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Updated: Mar 6, 2026

Sample Preparation to Bioinformatics Analysis of DNA Methylation: Association Strategy for Obesity and Related Trait Studies
Published on: May 6, 2022
Developmental pathways to adiposity begin before birth and are influenced by genotype, prenatal environment and
Xinyi Lin1, Ives Yubin Lim1,2, Yonghui Wu1
1Singapore Institute for Clinical Sciences, A*STAR, 30 Medical Drive, Singapore, 117609, Singapore.
Insights
Prenatal environment, genetics, and epigenetics influence childhood obesity risk. These factors impact birth weight and adiposity, offering insights for early obesity prevention strategies.
Area of Science:
- Developmental Biology
- Epigenetics
- Public Health
Background:
- Obesity is a global health concern with origins potentially rooted in the intrauterine environment.
- Suboptimal prenatal conditions may program fetal metabolism, increasing later-life obesity risk.
- The interplay between early exposures, genetics, and epigenetics in metabolic health is not fully understood.
Purpose of the Study:
- To comprehensively analyze the effects of prenatal environment, neonatal epigenetics (DNA methylation), and genotype on birth weight and childhood adiposity.
- To investigate the developmental origins of obesity by examining factors from gestation to early childhood.
Main Methods:
- Prospective mother-offspring cohort study (N=987) from birth to 48 months.
- Interrogation of 30 prenatal environmental variables, umbilical cord DNA methylation, and offspring genotype.
- Analysis of birth weight and adiposity, including longitudinal assessments.
Main Results:
- Eleven prenatal factors (maternal adiposity, smoking, glucose, fatty acids) linked to birth weight.
- Polygenic risk scores for adult adiposity also predicted birth weight and child adiposity.
- Seven neonatal methylation markers associated with birth weight; some linked to prenatal environment and metabolic pathways.
- Six methylation loci showed longitudinal associations with offspring size and adiposity.
Conclusions:
- Developmental pathways to adiposity commence before birth, influenced by environmental, genetic, and epigenetic factors.
- These early influences have lasting effects on offspring size, adiposity, and future metabolic health.
- Findings offer potential for early risk stratification and obesity prevention.
Background:
Obesity is an escalating health problem worldwide, and hence the causes underlying its development are of primary importance to public health. There is growing evidence that suboptimal intrauterine environment can perturb the metabolic programing of the growing fetus, thereby increasing the risk of developing obesity in later life. However, the link between early exposures in the womb, genetic susceptibility, and perturbed epigenome on metabolic health is not well understood. In this study, we shed more light on this aspect by performing a comprehensive analysis on the effects of variation in prenatal environment, neonatal methylome, and genotype on birth weight and adiposity in early childhood.
Methods:
In a prospective mother-offspring cohort (N = 987), we interrogated the effects of 30 variables that influence the prenatal environment, umbilical cord DNA methylation, and genotype on offspring weight and adiposity, over the period from birth to 48 months. This is an interim analysis on an ongoing cohort study.
Results:
Eleven of 30 prenatal environments, including maternal adiposity, smoking, blood glucose and plasma unsaturated fatty acid levels, were associated with birth weight. Polygenic risk scores derived from genetic association studies on adult adiposity were also associated with birth weight and child adiposity, indicating an overlap between the genetic pathways influencing metabolic health in early and later life. Neonatal methylation markers from seven gene loci (ANK3, CDKN2B, CACNA1G, IGDCC4, P4HA3, ZNF423 and MIRLET7BHG) were significantly associated with birth weight, with a subset of these in genes previously implicated in metabolic pathways in humans and in animal models. Methylation levels at three of seven birth weight-linked loci showed significant association with prenatal environment, but none were affected by polygenic risk score. Six of these birth weight-linked loci continued to show a longitudinal association with offspring size and/or adiposity in early childhood.
Conclusions:
This study provides further evidence that developmental pathways to adiposity begin before birth and are influenced by environmental, genetic and epigenetic factors. These pathways can have a lasting effect on offspring size, adiposity and future metabolic outcomes, and offer new opportunities for risk stratification and prevention of obesity.
Clinical Trial Registration:
This birth cohort is a prospective observational study, designed to study the developmental origins of health and disease, and was retrospectively registered on 1 July 2010 under the identifier NCT01174875 .
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