Risk Factors for Neural-Tube Defects Detected in Utero: A Prospective Community-Based Study from Addis Ababa.

BACKGROUND: A recent community-based study from Addis Ababa identifying Neural Tube Defect (NTD) cases by ultrasound examination of pregnant women showed a higher prevalence of 17 per 1000 fetuses. The risk factors behind the high prevalence remain unclear. METHODS: Altogether 891 of the 958 women participated in the ultrasound examination. Thirteen with unaffected twin pregnancies were excluded. Among 878 singleton pregnancies, 15 NTD cases were identified. Serum Folate, vitamin B12, and homocysteine levels were measured in case-mothers and a sub-set of 28 noncase mothers. Because of the modest sample size, exact logistic regression analysis was used to estimate associations between risk factors and NTDs. RESULTS: Serum vitamin status was generally poor for participants in the study. Still, relatively higher values of folate or vitamin B12 in serum, appeared to be protective for NTD (odds ratio [OR] = 0.61 per ng/ml, 95% Confidence interval [CI]: 0.42-0.85 and OR = 0.67 per 100 pg/ml, 95% CI: 0.41-1.02, respectively). High serum homocysteine was associated with higher risk of NTD (OR = 1.3 per µmol/l, 95% CI: 1.02-1.8). Women aged 30 years or more had an OR of 3.5 (95% CI: 1.1-12) for having a NTD child, and families with NTD children had lower household income. Women in the NTD group also had more spontaneous abortions or stillbirths in previous pregnancies. Self-reported intake of folate did not appear to protect against NTDs. CONCLUSIONS: Within this high-prevalence community, poor vitamin status was identified as a risk factor for NTDs detected at ultrasound examination. Improving food security and fortification of foods or food ingredients could be alternative measures.

Rare variants with large effects provide functional insights into the pathology of migraine subtypes, with and without aura.

Migraine is a complex neurovascular disease with a range of severity and symptoms, yet mostly studied as one phenotype in genome-wide association studies (GWAS). Here we combine large GWAS datasets from six European populations to study the main migraine subtypes, migraine with aura (MA) and migraine without aura (MO). We identified four new MA-associated variants (in PRRT2, PALMD, ABO and LRRK2) and classified 13 MO-associated variants. Rare variants with large effects highlight three genes. A rare frameshift variant in brain-expressed PRRT2 confers large risk of MA and epilepsy, but not MO. A burden test of rare loss-of-function variants in SCN11A, encoding a neuron-expressed sodium channel with a key role in pain sensation, shows strong protection against migraine. Finally, a rare variant with cis-regulatory effects on KCNK5 confers large protection against migraine and brain aneurysms. Our findings offer new insights with therapeutic potential into the complex biology of migraine and its subtypes.

Deficit of homozygosity among 1.52 million individuals and genetic causes of recessive lethality.

Genotypes causing pregnancy loss and perinatal mortality are depleted among living individuals and are therefore difficult to find. To explore genetic causes of recessive lethality, we searched for sequence variants with deficit of homozygosity among 1.52 million individuals from six European populations. In this study, we identified 25 genes harboring protein-altering sequence variants with a strong deficit of homozygosity (10% or less of predicted homozygotes). Sequence variants in 12 of the genes cause Mendelian disease under a recessive mode of inheritance, two under a dominant mode, but variants in the remaining 11 have not been reported to cause disease. Sequence variants with a strong deficit of homozygosity are over-represented among genes essential for growth of human cell lines and genes orthologous to mouse genes known to affect viability. The function of these genes gives insight into the genetics of intrauterine lethality. We also identified 1077 genes with homozygous predicted loss-of-function genotypes not previously described, bringing the total set of genes completely knocked out in humans to 4785.

Genetic effects on the timing of parturition and links to fetal birth weight.

The timing of parturition is crucial for neonatal survival and infant health. Yet, its genetic basis remains largely unresolved. We present a maternal genome-wide meta-analysis of gestational duration (n = 195,555), identifying 22 associated loci (24 independent variants) and an enrichment in genes differentially expressed during labor. A meta-analysis of preterm delivery (18,797 cases, 260,246 controls) revealed six associated loci and large genetic similarities with gestational duration. Analysis of the parental transmitted and nontransmitted alleles (n = 136,833) shows that 15 of the gestational duration genetic variants act through the maternal genome, whereas 7 act both through the maternal and fetal genomes and 2 act only via the fetal genome. Finally, the maternal effects on gestational duration show signs of antagonistic pleiotropy with the fetal effects on birth weight: maternal alleles that increase gestational duration have negative fetal effects on birth weight. The present study provides insights into the genetic effects on the timing of parturition and the complex maternal-fetal relationship between gestational duration and birth weight.

Prevalence of neural tube defects among pregnant women in Addis Ababa: a community-based study using prenatal ultrasound examination.

PURPOSE: The primary aim of this study was to estimate the prevalence of NTDs at ultrasound examination in communities of Addis Ababa and secondarily to provide a description of the dysmorphology of the NTD cases. METHODS: We enrolled 958 pregnant women from 20 randomly selected health centers in Addis Ababa during the period from October 1, 2018, to April 30, 2019. Of these 958 women, 891 had an ultrasound examination after enrollment, with a special focus on NTDs. We estimated the prevalence of NTDs and compared it with previously reported hospital-based birth prevalence estimates from Addis Ababa. RESULTS: Among 891 women, 13 had twin pregnancies. We identified 15 NTD cases among 904 fetuses, corresponding to an ultrasound-based prevalence of 166 per 10,000 (95% CI: 100-274). There were no NTD cases among the 26 twins. Eleven had spina bifida (122 per 10,000, 95% CI: 67-219). Among the 11 fetuses with spina bifida, three had a cervical and one had a thoracolumbar defect while the anatomical site for 7 was not registered. Seven of the 11 spina bifida defects had skin covering, while two of the cervical lesions were uncovered. CONCLUSION: We report a high prevalence of NTDs among pregnancies in communities of Addis Ababa based on screening by ultrasound. The prevalence was higher than in previous hospital-based studies in Addis, and the prevalence of spina bifida was particularly high.

An examination of mediation by DNA methylation on birthweight differences induced by assisted reproductive technologies.

BACKGROUND: Children born after assisted reproductive technologies (ART) differ in birthweight from those naturally conceived. It has been hypothesized that this might be explained by epigenetic mechanisms. We examined whether cord blood DNA methylation mediated the birthweight difference between 890 newborns conceived by ART (764 by fresh embryo transfer and 126 frozen thawed embryo transfer) and 983 naturally conceived newborns from the Norwegian Mother, Father, and Child Cohort Study (MoBa). DNA methylation was measured by the Illumina Infinium MethylationEPIC array. We conducted mediation analyses to assess whether differentially methylated CpGs mediated the differences in birthweight observed between: (1) fresh embryo transfer and natural conception and (2) frozen and fresh embryo transfer. RESULTS: We observed a difference in birthweight between fresh embryo transfer and naturally conceived offspring of - 120 g. 44% (95% confidence interval [CI] 26% to 81%) of this difference in birthweight between fresh embryo transfer and naturally conceived offspring was explained by differences in methylation levels at four CpGs near LOXL1, CDH20, and DRC1. DNA methylation differences at two CpGs near PTGS1 and RASGRP4 jointly mediated 22% (95% CI 8.1% to 50.3%) of the birthweight differences between fresh and frozen embryo transfer. CONCLUSION: Our findings suggest that DNA methylation is an important mechanism in explaining birthweight differences according to the mode of conception. Further research should examine how gene regulation at these loci influences fetal growth.

Variation in use of Caesarean section in Norway: An application of spatio-temporal Gaussian random fields.

AIMS: Caesarean section (CS) is a medical intervention performed in Norway when a surgical delivery is considered more beneficial than a vaginal. Because deliveries with higher risk are centralized to larger hospitals, use of CS varies considerably between hospitals. We describe how the use of CS varies geographically by municipality. Since indications for CS should have little variation across the relatively homogenous population of Norway, we expect fair use of CS to be evenly distributed across the municipalities. METHODS: Data from the Medical Birth Registry of Norway were used in our analyses (810,914 total deliveries, 133,746 CSs, 440 municipalities). We propose a spatial correlation model that takes the location into account to describe the variation in use of CS across the municipalities. The R packages R-INLA and TMB are used to estimate the yearly municipal CS rate and the spatial correlation between the municipalities. We also apply stratified models for different categories of delivering women (Robson groups). Estimated rates are displayed in maps and model parameters are shown in tables. RESULTS: The CS rate varies substantially between the different municipalities. As expected, there was strong correlation between neighbouring municipalities. Similar results were found for different Robson groups. CONCLUSIONS: The substantial difference in CS use across municipalities in Norway is not likely to be due to specific medical reasons, but rather to hospitals' different policies towards the use of CS. The policy to be either more or less restrictive to CS was not specific to any category of deliveries.

Wavelet Screening identifies regions highly enriched for differentially methylated loci for orofacial clefts.

DNA methylation is the most widely studied epigenetic mark in humans and plays an essential role in normal biological processes as well as in disease development. More focus has recently been placed on understanding functional aspects of methylation, prompting the development of methods to investigate the relationship between heterogeneity in methylation patterns and disease risk. However, most of these methods are limited in that they use simplified models that may rely on arbitrarily chosen parameters, they can only detect differentially methylated regions (DMRs) one at a time, or they are computationally intensive. To address these shortcomings, we present a wavelet-based method called 'Wavelet Screening' (WS) that can perform an epigenome-wide association study (EWAS) of thousands of individuals on a single CPU in only a matter of hours. By detecting multiple DMRs located near each other, WS identifies more complex patterns that can differentiate between different methylation profiles. We performed an extensive set of simulations to demonstrate the robustness and high power of WS, before applying it to a previously published EWAS dataset of orofacial clefts (OFCs). WS identified 82 associated regions containing several known genes and loci for OFCs, while other findings are novel and warrant replication in other OFCs cohorts.

Invited Commentary: Ionizing Radiation and Future Reproductive Health-Old Cohorts Still Deserve Attention.

Radiation from nuclear weapons or power plants has caused great concern among the public-concern that needs to be addressed with the best available data. Among the concerns associated with ionizing radiation are possible serious and far-reaching effects on reproductive health. Relevant data that can be used to address these concerns are scarce. The Hiroshima and Nagasaki bombings of World War II and the 1986 Chernobyl disaster in Ukraine are probably among the most dramatic and important sources of information on health effects, but much of the information is historical, and the exposed cohorts are getting old. In their accompanying article, Yamada et al. (Am J Epidemiol. 2021;190(11):2323-2333) revisit data on reproductive health outcomes in survivors of the Hiroshima and Nagasaki bombings during the years after the blasts. Exposure levels were very high, but after Yamada et al.'s reanalysis, effect estimates were low, and the evidence for overall effects on birth defects and perinatal mortality is still weak. The authors acknowledge that their data have limitations and that the generalizability of the findings is limited by the devastating conditions that prevailed in the 2 Japanese cities after the blasts.

Heritability curves: A local measure of heritability in family models.

Classical heritability models for family data split the phenotype variance into genetic and environmental components. For instance, the ACE model in twin studies assumes the phenotype variance decomposes as a2 + c2 + e2 , representing (additive) genetic effects, common (shared) environment, and residual environment, respectively. However, for some phenotypes it is biologically plausible that the genetic and environmental components may vary over the range of the phenotype. For instance, very large or small values of the phenotype may be caused by "sporadic" environmental factors, whereas the mid-range phenotype variation may be more under the control of common genetic factors. This article introduces a "local" measure of heritability, where the genetic and environmental components are allowed to depend on the value of the phenotype itself. Our starting point is a general formula for local correlation between two random variables. For estimation purposes, we use a multivariate Gaussian mixture, which is able to capture nonlinear dependence and respects certain distributional constraints. We derive an analytical expression for the associated correlation curve, and show how to decompose the correlation curve into genetic and environmental parts, for instance, a2 (y) + c2 (y) + e2 (y) for the ACE model, where we estimate the components as functions of the phenotype y. Furthermore, our model allows switching, for instance, from the ACE model to the ADE model within the range of the same phenotype. When applied to birth weight (BW) data on Norwegian mother-father-child trios, we conclude from the model that low and high BW are less heritable traits than medium BW. We also demonstrate switching between the ACE and ADE model when studying body mass index in adult monozygotic and dizygotic twins.

Gene-methylation interactions: discovering region-wise DNA methylation levels that modify SNP-associated disease risk.

BACKGROUND: Current technology allows rapid assessment of DNA sequences and methylation levels at a single-site resolution for hundreds of thousands of sites in the human genome, in thousands of individuals simultaneously. This has led to an increase in epigenome-wide association studies (EWAS) of complex traits, particularly those that are poorly explained by previous genome-wide association studies (GWAS). However, the genome and epigenome are intertwined, e.g., DNA methylation is known to affect gene expression through, for example, genomic imprinting. There is thus a need to go beyond single-omics data analyses and develop interaction models that allow a meaningful combination of information from EWAS and GWAS. RESULTS: We present two new methods for genetic association analyses that treat offspring DNA methylation levels as environmental exposure. Our approach searches for statistical interactions between SNP alleles and DNA methylation (G ×Me) and between parent-of-origin effects and DNA methylation (PoO ×Me), using case-parent triads or dyads. We use summarized methylation levels over nearby genomic region to ease biological interpretation. The methods were tested on a dataset of parent-offspring dyads, with EWAS data on the offspring. Our results showed that methylation levels around a SNP can significantly alter the estimated relative risk. Moreover, we show how a control dataset can identify false positives. CONCLUSIONS: The new methods, G ×Me and PoO ×Me, integrate DNA methylation in the assessment of genetic relative risks and thus enable a more comprehensive biological interpretation of genome-wide scans. Moreover, our strategy of condensing DNA methylation levels within regions helps overcome specific disadvantages of using sparse chip-based measurements. The methods are implemented in the freely available R package Haplin ( https://cran.r-project.org/package=Haplin ), enabling fast scans of multi-omics datasets.

Design efficiency in genetic association studies.

Selecting the best design for genetic association studies requires careful deliberation; different study designs can be used to scan for different genetic effects, and each design has its own set of strengths and limitations. A variety of family and unrelated control configurations are amenable to genetic association analyses, including the case-control design, case-parent triads, and case-parent triads in combination with unrelated controls or control-parent triads. Ultimately, the goal is to choose the design that achieves the highest statistical power using the lowest cost. For given parameter values and genotyped individuals, designs can be compared directly by computing the power. However, a more informative and general design comparison can be achieved by studying the relative efficiency, defined as the ratio of variances of two different parameter estimators, corresponding to two separate designs. Using log-linear modeling, we derive the relative efficiency from the asymptotic variance of the parameter estimators and relate it to the concept of Pitman efficiency. The relative efficiency takes into account the fact that different designs impose different costs relative to the number of genotyped individuals. We show that while optimal efficiency for analyses of regular autosomal effects is achieved using the standard case-control design, the case-parent triad design without unrelated controls is efficient when searching for parent-of-origin effects. Due to the potential loss of efficiency, maternal genes should generally not be adjusted for in an initial genome-wide association study scan of offspring genes but instead checked post hoc. The relative efficiency calculations are implemented in our R package Haplin.

Haplin power analysis: a software module for power and sample size calculations in genetic association analyses of family triads and unrelated controls.

BACKGROUND: Log-linear and multinomial modeling offer a flexible framework for genetic association analyses of offspring (child), parent-of-origin and maternal effects, based on genotype data from a variety of child-parent configurations. Although the calculation of statistical power or sample size is an important first step in the planning of any scientific study, there is currently a lack of software for genetic power calculations in family-based study designs. Here, we address this shortcoming through new implementations of power calculations in the R package Haplin, which is a flexible and robust software for genetic epidemiological analyses. Power calculations in Haplin can be performed analytically using the asymptotic variance-covariance structure of the parameter estimator, or else by a straightforward simulation approach. Haplin performs power calculations for child, parent-of-origin and maternal effects, as well as for gene-environment interactions. The power can be calculated for both single SNPs and haplotypes, either autosomal or X-linked. Moreover, Haplin enables power calculations for different child-parent configurations, including (but not limited to) case-parent triads, case-mother dyads, and case-parent triads in combination with unrelated control-parent triads. RESULTS: We compared the asymptotic power approximations to the power of analysis attained with Haplin. For external validation, the results were further compared to the power of analysis attained by the EMIM software using data simulations from Haplin. Consistency observed between Haplin and EMIM across various genetic scenarios confirms the computational accuracy of the inference methods used in both programs. The results also demonstrate that power calculations in Haplin are applicable to genetic association studies using either log-linear or multinomial modeling approaches. CONCLUSIONS: Haplin provides a robust and reliable framework for power calculations in genetic association analyses for a wide range of genetic effects and etiologic scenarios, based on genotype data from a variety of child-parent configurations.

A comparison of DNA methylation in newborn blood samples from infants with and without orofacial clefts.

BACKGROUND: Isolated orofacial clefts are among the most common congenital birth defects. Although the underlying biological mechanisms remain largely unknown, clefts are thought to be complex disorders influenced by genetic, environmental, and potentially epigenetic factors. METHODS: In blood samples from 2- to 3-day-old infants (n = 747) collected in a nationwide population-based study of orofacial clefts in Norway, we measured DNA methylation profiles for more than 450,000 CpGs and then conducted epigenome-wide association analyses (EWAS). We tested methylation profile difference at each CpG between controls (n = 436) and each of the cleft subtypes (92 cleft lip only, CLO; 84 cleft palate only, CPO; 132 cleft lip and palate, CLP). We also compared controls to various combinations of case groups and compared case subtypes to each other. Finally, using the EWAS results, we searched for larger differentially methylated regions (DMRs) associated with orofacial clefts. RESULTS: In EWAS comparing controls to individual cleft subtypes, we found no significant associations at a Bonferroni P value threshold of 10-7. After pooling case groups, we found two significantly differentially methylated CpGs: cg09696939 near gene BICC1 is associated with CLO+CLP (P = 9.58 × 10-8); cg26985354 in gene CLASRP is associated with CPO+CLP (P = 7.38 × 10-8). In DMR analysis, we identified a total of 56 significant regions when comparing controls to individual cleft subtypes (10 for CLO, 6 for CPO, 41 for CLP). Only one DMR is shared among the three cleft groups. In combined case group analysis, we found 26 DMRs for CLP+CLO, 31 for CLP+CPO, and 37 when all subtypes are combined. Finally, in case-case comparisons of subtypes, we identified 10 DMRs when comparing CLP to CPO, 9 in CLP compared to CLO, and 13 in CLP compared to CPO. CONCLUSIONS: We identified two individual CpGs and multiple DMRs that differ between controls and cleft case subtypes. Although we find some evidence for the possible role of DNA methylation in etiology of orofacial clefts, our study does not support previous reports of widespread differences in blood DNA methylation between babies with and without facial clefts.

Analysis of Parent-of-Origin Effects on the X Chromosome in Asian and European Orofacial Cleft Triads Identifies Associations with DMD, FGF13, EGFL6, and Additional Loci at Xp22.2.

Background: Although both the mother's and father's alleles are present in the offspring, they may not operate at the same level. These parent-of-origin (PoO) effects have not yet been explored on the X chromosome, which motivated us to develop new methods for detecting such effects. Orofacial clefts (OFCs) exhibit sex-specific differences in prevalence and are examples of traits where a search for various types of effects on the X chromosome might be relevant. Materials and Methods: We upgraded our R-package Haplin to enable genome-wide analyses of PoO effects, as well as power simulations for different statistical models. 14,486 X-chromosome SNPs in 1,291 Asian and 1,118 European case-parent triads of isolated OFCs were available from a previous GWAS. For each ethnicity, cleft lip with or without cleft palate (CL/P) and cleft palate only (CPO) were analyzed separately using two X-inactivation models and a sliding-window approach to haplotype analysis. In addition, we performed analyses restricted to female offspring. Results: Associations were identified in "Dystrophin" (DMD, Xp21.2-p21.1), "Fibroblast growth factor 13" (FGF13, Xq26.3-q27.1) and "EGF-like domain multiple 6" (EGFL6, Xp22.2), with biologically plausible links to OFCs. Unlike EGFL6, the other associations on chromosomal region Xp22.2 had no apparent connections to OFCs. However, the Xp22.2 region itself is of potential interest because it contains genes for clefting syndromes [for example, "Oral-facial-digital syndrome 1" (OFD1) and "Midline 1" (MID1)]. Overall, the identified associations were highly specific for ethnicity, cleft subtype and X-inactivation model, except for DMD in which associations were identified in both CPO and CL/P, in the model with X-inactivation and in Europeans only. Discussion/Conclusion: The specificity of the associations for ethnicity, cleft subtype and X-inactivation model underscores the utility of conducting subanalyses, despite the ensuing need to adjust for additional multiple testing. Further investigations are needed to confirm the associations with DMD, EGF16, and FGF13. Furthermore, chromosomal region Xp22.2 appears to be a hotspot for genes implicated in clefting syndromes and thus constitutes an exciting direction to pursue in future OFCs research. More generally, the new methods presented here are readily adaptable to the study of X-linked PoO effects in other outcomes that use a family-based design.

A Genome-Wide Search for Gene-Environment Effects in Isolated Cleft Lip with or without Cleft Palate Triads Points to an Interaction between Maternal Periconceptional Vitamin Use and Variants in ESRRG.

Background: It is widely accepted that cleft lip with or without cleft palate (CL/P) results from the complex interplay between multiple genetic and environmental factors. However, a robust investigation of these gene-environment (GxE) interactions at a genome-wide level is still lacking for isolated CL/P. Materials and Methods: We used our R-package Haplin to perform a genome-wide search for GxE effects in isolated CL/P. From a previously published GWAS, genotypes and information on maternal periconceptional cigarette smoking, alcohol intake, and vitamin use were available on 1908 isolated CL/P triads of predominantly European or Asian ancestry. A GxE effect is present if the relative risk estimates for gene-effects in the offspring are different across exposure strata. We tested this using the relative risk ratio (RRR). Besides analyzing all ethnicities combined ("pooled analysis"), separate analyses were conducted on Europeans and Asians to investigate ethnicity-specific effects. To control for multiple testing, q-values were calculated from the p-values. Results: We identified significant GxVitamin interactions with three SNPs in "Estrogen-related receptor gamma" (ESRRG) in the pooled analysis. The RRRs (95% confidence intervals) were 0.56 (0.45-0.69) with rs1339221 (q = 0.011), 0.57 (0.46-0.70) with rs11117745 (q = 0.011), and 0.62 (0.50-0.76) with rs2099557 (q = 0.037). The associations were stronger when these SNPs were analyzed as haplotypes composed of two-SNP and three-SNP combinations. The strongest effect was with the "t-t-t" haplotype of the rs1339221-rs11117745-rs2099557 combination [RRR = 0.50 (0.40-0.64)], suggesting that the effects observed with the other SNP combinations, including those in the single-SNP analyses, were mainly driven by this haplotype. Although there were potential GxVitamin effects with rs17734557 and rs1316471 and GxAlcohol effects with rs9653456 and rs921876 in the European sample, respectively, none of the SNPs was located in or near genes with strong links to orofacial clefts. GxAlcohol and GxSmoke effects were not assessed in the Asian sample because of a lack of observations for these exposures. Discussion/Conclusion: We identified significant interactions between vitamin use and variants in ESRRG in the pooled analysis. These GxE effects are novel and warrant further investigations to elucidate their roles in orofacial clefting. If validated, they could provide prospects for exploring the impact of estrogens and vitamins on clefting, with potential translational applications.

Parent-of-origin-environment interactions in case-parent triads with or without independent controls.

With case-parent triad data, one can frequently deduce parent of origin of the child's alleles. This allows a parent-of-origin (PoO) effect to be estimated as the ratio of relative risks associated with the alleles inherited from the mother and the father, respectively. A possible cause of PoO effects is DNA methylation, leading to genomic imprinting. Because environmental exposures may influence methylation patterns, gene-environment interaction studies should be extended to allow for interactions between PoO effects and environmental exposures (i.e., PoOxE). One should thus search for loci where the environmental exposure modifies the PoO effect. We have developed an extensive framework to analyze PoOxE effects in genome-wide association studies (GWAS), based on complete or incomplete case-parent triads with or without independent control triads. The interaction approach is based on analyzing triads in each exposure stratum using maximum likelihood estimation in a log-linear model. Interactions are then tested applying a Wald-based posttest of parameters across strata. Our framework includes a complete setup for power calculations. We have implemented the models in the R software package Haplin. To illustrate our PoOxE test, we applied the new methodology to top hits from our previous GWAS, assessing whether smoking during the periconceptional period modifies PoO effects on cleft palate only.

Maternal BMI at the start of pregnancy and offspring epigenome-wide DNA methylation: findings from the pregnancy and childhood epigenetics (PACE) consortium.

Pre-pregnancy maternal obesity is associated with adverse offspring outcomes at birth and later in life. Individual studies have shown that epigenetic modifications such as DNA methylation could contribute. Within the Pregnancy and Childhood Epigenetics (PACE) Consortium, we meta-analysed the association between pre-pregnancy maternal BMI and methylation at over 450,000 sites in newborn blood DNA, across 19 cohorts (9,340 mother-newborn pairs). We attempted to infer causality by comparing the effects of maternal versus paternal BMI and incorporating genetic variation. In four additional cohorts (1,817 mother-child pairs), we meta-analysed the association between maternal BMI at the start of pregnancy and blood methylation in adolescents. In newborns, maternal BMI was associated with small (<0.2% per BMI unit (1 kg/m2), P < 1.06 × 10-7) methylation variation at 9,044 sites throughout the genome. Adjustment for estimated cell proportions greatly attenuated the number of significant CpGs to 104, including 86 sites common to the unadjusted model. At 72/86 sites, the direction of the association was the same in newborns and adolescents, suggesting persistence of signals. However, we found evidence for acausal intrauterine effect of maternal BMI on newborn methylation at just 8/86 sites. In conclusion, this well-powered analysis identified robust associations between maternal adiposity and variations in newborn blood DNA methylation, but these small effects may be better explained by genetic or lifestyle factors than a causal intrauterine mechanism. This highlights the need for large-scale collaborative approaches and the application of causal inference techniques in epigenetic epidemiology.