Associations between fasting glucose rate-of-change and the missense variant, rs373863828, in an adult Samoan cohort.

BACKGROUND: The A allele of rs373863828 in CREB3 regulatory factor is associated with high Body Mass Index, but lower odds of type 2 diabetes. These associations have been replicated elsewhere, but to date all studies have been cross-sectional. Our aims were (1) to describe the development of type 2 diabetes and change in fasting glucose between 2010 and 2018 among a longitudinal cohort of adult Samoans without type 2 diabetes or who were not using diabetes medications at baseline, and (2) to examine associations between fasting glucose rate-of-change (mmol/L per year) and the A allele of rs373863828. METHODS: We describe and test differences in fasting glucose, the development of type 2 diabetes, body mass index, age, smoking status, physical activity, urbanicity of residence, and household asset scores between 2010 and 2018 among a cohort of n = 401 adult Samoans, selected to have a ~2:2:1 ratio of GG:AG: AA rs373863828 genotypes. Multivariate linear regression was used to test whether fasting glucose rate-of-change was associated with rs373863828 genotype, and other baseline variables. RESULTS: By 2018, fasting glucose and BMI significantly increased among all genotype groups, and a substantial portion of the sample developed type 2 diabetes mellitus. The A allele was associated with a lower fasting glucose rate-of-change (ß = -0.05 mmol/L/year per allele, p = 0.058 among women; ß = -0.004 mmol/L/year per allele, p = 0.863 among men), after accounting for baseline variables. Mean fasting glucose and mean BMI increased over an eight-year period and a substantial number of individuals developed type 2 diabetes by 2018. However, fasting glucose rate-of-change, and type 2 diabetes development was lower among females with AG and AA genotypes. CONCLUSIONS: Further research is needed to understand the effect of the A allele on fasting glucose and type 2 diabetes development. Based on our observations that other risk factors increased over time, we advocate for the continued promotion for diabetes prevention and treatment programming, and the reduction of modifiable risk factors, in this setting.

Noncommunicable disease risk behaviors and protective factors among children in Samoa: Retrospective trend analysis of global school-based health surveys in 2011 and 2017.

Pacific Island countries experience a high prevalence of noncommunicable diseases (NCDs), which may be prevented by reducing risk behaviors and strengthening protective factors in childhood and adolescence. To better inform preventative interventions, our objective was to use publicly available data from the Global School-based Student Health Survey (GSHS), to provide cross-sectional and trend estimates for the prevalence of NCD risk and protective factors among school-aged children in 2011 and 2017 in Samoa. Two waves of cross-sectional data included 4,373 children (51.98% female), with a median age of 15 years, who were mainly in school years 9-10 in Samoa. Retrospective analyses were adjusted for the GSHS multistage stratified cluster sample design. Weighted prevalences of overweight/obesity, dietary behaviors, physical activity, and sedentary behavior, oral and hand hygiene, emotional and mental health, and community protective factors were reported by study year. Logistic regressions were fitted to assess differences in the prevalence of risk and protective factors, adjusted for age group, sex, and school year. In 2011 and 2017, the prevalence of overweight/obesity remained consistently high in females (59.12% and 64.29%, p = 0.428) and increased from 44.21% to 53.65% in males (p = 0.039). Time spent sitting for long periods, smoking cigarettes, using other tobacco products, and drinking alcohol were lower in 2017 compared to 2011 (all p<0.05). Many children reported experiencing bullying (33.27% for females and 59.30% for males in 2017), while physical fighting was common among males (73.72% in 2011 and 57.28% in 2017). The high prevalence of obesity and related NCD risk factors require urgent public health action in Samoa. Alongside the continued reduction of tobacco and alcohol use, emotional and mental wellness should be prioritized in interventions and programs to promote healthy behaviors and lifestyle changes starting in childhood.

Validation of human telomere length multi-ancestry meta-analysis association signals identifies POP5 and KBTBD6 as human telomere length regulation genes.

Genome-wide association studies (GWAS) have become well-powered to detect loci associated with telomere length. However, no prior work has validated genes nominated by GWAS to examine their role in telomere length regulation. We conducted a multi-ancestry meta-analysis of 211,369 individuals and identified five novel association signals. Enrichment analyses of chromatin state and cell-type heritability suggested that blood/immune cells are the most relevant cell type to examine telomere length association signals. We validated specific GWAS associations by overexpressing KBTBD6 or POP5 and demonstrated that both lengthened telomeres. CRISPR/Cas9 deletion of the predicted causal regions in K562 blood cells reduced expression of these genes, demonstrating that these loci are related to transcriptional regulation of KBTBD6 and POP5. Our results demonstrate the utility of telomere length GWAS in the identification of telomere length regulation mechanisms and validate KBTBD6 and POP5 as genes affecting telomere length regulation.

Accelerometer-Based Estimates of Physical Activity and Sedentary Time Among Samoan Adults.

BACKGROUND: The prevalence of obesity-related cardiometabolic disease in Samoa is among the highest globally. While physical activity is a modifiable risk factor for obesity-related disease, little is known about physical activity levels among adult Samoans. Using wrist-worn accelerometer-based devices, this study aimed to characterize physical activity among Samoan adults. METHODS: Samoan adults (n = 385; 55% female, mean [SD] age 52 [10] y) wore Actigraph GT3X+ devices for 7 to 10 days. General linear models were used to examine mean daily minutes of sedentary time, light physical activity, and moderate to vigorous physical activity by various participant characteristics. RESULTS: Time spent in moderate to vigorous physical activity did not differ statistically between men (88 [5] min; 95% confidence interval [CI], 80-97) and women (78 [4] min; 95% CI, 70-86; P = .08). Women, however, spent more time than men in light physical activity: 380 (7) minutes (95% CI, 367-393) versus 344 (7) minutes (95% CI, 329-358; P < .001). While there were no differences in physical activity by census region, education, or occupation among women, men in urban areas spent significantly less time in moderate to vigorous physical activity than those in peri-urban and rural areas (P = .015). Women with class II/III obesity spent more time in sedentary activities than those with healthy weight or overweight/class I obesity (P = .048). CONCLUSIONS: This study characterizes physical activity among Samoan adults and highlights variation by sex, urbanicity, and weight status. In providing initial device-measured estimates of physical activity in Samoa, this analysis establishes a baseline from which the success of future attempts to intervene on physical activity may be assessed.

Child, family and household characteristics associated with physical activity in Samoan children aged 3-8 years: A cross-sectional study.

Physical activity is a key component of many obesity prevention strategies. The aim of this analysis was to identify child, family, and household characteristics associated with parent-reported physical activity in Samoan children aged 3-8 years. Children (n = 445; 51.2% female, mean age 5.4 years) were part of an ongoing, mixed-longitudinal study of child growth, development, and wellbeing (the Ola Tuputupua'e cohort). Bivariate analyses and multivariate generalized linear regressions were conducted to investigate the relationship of child, family, and household characteristics with physical activity level, measured using the Netherlands Physical Activity Questionnaire (NPAQ). Children were classified as being 'highly active' if they had NPAQ scores in the 75th percentile or above. Among the n = 111 children classified as 'highly active', n = 67 (60.4%) were boys. After adjusting for child, family, and household-level characteristics, hours of child sleep per night was the only variable significantly associated with odds of being highly active. Compared to children who slept less than 9 hours at night, those who slept 10-10.99 hours (OR: 5.97, 95% CI: 2.14-18.13) and 11+ hours (OR: 25.75, 95% CI: 8.14-90.12) had higher odds of being 'highly active'. Future research should examine the mechanisms driving the relationship between nighttime sleep and physical activity among Samoan children. Intervening on sleep duration and quality may improve physical activity and, in turn, obesity risk in this setting.

Associations of childhood BMI traits with blood pressure and glycated haemoglobin in 6-9-year-old Samoan children.

INTRODUCTION: Prevalence and risk factors for elevated glycated haemoglobin (HbA1c) and blood pressure (BP) are poorly understood among Pacific children. We examined associations of HbA1c and BP in 6-9 year-olds with body mass index (BMI) at ages 2, 5, and BMI velocity between 2-9 years in Samoa. METHODS: HbA1c (capillary blood) and BP were measured in n = 410 Samoan children who were part of an ongoing cohort study. Multilevel models predicted BMI trajectory characteristics. Generalized linear regressions assessed associations of childhood characteristics and BMI trajectories with HbA1c and BP treated as both continuous and categorical outcomes. Primary caregiver-reported childhood characteristics were used as covariates. RESULTS: Overall, 12.90% (n = 53) of children had high HbA1c (≥5.7%) and 33.17% (n = 136) had elevated BP. BMI at 5-years and BMI velocity were positively associated with high HbA1c prevalence in males. A 1 kg/m2 per year higher velocity was associated with a 1.71 (95% CI: 1.07, 2.75) times higher prevalence of high HbA1c. In females, higher BMI at 5-years and greater BMI velocity were associated with higher BP at 6-9 years (95% CI: 1.12, 1.40, and 1.42, 2.74, respectively). CONCLUSION: Monitoring childhood BMI trajectories may inform cardiometabolic disease screening and prevention efforts in this at-risk population.

Indication of mixed glucose and fatty acid use by inferred brown adipose tissue activity in Samoans.

OBJECTIVES: Despite the growing rates of global obesity and the known positive associations between brown adipose tissue (BAT) and cardiovascular health, little is known about the metabolic effects of BAT activity in Samoans, a population at high risk of obesity and type II diabetes. Here we assessed the potential effects of inferred BAT activity on metabolic health markers in Samoan adults exposed to mild cold. METHODS: Using point-of-care finger prick technology we measured fasting glucose, total cholesterol, high-density lipoprotein (HDL), and low-density lipoprotein (LDL) levels before and after 30 min of cold exposure among 61 individuals (38 females, 23 males, ages 31-54) from 'Upolu Island, Samoa. Respiratory quotient was measured by indirect calorimetry to determine substrate metabolism at room temperature and cold exposure. RESULTS: Fasting glucose levels decreased significantly (p < .001) after cold exposure while neither total cholesterol (p = .88), HDL (p = .312), nor LDL (p = .089) changed. Respiratory quotient decreased significantly (p = .009) between exposures, suggesting an increased preference for lipid metabolism as a response to cold. CONCLUSIONS: The observed effects of inferred BAT activity on biomarkers suggest BAT activity utilizes both glucose and lipid-derived fatty acids as fuel for thermogenesis. Our work provides evidence for the beneficial metabolic effects of BAT and emphasizes the need for the population-specific development of metabolic treatments involving BAT to ensure the successful and equitable minimization of extreme consequences of obesity and metabolic health.

When the cold gets under your skin: Evidence for brown adipose tissue activity in Samoan adults.

OBJECTIVES: Brown adipose tissue (BAT) is a heat-producing organ aiding nonshivering thermogenesis (NST) during cold stress. Due to its potential cold-adaptive role BAT has been predominantly studied in cold and temperate climate populations, but not among warm-climate adults. This work explores if BAT activity can be inferred in Samoans. MATERIALS AND METHODS: We inferred BAT activity by comparing metabolic rate and surface heat dissipation using indirect calorimetry and thermal imaging between room temperature and cold exposure among Samoans (N = 61, females: n = 38) from 'Upolu Island, Samoa. BAT activity was inferred using ANOVA linear regression models with the variables measured at cold exposure as outcomes. T-tests were used to compare changes in surface temperature between room temperature and cold exposure. RESULTS: Metabolic rate significantly increased after cooling. In both the supraclavicular area, a known BAT location, and the sternum, a non-BAT location, temperatures decreased significantly upon cold exposure. Differences in supraclavicular temperatures between room temperature and cold were significantly smaller than differences in sternum temperatures between exposures. These results suggest that BAT thermogenesis occurred in known BAT-locations and thus contributed to NST during cooling. CONCLUSIONS: This study adds to our understanding of BAT activity across different populations and climates. Further study may illuminate whether the cold-adaptive properties of BAT may have played a role in the successful expansion of populations across the globe, including warm-climate groups.

Association between age at menarche and cardiometabolic risk among Samoan adults.

OBJECTIVES: Recent studies suggest that early menarche may increase cardiometabolic morbidity and mortality. Yet few studies have examined this association in the Pacific Islands, where obesity prevalence is among the highest globally. We sought to examine associations between age at menarche and cardiometabolic risk in Samoa. METHODS: Participants were from the Soifua Manuia study (n = 285, age 32-72 years) conducted in Samoa from 2017 to 2019. Logistic regressions were conducted to estimate odds of obesity, hypertension, diabetes, dyslipidemia, and metabolic syndrome per one-year increase in age at menarche. Linear regressions were conducted to examine associations between age at menarche and continuous measures of adiposity, blood pressure, insulin resistance, and serum lipids. RESULTS: Median age at menarche was 14 years (IQR = 2). After controlling for relevant covariates, each one-year increase in age at menarche was associated with a 15% decrease (OR = 0.85, 95% CI: 0.72-1.01, p = .067) in odds of hypertension, but a 21% increase (OR = 1.21, 95% CI: 1.01-1.45, p = .044) in odds of diabetes and 18% increase (OR = 1.18, 95% CI: 0.98-1.42, p = .081) in odds of high total cholesterol. Each additional year in age at menarche was associated with a 1.60 ± 0.52 kg (p = .002) decrease in lean mass and 1.56 ± 0.51 kg (p = .003) decrease in fat-free mass. CONCLUSIONS: Associations between age at menarche and cardiometabolic risk may be population-specific and are likely influenced by both current and historical nutritional and epidemiological contexts. Prospective studies are needed to clarify the role of childhood adiposity and other early life exposures on age at menarche and subsequent cardiometabolic risk.

Improving imputation quality in Samoans through the integration of population-specific sequences into existing reference panels.

Genotype imputation is fundamental to association studies, and yet even gold standard panels like TOPMed are limited in the populations for which they yield good imputation. Specifically, Pacific Islanders are poorly represented in extant panels. To address this, we constructed an imputation reference panel using 1,285 Samoan individuals with whole-genome sequencing, combined with 1000 Genomes (1000G) samples, to create a reference panel that better represents Pacific Islander, specifically Samoan, genetic variation. We compared this panel to 1000G and TOPMed panels based on imputed variants using genotyping array data for 1,834 Samoan participants who were not part of the panels. The 1000G + 1285 Samoan panel yielded up to 2.25-2.76 times more well-imputed (r 2 ≥ 0.80) variants than TOPMed and 1000G. There was improved imputation accuracy across the minor allele frequency (MAF) spectrum, although it was more pronounced for variants with 0.01 ≤ MAF ≤ 0.05. Imputation accuracy (r 2 ) was greater for population-specific variants (high fixation index, F ST ) and those from larger haplotypes (high LD score). The gain in imputation accuracy over TOPMed was largest for small haplotypes (low LD score), reflecting the Samoan panel's ability to capture population-specific variation not well tagged by other panels. We also augmented the 1000G reference panel with varying numbers of Samoan samples and found that panels with 48 or more Samoans included outperformed TOPMed for all variants with MAF ≥ 0.001. This study identifies variants with improved imputation using population-specific reference panels and provides a framework for constructing other population-specific reference panels.

Characterization of sleep apnea among a sample of adults from Samoa.

Sleep apnea is a public health concern around the world, but little research has been dedicated to examining this issue in low- and middle-income countries, including Samoa. Using data collected through the Soifua Manuia ("Good Health") study, which aimed to investigate the impact of the body mass index (BMI)-associated genetic variant rs373863828 in CREB3 Regulatory Factor ( CREBRF ) on metabolic traits in Samoan adults, we examined the sample prevalence and characteristics of sleep apnea using data collected with a validated home sleep apnea device (WatchPAT, Itamar). A total of 330 participants (sampled to overrepresent the obesity-risk allele of interest) had sleep data available. Participants (53.3% female) had a mean (SD) age of 52.0 (9.9) years and BMI of 35.5 (7.5) kg/m 2 and 36.3% of the sample had type 2 diabetes. Based on the 3% and 4% apnea hypopnea indices (AHI) and the 4% oxygen desaturation index (ODI), descriptive analyses revealed that many participants had potentially actionable sleep apnea defined as >5 events/hr (87.9%, 68.5%, and 71.2%, respectively) or clinically actionable sleep apnea defined as ≥15 events/hr (54.9%, 31.5%, and 34.5%, respectively). Sleep apnea was more severe in men; for example, clinically actionable sleep apnea (≥15) based on the AHI 3% definition was observed in 61.7% of men and 48.9% of women. Correction for non-representational sampling related to the CREBRF obesity-risk allele resulted in only slightly lower estimates. Across the AHI 3%, AHI 4%, and ODI 4%, multiple linear regression revealed associations between a greater number of events/hr and higher age, male sex, higher body mass index, higher abdominal-hip circumference ratio, and geographic region of residence. Our study identified a much higher frequency of sleep apnea in Samoa compared with published data from other studies, but similar predictors. Continued research addressing generalizability of these findings, as well as a specific focus on diagnosis and affordable and equitable access to treatment, is needed to alleviate the burden of sleep apnea in Samoa and around the world.

Scabies prevalence after ivermectin-based mass drug administration for lymphatic filariasis, Samoa 2018-2019.

BACKGROUND: Scabies is a common skin infestation caused by the Sarcoptes scabei mite. Ivermectin, one of three drugs used in mass drug administration (MDA) for lymphatic filariasis, is also effective for treating scabies. Ivermectin-based MDA was first conducted in Samoa in August 2018, with ivermectin being offered to those aged ≥5 years. Here, we report scabies prevalence in Samoa after MDA. METHODS: We conducted household surveys 1.5-3.5 months (Survey 1) and 6-8 months (Survey 2) after the 2018 MDA in 35 primary sampling units. We conducted clinical examination for scabies-like rash and used International Alliance for the Control of Scabies classification criteria. We estimated scabies prevalence by age, gender and region. Multivariable logistic regression was used to assess factors associated with prevalence. RESULTS: We surveyed 2868 people (499 households) and 2796 people (544 households) aged 0-75 years in Surveys 1 and 2, respectively. Scabies prevalence increased from 2.4% (95% CI 2.1-2.7%) to 4.4% (95% CI 4.0-4.9%) between surveys. Scabies was associated with younger age (0-4 years: aOR 3.5 [2.9-4.2]; 5-15 years: aOR 1.6 [1.4-1.8] compared to ≥16 years), female gender (aOR 1.2 [95% CI 1.1-1.4]; region (aOR range from 1.4 [1.1-1.7] to 2.5 [2.1-3.1] between regions), large households (aOR 2.6 [2.0-3.4] households ≥13), and not taking MDA in 2018 (aOR 1.3 [95% CI 1.1-1.6]). CONCLUSIONS: We found moderate prevalence of scabies in two population-representative surveys conducted within 8 months of the 2018 MDA for lymphatic filariasis. Prevalence appeared to increase between the surveys, and ongoing surveillance is recommended, particularly in young children.

A Polynesian-specific missense CETP variant alters the lipid profile.

Identifying population-specific genetic variants associated with disease and disease-predisposing traits is important to provide insights into the genetic determinants of health and disease between populations, as well as furthering genomic justice. Various common pan-population polymorphisms at CETP associate with serum lipid profiles and cardiovascular disease. Here, sequencing of CETP identified a missense variant rs1597000001 (p.Pro177Leu) specific to Maori and Pacific people that associates with higher HDL-C and lower LDL-C levels. Each copy of the minor allele associated with higher HDL-C by 0.236 mmol/L and lower LDL-C by 0.133 mmol/L. The rs1597000001 effect on HDL-C is comparable with CETP Mendelian loss-of-function mutations that result in CETP deficiency, consistent with our data, which shows that rs1597000001 lowers CETP activity by 27.9%. This study highlights the potential of population-specific genetic analyses for improving equity in genomics and health outcomes for population groups underrepresented in genomic studies.

Prevalence of malnutrition among Samoan children aged 5 to 11 years in 2019-2020.

BACKGROUND: Globally, rapid economic development, urbanisation, and nutrition transitions have led to rising levels of malnutrition in all forms. AIM: The study objective was to document the prevalence of overweight/obesity, underweight, stunting, and anaemia among Samoan children in 2019-2020. SUBJECTS AND METHODS: Children from the Ola Tuputupua'e "Growing Up" in Samoa study at ages 5-11 years with complete physical assessments were included. Overweight/obesity, underweight, and stunting were classified using World Health Organisation Z-scores for body mass index-for-age (BMIZ> +1), weight-for-age (WAZ< -2SD), and height-for-age (HAZ< -2SD), respectively. Anaemia was defined as haemoglobin concentration <11.5 g/dL. Prevalence was compared by child age, sex, and census region of residence (representing urbanicity and exposure to nutrition transition) using Wilcoxon two-sample, Chi-square, or Fisher's exact tests. RESULTS: The prevalence of overweight/obesity, underweight, stunting, and anaemia was 36.2%, 0.5%, 1.6%, and 31.6%, respectively. Overweight/obesity in children was positively associated with age and highly prevalent in periurban and urban regions. While children living in the rural region with the lowest exposure to nutrition transition had the highest prevalence of mild-to-moderate stunting, anaemia prevalence was lower compared to those in the urban region. No sex differences in malnutrition were observed. CONCLUSION: Moderate-to-high levels of overweight/obesity and anaemia call for comprehensive intervention strategies.

Association of rs9939609 in FTO with BMI among Polynesian peoples living in Aotearoa New Zealand and other Pacific nations.

The fat mass and obesity associated (FTO) locus consistently associates with higher body mass index (BMI) across diverse ancestral groups. However, previous small studies of people of Polynesian ancestries have failed to replicate the association. In this study, we used Bayesian meta-analysis to test rs9939609, the most replicated FTO variant, for association with BMI with a large sample (n = 6095) of Aotearoa New Zealanders of Polynesian (Maori and Pacific) ancestry and of Samoan people living in the Independent State of Samoa and in American Samoa. We did not observe statistically significant association within each separate Polynesian subgroup. Bayesian meta-analysis of the Aotearoa New Zealand Polynesian and Samoan samples resulted in a posterior mean effect size estimate of +0.21 kg/m2, with a 95% credible interval [+0.03 kg/m2, +0.39 kg/m2]. While the Bayes Factor (BF) of 0.77 weakly favors the null, the BF = 1.4 Bayesian support interval is [+0.04, +0.20]. These results suggest that rs9939609 in FTO may have a similar effect on mean BMI in people of Polynesian ancestries as previously observed in other ancestral groups.

Cross-sectional and prospective associations between household socioeconomic resources, appetite traits, and body size among Samoan infants.

In high-income countries, household socioeconomic resources (as measured by education, occupation, income, and/or household assets) and childhood obesity risk tend to be negatively associated. This association may arise in part because children from households with fewer resources are exposed to obesogenic environments that shape appetite trait development. In contrast, many low- and middle-income countries (LMICs) exhibit a positive association between socioeconomic resources and child body size. There is less evidence from LMIC settings about when during development this association emerges and whether appetite traits play a mediatory role. To explore these questions, we examined cross-sectional and longitudinal associations between socioeconomic resources, appetite traits, and body size among infants in Samoa, an LMIC in Oceania. Data were from the Foafoaga O le Ola prospective birth cohort of 160 mother-infant dyads. Appetite traits were characterized using the Baby and Child Eating Behavior Questionnaires and household socioeconomic resources were quantified using an asset-based measure. While infant body size and household socioeconomic resources were positively associated in both cross-sectional and prospective analyses, we found no evidence that appetite traits mediate this relationship. These results suggest that other aspects of the food environment, such as food security and feeding style, may explain the positive association between socioeconomic resources and body size observed in many LMICs.

Structural variation across 138,134 samples in the TOPMed consortium.

Ever larger Structural Variant (SV) catalogs highlighting the diversity within and between populations help researchers better understand the links between SVs and disease. The identification of SVs from DNA sequence data is non-trivial and requires a balance between comprehensiveness and precision. Here we present a catalog of 355,667 SVs (59.34% novel) across autosomes and the X chromosome (50bp+) from 138,134 individuals in the diverse TOPMed consortium. We describe our methodologies for SV inference resulting in high variant quality and >90% allele concordance compared to long-read de-novo assemblies of well-characterized control samples. We demonstrate utility through significant associations between SVs and important various cardio-metabolic and hemotologic traits. We have identified 690 SV hotspots and deserts and those that potentially impact the regulation of medically relevant genes. This catalog characterizes SVs across multiple populations and will serve as a valuable tool to understand the impact of SV on disease development and progression.

Structural variation across 138,134 samples in the TOPMed consortium.

Ever larger Structural Variant (SV) catalogs highlighting the diversity within and between populations help researchers better understand the links between SVs and disease. The identification of SVs from DNA sequence data is non-trivial and requires a balance between comprehensiveness and precision. Here we present a catalog of 355,667 SVs (59.34% novel) across autosomes and the X chromosome (50bp+) from 138,134 individuals in the diverse TOPMed consortium. We describe our methodologies for SV inference resulting in high variant quality and >90% allele concordance compared to long-read de-novo assemblies of well-characterized control samples. We demonstrate utility through significant associations between SVs and important various cardio-metabolic and hematologic traits. We have identified 690 SV hotspots and deserts and those that potentially impact the regulation of medically relevant genes. This catalog characterizes SVs across multiple populations and will serve as a valuable tool to understand the impact of SV on disease development and progression.

Compound heterozygous splicing variants expand the genotypic spectrum of EMC1-related disorders.

EMC1 encodes subunit 1 of the endoplasmic reticulum (ER) membrane protein complex (EMC), a transmembrane domain insertase involved in membrane protein biosynthesis. Variants in EMC1 are described as a cause of global developmental delay, hypotonia, cortical visual impairment, and commonly, cerebral atrophy on MRI scan. We report an individual with severe global developmental delay and progressive cerebellar atrophy in whom exome sequencing identified a heterozygous essential splice-site variant in intron-3 of EMC1 (NM_015047.3:c.287-1G>A). Whole genome sequencing (WGS) identified a deep intronic variant in intron-20 of EMC1 (NM_015047.3:c.2588-771C>G) that was poorly predicted by in silico programs to disrupt pre-mRNA splicing. Reverse Transcription-PCR (RT-PCR) revealed stochastic activation of a pseudo-exon associated with the c.2588-771C>G variant and mis-splicing arising from the c.287-1G>A variant. This case highlights the utility of WGS and RNA studies to identify and assess likely pathogenicity of deep intronic variants and expands the genotypic and phenotypic spectrum of EMC1-related disorders.

Prediction of fat mass from anthropometry at ages 7 to 9 years in Samoans: a cross-sectional study in the Ola Tuputupua'e cohort.

BACKGROUND/OBJECTIVE: With increasing obesity prevalence in children globally, accurate and practical methods for quantifying body fat are critical for effective monitoring and prevention, particularly in high-risk settings. No population is at higher risk of obesity than Pacific Islanders, including children living in the independent nation of Samoa. We developed and validated sex-specific prediction models for fat mass in Samoan children. SUBJECTS/METHODS: Dual X-ray absorptiometry (DXA) assessments of fat mass and weight, height, circumferences, and skinfolds were obtained from 356 children aged 7-9 years old in the Ola Tuputupua'e "Growing Up" study. Sex-specific models were developed from a randomly selected model development sample (n = 118 females, n = 120 males) using generalized linear regressions. In a validation sample (n = 59 females; n = 59 males), Lin's concordance and Bland-Altman limits-of-agreement (LoA) of DXA-derived and predicted fat mass from this study and other published models were examined to assess precision and accuracy. RESULTS: Models to predict fat mass in kilograms were: e^[(-0.0034355 * Age8 - 0.0059041 * Age9 + 1.660441 * ln (Weight (kg))-0.0087281 * Height (cm) + 0.1393258 * ln[Suprailiac (mm)] - 2.661793)] for females and e^[-0.0409724 * Age8 - 0.0549923 * Age9 + 336.8575 * [Weight (kg)]-2 - 22.34261 * ln (Weight (kg)) [Weight (kg)]-1 + 0.0108696 * Abdominal (cm) + 6.811015 * Subscapular (mm)-2 - 8.642559 * ln (Subscapular (mm)) Subscapular (mm)-2 - 1.663095 * Tricep (mm)-1 + 3.849035]for males, where Age8 = Age9 = 0 for children at age 7 years, Age8 = 1 and Age9 = 0 at 8 years, Age8 = 0 and Age9 = 1 at 9 years. Models showed high predictive ability, with substantial concordance (ρC > 0.96), and agreement between DXA-derived and model-predicted fat mass (LoA female = -0.235, 95% CI:-2.924-2.453; male = -0.202, 95% CI:-1.977-1.572). Only one of four existing models, developed in a non-Samoan sample, accurately predicted fat mass among Samoan children. CONCLUSIONS: We developed models that predicted fat mass in Samoans aged 7-9 years old with greater precision and accuracy than the majority of existing models that were tested. Monitoring adiposity in children with these models may inform future obesity prevention and interventions.