soft tissues (fat and muscle) may be informative.