Objective 1: To generate and supplement existing genetic, epigenomic and metabolomic data across five large European cohort studies to provide an unparalleled resource for investigating associations between early life factors and subsequent obesity, neurodevelopmental and mental health outcomes.

Objective 2: To integrate inter-generational phenotypic, genetic, epigenomic and metabolomic data across the five cohort studies through harmonization of data and meta-analysis.

Objective 3: To identify causal relationships between prenatal exposures and metabolic and neurodevelopmental outcomes using a variety of state-of-the-art causal analytic methods including Mendelian randomization, maternal-paternal, between-sibling and cross-cohort comparisons.

Objective 4: To synthesise information to inform and prioritise future interventions and public health policy that will have a meaningful and lasting impact upon the incidence of these health challenges.

The primary intent of ROHgen is to investigate the influence of ROH on complex traits; to show for which traits and end points there is evidence of recessive effects, how strong they are and eventually potentially to count and map these effects. This will be done by conducting the same analyses across many cohorts and then sharing various statistics relating to ROH or trait associations for central meta-analysis.

Hypothesis: ROHs are associated with health-related outcomes and quantitative traits of interest.

The FP7 funded GEFOS consortium identified a range of BMD-related loci by GWAS (1). This Horizon 2020 application (PI Fernando Rivadeneira, Erasmum Medical Centre, Netherlands) represents an extension of this program, intended to identify further BMD related loci by harnessing whole gemome sequencing technology. It is intended that ALSPAC will contribute to work package (WP) 2, 3 and 6.

In WP2, a musculoskeletal (MSK) chip with GWAS and customized content, which after genotyping ~60,000 young and elderly individuals from 36 studies previously involved in GEFOS (mostly European), will allow the discovery of common, less frequent and rare variants; together with fine mapping of gene regions associated with traits and pathological conditions of the MSK system including BMD, fracture risk, sarcopenia and frailty. ALSPAC mothers will form part of a replication cohort for novel genotype-BMD associations arising from this MSK chip.

In WP3, BMD associated variants will be analysed in relation to different endophenotypes, based on our previous studies suggesting different genetic influences on trabecular and cortical bone (2-4). Associations will be analysed between genetic markers of interest and cortical bone phenotypes obtained in ALSPAC off spring as measured by tibial pQCT, and trabecular bone phenotypes as obtained in ALSPAC mothers by radial pQCT.

In WP6, genetic influences on BMD identified in WP2 will be examined using a lifecourse approach, by comparing the strength of associations (as reflected by beta coefficients) across different times of life. Results from ALSPAC offspring (total body DXA at age 9 and 17, hip DXA at 13 and 17), and ALSPAC mothers (pre versus postmenopausal hip BMD) will contribute to these analyses.

It is envisaged that ALSPAC genetic data will be in the form of genome wide data imputed to 1000 genomes, as previously obtained. In the case of rare variants of interest which are not covered by imputation, there may be a need for custom genotyping. Bone outcomes will comprise DXA and pQCT measures as previously obtained in ALSPAC off spring and mothers.

Our proposed study of pursuit and saccade eye movemets in the ALSPAC cohort will allow many hypotheses to be tested but initially we will concentrate on:

Variation in anti-saccade task accuracy with IQ (as per Evdokimifdis et al)

Variation in smooth pursuit and saccade function with PLIKS score (as part of Zammit et al's programme)

Variation in sacccade fuction as a measure of executive control, according to previous exposure to potential neurotoxins such as tobacco, alocohol, cannabis, other drugs

Variation in oculomotor parameters according to previous stressful experiences - this is relevant to the current popularity of eye-movemet based thereapy for post-traumatic stress disorder.

Variations in oculomotor control according to genotype for specific candidate genes and as the phenotype for GWAS studies of genetic predictors of oculomotor control

Further researc questions will be developed in line with current literature and withstrategic funding calls.

The aim of the study is to explore the association of distinctive facial features with candidate genes reported to be associated with facial development.

We intend to replicate the findings reported by Claes et al 2014 where the authors found an association of 20 genes with distinctive facial features. This study uses a novel technique bootstrapped response-based imputation modelling to explore the relationships of sex, genomic ancestry and a set of craniofacial candidate genes. The procedure will be replicated on 4747 3D 15 year old facial shells. In addition an additional 30 genes which did not show any association in Claes' sample of 592 will be explored using the ALSPAC cohort.

Essentially the proposed method uses dense spatially dense quasi-landmarks on 3D images (greater than 7,000), principal component analyses and a new partial least squares regression (bootstrapped response-based imputation modelling (BRIM) to measure and model facial variation.

By simultaneously modeling facial shape variation as a function of sex and genomic ancestry along with genetic markers in craniofacial candidate genes, the effects of sex and ancestry can be removed from the model thereby providing the ability to extract the effects of individual genes.

Although the combined impact of genetic variants on phenotypic traits has become of increased interest over the last few years, there has so far been little research undertaken to understand the combined impact of variants on DNA methylation. We intend to apply collapsing approaches to collapsed methylation scores to investigate this. This could be an attractive approach in contrast to individual CpG site analyses for many reasons, such as computional efficiency, reducing the burden of multiple testing, smoothing out artefacts and representing the underlying biology in a different form by collapsing across functional units (e.g. CpG islands, including/excluding shores, entire promoter regions). Furthermore, the manner in which methylation data is collapsed is an aspect of this work which will need to be evaluated. There are currently some methods out there which could be used for this purpose, although so far they have mainly been used to investigate the relationship between methylation and phenotypic traits.

As pairwise association analyses for individual CpG sites is currently being undertaken using the 450K methylation data in ALSPAC, this should provide a useful comparison for this proposed approach.

There is an observational relationship between dietary intake of dairy/calcium and subsequent risk of osteoporosis/BMI. However, many of these studies are observational in nature and thus subject to confounding. We would like to investigate this relationship using Mendelian Randomization in ALSPAC and in other cohorts that contain these data. Our intention is to use variants related to (i) dairy intake, and (ii) calcium intake/levels (as identified through previous GWAS or through GWAS in ALSPAC) to investigate the relationship between these exposures and (i) bone related phenotypes, height, weight and BMI and (ii) metabolomic measures in ALSPAC.

AIMS

There are two main aims of the proposed study. The first aim is to examine the longitudinal predictors of later reading and writing levels in unselected populations. More specifically the longitudinal predictive role of early oral language and literacy skills assessed at different developmental points will be examined. In this way, it will be possible to use the smaller cohorts, from such as the clinics 25 months and 49 months to examine the prospective longitudinal relations between early oral language and later literacy skills as well as educational and vocational outcomes. The second aim of the study is to conduct a retrospective analysis of the data and examine the early markers of two main subtypes of reading difficulties, namely dyslexia (specific reading impairment) and specific reading comprehension impairment. The early markers of later writing difficulties will also be examined. Prior research on the relationship between reading comprehension and text writing reported only moderate relations suggesting that the comprehension and production of written text call upon similar as well as distinct cognitive-linguistic skills. There is currently very limited understanding of the early markers of text writing difficulties.

Here I propose to include questions on emotional, physical and sexual abuse to the next ALSPAC YPs questionnaire. This proposal is directly linked to approved project B2134. As noted above, there is an inceasing interest in abuse as a novel cardiometabolic risk factor. As part of project B2134 I propose to study this association in ALSPAC mothers and fathers. Collecting these data in the YPs will allow to do so in this cohort as well and will enhance ALSPAC as a resource to study intergenarational, familial patterns of abuse.