Identifying genetic and environmental risk factors for cleft using genome wide association study data

The Cleft Collective is a set of studies of over 2500 families from across the UK who are affected by cleft lip/palate, whose long-term goals are to develop effective treatments to reduce the risk of cleft and to improve the physical, functional and emotional wellbeing of people born with a cleft. Since the study was established in 2012, we have built one of the world's largest banks of biological samples from children born with a cleft and their parents, in addition we have secured funding to generate genetic data on this cohort. We represent a cleft study of more than 1000 families collected and recruited in Bonn Germany which has DNA samples but does not currently have funding for genotyping. We are now hoping to take advantage of these impressive endeavours by seeking funding to generate genetic data on the Bonn study and then analyse both studies to identify genetic variants which cause cleft both among children born with a cleft and their mothers. We will also use this information to identify non-genetic (environmental) factors that cause clefts using an analytical technique called Mendelian randomization. An improved understanding of these causes will be vital in helping us to achieve our long-term goals, and it will also provide a valuable resource to other researchers from around the world. Findings from this work will be directly relevant to the large global community of people born with a cleft (approximately 1 in every 650 births), but also to the needs of people affected by craniofacial abnormalities and conditions related to cleft which may have many of the same risk factors.

Approximately 1 in every 650 children born in the UK each year will have an orofacial cleft. The Cleft Collective (CC) is a set of cohort studies of children born with a cleft across the UK and their families set up in 2012 which to date has recruited over 2500 families. In addition, a similar family study including around 1000 families has been recruited in Bonn Germany. Both studies have banks of biological samples (blood, cleft tissue or saliva) collected from participants and the CC has funding to genotype participants using a genome wide association study chip.
The aim of this project is to genotype the Bonn sample using the same chip as the CC and use data from both studies to carry-out genome wide association studies (GWAS) to determine whether there are further common variants (not so far detected) associated with cleft lip and/or cleft palate. We will carry-out GWAS by cleft subtypes to look for subtype-specific genetic variants, carry-out a GWAS of mothers of children born with a cleft to determine whether there are maternal genetic variants that increase the risk of having a child with a cleft and investigate parent-child gene interactions in cleft. In order to identify non-genetic modifiable risk factors for cleft we will carry-out two sample hypothesis-driven and hypothesis-free Mendelian randomization using GWAS data from mothers to determine whether exposures in pregnancy are likely to cause cleft. This is an analytical technique pioneered and advanced by researchers at the University of Bristol, which uses genetic variants as surrogates for environmental exposures to overcome problems of confounding, measurement error and reverse causation which are inherent in observation studies. The analyses listed above will allow us to identify the causes of cleft, and determine subtype specific risk factors, and inform public health policy to reduce the occurrence of cleft.

The Cleft Collective Cohort Studies have involved individuals with a cleft and parents of children with a cleft from the design stage of the study; they have had input into the development of the study design, protocols and questionnaires. The research agenda is driven by the James Lind Alliance priorities (http://www.jla.nihr.ac.uk/priority-setting-partnerships/cleft-lip-and-palate) which brings together patients, carers and health care staff to set priorities for research.
Around one in every 650 babies born in the UK have a cleft, whilst the cleft is normally repaired within the first year of life, further treatments for related speech, hearing and psychological problems are common and often further surgery is required as the child grows. Therefore this condition has considerable morbidity associated with it. In addition, in developing countries the presence of a cleft is still associated with substantially higher mortality rates than for the general population. In order to prevent clefts from occurring Midwives and public health specialists need clear messages on causal modifiable risk factors which they can use to inform the public. In addition the public themselves can only take action to reduce the risk of having a child with cleft if they have evidence based information on causal risk factors. This will come from the Mendelian randomization work proposed in this grant. Where the evidence suggests that an exposure is unlikely to make a substantial contribution to cleft this will be lead to deprioritisation of that particular risk factor from further research. Similarly, where we find genetic risk factors for cleft, this information will be shared with genetic counsellors and other health professionals who are in contact with those directly affected.
The pathways for feeding back to the relevant health professionals and in translating our findings to practice are very clear. We work very closely with all 17 Cleft centres and with a multidisciplinary group of professional across the UK in order to recruit patients into the Cleft Collective and we feedback research findings to them on a regular basis. We intend to present our findings at the annual Craniofacial Society of Great Britain and Ireland conference which attracts a wide audience of health care professionals working in the cleft field. We also plan to organise a workshop on Cleft Genetics at the outset of this study for those working in this area of research, to generate collaboration and encourage use of the data generated in this study.
We will disseminate the findings from this research to those taking part in the Cleft Collective cohort studies via social media, newsletters and a webinar in doing so hopefully encourage participation and retention in this research. We will also disseminate this research to the wider cleft community by presenting at the Cleft Lip and Palate Association Conference (CLAPA) and seek to inform the general public about cleft by participating in science festivals.
The genetics data and detailed phenotype information and summary statistics generated in this project will be available to academics and healthcare workers to carry out research on cleft and on related conditions, such as hearing outcomes and speech outcomes, and we will promote the use of this data via dissemination and training.