Proposal summaries

These are research proposals that have been approved by the ALSPAC exec. The titles include a B number which identifies the proposal and the date on which the proposals received ALSPAC exec approval.

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B833 - Cognitive Function and Social Learning - 08/06/2009

B number: 
B833
Principal applicant name: 
Dr Elise Robinson (Harvard School of Public Health, USA)
Co-applicants: 
Prof Marcus Munafo (University of Bristol, UK), Dr Kerim Munir (Harvard School of Public Health, USA)
Title of project: 
Cognitive Function and Social Learning.
Proposal summary: 

Autistic disorders affect an estimated 60 per 10,000 individuals (1, 2). The traits charateristic of autism spectrum disorders (social communication and language delays, restricted and repetitive interests), however, are normally distributed within the general population (3).

There is substantial IQ- and sex-based variability in the prevalence of both clinical and sub-clinical social communication deficit (4, 5). Specifically, there is evidence that IQ is protective against disordered social communication behavior in women, but less so in men. The degree to which this relationship is stable over time is unclear. Studies examining the longitudinal trajectory of social communication behavior are limited; those including members of the general population have been conducted exclusively among males (6). Further, the relationship between IQ and social developmental trajectory has yet to be established. The primary purpose of this project is to investigate the relationship between social/communication behavior and IQ. Specifically, we are interested in determining whether the longitudinal relationship between social behavior and IQ is modified by gender. The primary hypotheses of this study are outlined below:

1. Social and communication skills (assessed via the Social and Communication Disorders Checklist) will improve for some individuals over time. SCDC scores will be tracked at years 7.5, 10, 13/14, and 15/16.

1a. Higher IQ will predict greater improvement in social and communication skills in women but not in men. IQ will be assessed using the WISC-III at 8 and the WASI at 15/16 (scores will be averaged).

1b. Amongst individuals with diagnosed autistic disorder, asperger's disorder, or pervasive developmental disorder not otherwise specified, higher IQ will predict greater improvement in social and communication skills in women but not in men. Autism will be assessed using NHS data linked to ALSPAC by Williams and colleagues (7).

1c. These relationships will hold after controlling for a number of factors potentially related to both IQ and social behavior as measured. Covariates of interest include: language ability (CCC, WOLD); socioeconomic position (family educational background, indices of multiple deprivation, parental employment status, ethnicity, household income); child behavior (1970 birth cohort scales); hyperactiviy (SCQ); literacy and numeracy (WORD) and; prosocial behavior (parent and teacher reports, CHAMP). These covariates will also be assessed for distributional equivalency between sexes and across IQ groups.

Questions regarding phenotypic consistency are implicit within the above analyses. There exists substantial documentation regarding phenotypic heterogeneity in autism (8, 9). Said heterogeneity influences in the maner in which autism research should be conducted and interpreted (10). The variety of measured ASD-correlates in the ALSPAC data set affords a unique opportunity to examine heterogeneity within a representative sample of individuals diagnosed with autism. Specifically, it permits analysis of phenotypic patterning within subgroups. The secondary aim of this project is to assess the phenotypic consistency of autism 1) across the IQ spectrum and 2) between genders. The primary points of comparison will be the following:

2a. The conditional probability of a diagnosis of autism per a given SCDC score.

2b. Evidence of early childhood social/communication delay relative to overall development. Communication delay will be assessed via the communication and social subscales of the Denver at 6, 18, and 30 months and the MacArthur at 15, 24, and 36 months. Overall development in early childhood will be assessed through the remainder of the Denver at 6, 18, and 30 months and the Griffiths (18 months).

2c. The prevalence of associated phenotypes (Theory of Mind, Non-verbal information)

All longitudinal analyses will be conducted using generalized linear mixed effects models (11). The hypotheses of this project are in line with GLMM as, using this method, population averages are interpreted as conditional upon a system of random effects (individual trajectories). Using a mixed (random) effects technique, we will be able to a) control for within-individual clustering of social communication scores across time and b) evaluate between-individual heterogeneity in trajectories. We will use time-variant predictors when available. Accordingly, many covariates (e.g. verbal ability) have been requested at multiple time points. The comparisons involved in questions 2a-c involve basic statistical associations (probabilities, percents). All analyses will be conducted in SAS v. 9.2.

References

1. Yeargin-Allsopp M, Rice C, Karapurkar T, Doernberg N, Boyle C, Murphy C. Prevalence of Autism in a US Metropolitan Area. Journal of the American Medical Association. 2003;289:49-55.

2. Bertrand J, Mars A, Boyle C, Bove F, Yeargin-Allsopp M, Decoufle P. Prevalence of Autism in a United States Populations: The Brick Township, New Jersey, Investigation. Pediatrics. 2001;108:1155-1161.

3. Constantino J, Todd R. Autistic traits in the general population. Archives of General Psychiatry. 2003;60:524-530.

4. Fombonne E. Epidemiological Surveys of Autism and Other Pervasive Developmental Disorders: An Update. Journal of Autism and Developmental Disorders. 2003;33(4):365-382.

5. Skuse D, Mandy W, Steer C, et al. Social Communication Competence and Functional Adaptation in a General Population of Children: Preliminary Evidence for Sex-by-Verbal IQ Differential Risk. Journal of the American Academy of Child and Adolescent Psychiatry. 2009;48(2):128-137.

6. Constantino J, Abbacchi A, Lavesser P, et al. Developmental course of autistic social impairment in males. Development and Psychopathology. 2009;21:127-138.

7. Williams E, Thomas K, Sidebotham H, Emond A. Prevalence and characteristics of autism spectrum disorders in the ALSPAC cohort. Developmental Medicine and Child Neurology. 2008;50:672-677.

8. Spence S, Cantor R, Chung L, Kim S, Geschwind D, Alarcon M. Stratification Based on Language-Related Endophenotypes in Autism: Attempt to Replicate Reported Linkage. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics. 2006; 141B: 591-598.

9. Spiker D, Lotspeich L, Dimicell S, Myers R, Risch N. Behavioral phenotypic variation in autism multiplex families: Evidence for a continuous severity gradient. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics. 2002; 114: 129-136.

10. Happe F, Ronald A, Plomin R. Time to give up on a single explanation for autism. Nature Neuroscience. 2006;9:1218-1220.

11. Fitzmaurice G, Laird N, Ware J. Applied Longitudinal Analysis. Hoboken, NJ: Wiley; 2004.

Date proposal received: 
Monday, 8 June, 2009
Date proposal approved: 
Monday, 8 June, 2009
Keywords: 
Cognitive Function
Primary keyword: 

B830 - Attention Deficit Hyperactivity Disorder in Children with Learning Disability - 05/06/2009

B number: 
B830
Principal applicant name: 
Prof Anita Thapar (University of Cardiff, UK)
Co-applicants: 
Dr Alka Ahuja (University of Cardiff, UK)
Title of project: 
Attention Deficit Hyperactivity Disorder in Children with Learning Disability.
Proposal summary: 

Attention Deficit Hyperactivity Disorder (ADHD) otherwise known as Hyperkinetic disorder (ICD 10) is an extremely disabling condition, affecting 1.4-6% of children. It is now the commonest reason for follow-up in Child and Adolescent Mental Health Services as well as being seen in Community Child Health Services. Behavioural, social and educational problems as well as increased rates of adult difficulties including criminality and drug misuse are associated with ADHD in children with normal intelligence. In contrast, virtually nothing is known about ADHD in children with learning disability (LD/mental retardation) as sub average intelligence (IQless than 70) has traditionally been used as an exclusion criterion in studies of ADHD. Neither the DSM-IV nor the ICD-10 gives detailed consideration to the diagnosis of ADHD/Hyperkinetic disorder among children with LD.

At one time, clinical lore suggested that ADHD did not occur in children with LD, and any inappropriate behaviour children with LD showed was secondary to mental impairment. That view is not supported by current evidence. More recent studies have shown that ADHD occurs more commonly in these children but may be underdiagnosed due to issues such as '' diagnostic overshadowing'', the tendency by which clinicians tend to overlook additional psychiatric diagnosis once a diagnosis of learning disability is made; or ''masking'' in which the clinical characteristics of a mental disorder are masked by a cognitive, language or speech deficit.While available evidence suggests that ADHD may be more common among children with learning disability, research has been hindered as most studies of ADHD in children with LD do not use standardised diagnostic interviews and criteria. Also this sub-group of children with ADHD and learning disability are excluded from virtually all aetiological and treatment studies. Thus it is not known whether the clinical presentation, pattern of correlates and aetiology of ADHD differs in children with learning disability. This may have ethical implications as not much is known about the diagnosis and treatment in this group of children and hence they are frequently undiagnosed and untreated.

Although there is evidence that ADHD does occur in those with LD a crucial clinical issue is whether or not ADHD in this group is the same entity as that found in those without learning disability; that is can those with both ADHD and LD be viewed as having "true" ADHD. As this sub-group is almost always excluded from research, it remains unknown whether they are similar to children with ADHD and normal IQ in terms of clinical and aetiological correlates. Our preliminary pilot study analyses using a sample of children with ADHD with low IQ test scores showed that lower IQ, is associated with increased ADHD symptom severity and conduct disorder symptoms. This suggests that ADHD and LD may represent a clinically more severe variant of ADHD.On the basis of pilot data, we hypothesise that children with ADHD and LD will show a similar clinical presentation and pattern of genetic and psychosocial correlates to those found in children with ADHD and IQ within the normal range. If our hypothesis is correct, then children with ADHD and LD are likely to benefit from stimulant and other treatments that are known to be effective in those with ADHD without LD and our work will provide impetus for therapeutic trials in this important and disadvantaged group. Moreover, the findings will further highlight that children with ADHD and learning disability should not necessarily be excluded from aetiological and other clinical studies.

AIMS OF THE STUDY:

The aim of this study is to

1) Collect and comprehensively assess a sample of 100 children with ADHD and learning disability.

2) Compare this group with two other groups-a well-characterised sample of children with ADHD who have normal intelligence (IQgreater than 70) that has already been collected and a control group of children with low IQ alone on a) clinical characteristics b) genetic and psychosocial correlates that are known to be associated with ADHD.

The control group of children with low IQ and no clinical comordity have been difficult to recruit from a clinical setting and the ALSPAC would be ideally placed to provide the clinical and cognitive data required for this group of children.

Current data requested:

ADHD -

DAWBA data on Attention & Activity from parent questionnaires at ages 91mths and 128 months

DAWBA data on Attention, Activity and Impulsiveness from teacher questionnaires at Yr 3 & Yr 6

Antisocial Behaviour -

DAWBA data on Awkward & Troublesome Behaviour from parent questionnaires at ages 91mths and 128 mths

DAWBA data on Awkwardness & Troublesome Behaviour from teacher questionnaires at Yr 3 & Yr 6

Antisocial Behaviour questions from Focus@8 and Focus@10 from the child

Cognitive measures -

WISC IQ measure from Focus@8, including digit span subtest, full scale IQ, pe rformance IQ and verbal IQ measure

Other Measures:

Demographic measures -

Sex,

Age at each assessment,

whether from a multiple birth

Social class (maternal education and housing type),

Ethnicity.

Date proposal received: 
Friday, 5 June, 2009
Date proposal approved: 
Friday, 5 June, 2009
Keywords: 
ADHD
Primary keyword: 

B829 - Testing for shared genetic liability between maternal smoking during pregnancy and ADHD - 05/06/2009

B number: 
B829
Principal applicant name: 
Dr Kate Langley (University of Cardiff, UK)
Co-applicants: 
Prof Anita Thapar (University of Cardiff, UK), Dr Stan Zammitt (University of Bristol, UK)
Title of project: 
Testing for shared genetic liability between maternal smoking during pregnancy and ADHD.
Proposal summary: 

Attention deficit hyperactivity disorder (ADHD) is a common, extremely disabling disorder which has major adverse squalae in childhood and later life. Despite being such an important clinical problem, the aetiology and pathogenesis of ADHD is poorly understood. Available evidence suggests that both genetic and environmental risk factors are important.

Association studies have suggested that maternal smoking during pregnancy may be an environmental risk factor for ADHD. However, there is a growing body of evidence to suggest that these associations are due to shared genetic liability between smoking and ADHD, rather than there being a causal environmental effect.

Using a novel design looking at children born through IVF, we have shown that where mothers are not genetically related to the child they carry in pregnancy (e.g. children conceived following egg donation) no significant association is observed between maternal smoking during pregnancy and ADHD symptoms. Conversely when the mother is genetically related to the child she carries (e.g. children conceived following sperm donation) a significant association between smoking during pregnancy and ADHD is observed. This suggests that the association may arise because of shared genetic liability for maternal smoking and child ADHD. Similarly, studies looking at the children of twins and discordant sibling pairs where the mother smokes during one pregnancy but not the other, also indicate that there is a genetic or familial influence on the links between maternal smoking during pregnancy and child behaviour.

Although these studies are suggestive of shared genetic liability, the evidence is still incomplete.

The aim of this proposal is to further explore the causal pathways for association between maternal smoking during pregnancy and childhood ADHD and the possibility that this is due to shared genetic liability.

1). Firstly, we propose to compare the risk for child ADHD when mothers and fathers smoked during the pregnancy; any true environmental effect (taking into account passive smoking effects) would be observed only in those who are exposed to smoke in utero via their mother whilst an equal risk from the father would be indicative of shared genetic liability.

2). We also propose to look at a specific gene variant in the CHRNA3 gene (rs1051730) which has been shown across a number of studies to be associated with increased risk of cigarette smoking and in the ALSPAC sample with smoking during pregnancy, again comparing differential risk passed from the mother and father.

3). Using this genetic information, we aim to look at the child's genotype: If there is shared genetic liability for this particular variant-then we would expect to find association between this SNP and childhood ADHD symptoms. In the future this pilot work could lead to applying for funding to test other variants in relation to the shared genetic liability between smoking and ADHD.

4). Stan Zammit to lead:

Although there have been fewer studies that have examined the relationship between maternal substance use and psychosis, effects on psychosis are equally plausible given the diverse detrimental effects of in-utero exposure to tobacco on cerebral development and function, and also given the evidence that such exposure can lead to cognitive deficits that are an established risk factor for psychosis. In fact, within ALSPAC, we observed that maternal smoking during pregnancy was associated with increased risk of child psychotic experiences, whereas paternal smoking during pregnancy was not associated (although confidence intervals for maternal and paternal smoking overlapped). High levels of maternal alcohol use during pregnancy were also associated with child psychotic symptoms. We would therefore like to examine whether maternal and child genetic variants associated with smoking behaviour are associated with risk of child psychotic experiences.

Date proposal received: 
Friday, 5 June, 2009
Date proposal approved: 
Friday, 5 June, 2009
Keywords: 
ADHD, Pregnancy, Smoking
Primary keyword: 

B825 - Replication of associations seen in Duke Genetics of Memory and Epilepsy Studies - 03/06/2009

B number: 
B825
Principal applicant name: 
Dr Elizabeth T Cirulli (Duke University, USA)
Co-applicants: 
Dr Anna Need (Duke University, USA), Dr David Goldstein (Duke University, USA), Dr Beate St. Pourcain (University of Bristol, UK), Prof George Davey Smith (University of Bristol, UK)
Title of project: 
Replication of associations seen in Duke Genetics of Memory and Epilepsy Studies.
Proposal summary: 

We will provide a list of 235 SNPs that have been found to be associated with performance in our cohort. We genotyped our samples using the Illumina HumanHap550 or 610 and will pick the top 10 (approximately) associations from each of the 23 phenotypes examined in our cohort for followup in the ALSPAC cohort. We would like the p-values, betas, standard errors, and direction of effect by allele for a linear regression between each of these SNPs and each of the cognition phenotypes available in the ALSPAC cohort (with covariates such as age and gender included in the model). Since our cohort is composed of individuals over the age of 18, we would prefer the cognition data to be from a timepoint past childhood.

Our analysis was done in a sample of 291 Caucasians for the following tests: Green Story Recall Immediate and Delayed, TrailsA, TrailsB, WAIS Digit Span Forward, WAIS Digit Span Backward, Controlled Oral Word Association, Animals, WAIS Digit Symbol, WAIS Symbol Search, Stroop Color-Word, and the first principal component of these 11 phenotypes. Analysis was performend in a partially overlapping sample of 656 Caucasians and Asians for the following tests from Cantab: paired associates learning (PAL) (2 phenotypes from test), spatial working memory (SWM) (2 phenotypes from test), verbal recognition memory - immediate recall (VRM), pattern recognition memory (PRM), intra-extradimensional set shifting (IED), rapid visual processing (RVP), spatial span (SSP), spatial recognition memory (SRM), and the first principal component from these 10 phenotypes. Cognition phenotypes that are most similar to these measures would be ideal for comparison.

Date proposal received: 
Wednesday, 3 June, 2009
Date proposal approved: 
Wednesday, 3 June, 2009
Keywords: 
Genetics
Primary keyword: 

B828 - Investigation of BMI T2D alleles and cognition - 02/06/2009

B number: 
B828
Principal applicant name: 
Prof Michael O'Donovan (University of Cardiff, UK)
Co-applicants: 
Dr Beate St. Pourcain (University of Bristol, UK), Dr Stanley Zammit (University of Bristol, UK)
Title of project: 
Investigation of BMI, T2D alleles, and cognition.
Proposal summary: 

It is widely accepted that there is an increased prevalence of cardiovascular risk factors in the schizophrenic population. There is also increasing evidence that some of the second generation antipsychotics may contribute additionally to a number of cardiovascular risk factors, particularly type 2 diabetes, obesity, and dyslipidemias. There is also some evidence that many of these factors may contribute risk to cognitive impairment, including dementia (Biessels et al 2006;Qiu et al 2005;Kivipeklto et al 2005) and more subtle cognitive decrements in non-psychiatric populations (reviewed by van den Berg et al 2008). Whether these factors are causal is less clear, but is a question that has obvious importance for public health.

We have become interested in this issue from the perspective of schizophrenia patients given their already impaired cognitive function and the greater prevalence of obesity and type 2 diabetes. Pilot data generated from subjects recruited for projects conducted by the Conte Center for the Neuroscience of Mental Disorders (CCNMD) at the Mount Sinai School of Medicine (a subset of which has been reported on previously, Friedman et al 2008) provides some evidence for association between increased weight and poor cognitive function. Analyses were conducted on 153 subjects (100 with schizophrenia, 53 non-psychiatric) with complete medical and cognitive data. Our analyses provided evidence for an inverse correlation between increased BMI and performance on delayed and immediate memory tasks. There was no evidence for caseness as an interaction term, suggesting the findings might generalize to the population. These pilot data provide some support for the hypothesis for a relationship between BMI and cognitive impairment. While the findings are preliminary, if correct may not reflect causality, and if they do, they may result from pathological changes that are not likely to occur to any appreciable extent, we are interested in exploring an alternative possibility of more direct causal links. Thus, we wish to use the ALSPAC data a) to explore relationships between BMI in childhood and cognition and b) to explore relationships between cognition and alleles that are known to be associated with increased BMI and T2D using the Mendelian randomization approach to test for possible causality.

G.J. Biessels, S. Staekenborg, E. Brunner, C. Brayne, P. Scheltens, Risk of dementia in

diabetes mellitus: a systematic review, Lancet Neurol. 5 (2006) 64-74.

C. Qiu, B. Winblad, L. Fratiglioni, The age-dependent relation of blood pressure to

cognitive function and dementia, Lancet Neurol. 4 (2005) 487-499.

M. Kivipelto, T. Ngandu, L. Fratiglioni, M. Viitanen, I. Kareholt, B. Winblad, E.L.

Helkala, J. Tuomilehto, H. Soininen, A. Nissinen, Obesity and vascular risk factors at

midlife and the risk of dementia and Alzheimer disease, Arch.Neurol. 62 (2005)

1556-1560.

van den Berg E, Kloppenborg RP, Kessels RP, Kappelle LJ, Biessels GJ.Type 2 diabetes mellitus, hypertension, dyslipidemia and obesity: A systematic comparison of their impact on cognition. Biochim Biophys Acta. 2009 May;1792(5):470-81. Epub 2008 Sep 23.

WHO. Obesity and overweight. World Health Organization. 2006. Available from: http://www.who.int/mediacentre/factsheets/fs311/en/print.html (accessed 26 August 2008).

Friedman JI, Tang C, Carpenter D, Buchsbaum M, Schmeidler J, Flanagan L, Golembo S, Kanellopoulou I, Ng J, Hof PR, Harvey PD, Tsopelas ND, Stewart D, Davis KL. Diffusion tensor imaging findings in first-episode and chronic schizophrenia patients. Am J Psychiatry. 2008 Aug;165(8):1024-32.

Date proposal received: 
Tuesday, 2 June, 2009
Date proposal approved: 
Tuesday, 2 June, 2009
Keywords: 
Genetics
Primary keyword: 

B827 - Genes and intelligence Do genes make us smarter - 02/06/2009

B number: 
B827
Principal applicant name: 
Prof Jean Golding (University of Bristol, UK)
Co-applicants: 
Prof Alan Emond (University of Bristol, UK), Prof John Henderson (University of Bristol, UK), Prof Marcus Pembrey (University of Bristol, UK), Dr Susan Ring (University of Bristol, UK), Prof George Davey Smith (University of Bristol, UK), Prof Debbie A Lawlor (University of Bristol, UK)
Title of project: 
Genes and intelligence: Do genes make us smarter?
Proposal summary: 

Multiple genome wide and candidate gene analysis have been performed in order to identify genetic varaints that explain the inter-individual differences in intelligence(Butcher, L. M. et al., 2005; Butcher, L. M., Davis, O. S., Craig, I. W., & Plomin, R., 2008; Plomin, R., 1999; Plomin, R. et al., 2004; Plomin, R. et al., 2001; Buyske, S. et al., 2006; Dick, D. M. et al., 2006; Luciano, M. et al., 2006; Posthuma, D. et al., 2005, for a review see Posthuma and de Geus (Posthuma, D. & de Geus, E. J. C., 2006)) but so far results are far from clear. Of all reported genetic association studies in the literature, only 4% have shown replicable association according to a 2002 search (Hirschhorn, J. N., Lohmueller, K., Byrne, E., & Hirschhorn, K., 2002). Using data from the IMAGE project, we performed a GWAS on IQ using data from 947 European Caucasian nuclear families (2844 individuals) from eight countries (Belgium, England, Germany, Holland, Ireland, Israel, Spain, and Switzerland) that were included in the analysis. Families were recruited based on having one child with ADHD (Attention-Deficit/Hyperactivity Disorder) and another who would provide DNA and quantitative trait data. In addition, both parents had to be available for DNA-sampling. IQ scores were available for 634 probands (for which we also had genotyping data), of which 554 are males, with a mean age of 10.99 (SD 2.74). IQ was measured with WISC-III-R (Wechsler Intelligence scales for children) (Wechsler, D, 1991) or the WAIS-III-R (Wechsler Adult Intelligence Scale) (Wechsler, D, 1997) when appropriate (for children aged 17 and older). The vocabulary, similarities, picture completion and block design subtests from the WISC were used to obtain an estimate of child's IQ (prorated following procedures described by Sattler) (Sattler, J. M., 1992). Age-appropriate national population norms were available for each participating site and these were used to derive standardized estimates of intelligence (Sonuga-Barke, E. J. et al., 2008). Standardized Full Scale IQ scores ranged from 56 to 154, with a mean of 100.7 (SD 15.6).

The IMAGE consotium makes part o the Genetic Association Information Network (GAIN) a public-private partnership of FNIH (Foundation for the National Institutes of Health, Inc.) that currently involves NIH, Pfizer, Affymetrix, Perlegen Sciences, Abbott, and the Eli and the Edythe Broad Institute (of MIT and Harvard University (http,//www.fnih.org)). Genotyping was conducted at Perlegen Sciences using their genotyping platform, which comprises approximately 600,000 tagging SNPs designed to be in high linkage disequilibrium with untyped SNPs for the HapMap populations. Genotype data were cleaned by NCBI (The National Center for Biotechnology Information). Quality Control analyses were processed using the GAIN QA/QC Software Package (version 0.7.4) developed by Goncalo Abecasis and Shyam Gopalakrishnan at the University of Michigan. Details of the genotyping and data cleaning process for the ADHD GAIN study (Study Accession, phs000016.v1.p1) have been reported elsewhere (Neale, B. M. et al., 2008a). Briefly, we selected only SNPs with minor allele frequency (MAF) >= 0.05 and Hardy-Weinberg equilibrium (HWE) (P >= 1x10-6). Genotypes causing Mendelian inconsistencies were identified by PLINK and removed (http,//pngu.mgh.harvard.edu/purcell/plink/) (Purcell, S. et al., 2007a). We additionally removed SNPs that failed the quality control metrics for the other two GAIN Perlegen studies (for Major Depression Disorder (dbGAP Study Accession, phs000020.v1.p1) and Psoriasis (dbGAP Study Accession, phs000019.v1.p1). With this filtering, 384.401 SNPs were retained in the final dataset. To increase coverage in the targeted genomic areas, we used the imputation approach implemented in PLINK (v1.04), which imputes genotypes of SNPs that are not directly genotyped in the dataset, but that are present on a reference panel. The PLINK algorithm is an extension of multimarker tagging. The reference panel used consisted of 2,543,285 polymorphic autosomal SNPs genotyped on the 60 HapMap CEU founders which are publicly available for download from the HapMap website (http://www.hapmap.org). A threshold of 0.80 confidence level was set for a hard call to be included in further association testing. Most likely genotypes on imputed SNPs were then included in association analyses. Gene coverage was determined by the sum of the typed and imputed SNPs as well as the tagged SNPs divided by the total known common SNPs within a gene, using WGAviewer (Ge, D. et al., 2008). Association analysis of 634 ADHD probands was conducted using the linear procedure implemented in PLINK using the prorated IQ score as quantitative outcome and adjusting for the language in which the IQ tests were done. Initial findings show several SNPs with interesting (non geneome wide significant) association p values (p less than 10E-06) including a haplotype block on chromosome 3 (rs7643566, rs6800161, rs9860985, rs7642425, rs1602, rs480668, rs6583190 and rs553783 (uncorrected p values = 5.32E-6)) also SNP rs11594325 (uncorrected p value = 6.43 E-6) in the PRKG1 gene on chromosome 10 and SNP rs2134947 (uncorrected p value=9.47E-7) in the CNTN5 genme on chromosme 11. In order to validate these findings, an independent replication sample is needed. We propose to use the genetic and IQ information available from the ALSPAC study in order to replicate these association findings. ALSPAC, as a birth cohort is comparable to an ADHD sample as IMAGE in terms og IQ because the selection criteria applied for the IMAGE participants only required that the IQ was equal or higher than 70, meaning that the distribution of the trait in our ADHD sample is perfectly normal (overall mean IQ [all probands] = 100.0, SD=15.4). Also, the proportion of IQ values lower that this threshold is low, skewing our IQ distribution only slightly, skewness 0.103, SE=0.070), this will not influence our comparison with cohort such as ALSPAC.

Date proposal received: 
Tuesday, 2 June, 2009
Date proposal approved: 
Tuesday, 2 June, 2009
Keywords: 
Genetics, Intelligence, Genes
Primary keyword: 

B824 - Autistic Traits in the General Population associated and causal risk factors - 01/06/2009

B number: 
B824
Principal applicant name: 
Prof David Skuse (University College London, UK)
Co-applicants: 
Dr William Mandy (University College London, UK)
Title of project: 
Autistic Traits in the General Population: associated and causal risk factors.
Proposal summary: 

Autism is coming to be conceptualised as a dimensional disorder, located at the extreme of the distribution of traits found in the general population (Constantino and Todd, 2004). This raises two questions of theoretical and clinical significance:

1. At what point do autistic traits become functionally impairing in the general population of children?

2. Do risk factors for autistic social communication could operate right across the range of impairment, and not just on those at the extreme of the distribution?

We examined these questions using data from ALSPAC (Skuse, Mandy, Steer et al., 2009), looking at the associations between a parent-report measure of social communication impairment (the Social Communication Disorders Checklist (SCDC); Skuse, Mandy & Scourfield, 2005) and independent measures of intelligence and teacher-reported functional impairment (Strengths and Difficulties Questionnaire (SDQ); Goodman et al., 2003). Two notable, novel findings emerged from this study (Constantino, 2009).

Firstly we demonstrated that in middle childhood even mild, sub-clinical social communication impairments are associated with social, emotional and behavioural impairments at school. This was true across the range of social communication impairment, with no step-function or obvious threshold above which social communication traits became clinically significant. This has implications for teachers and clinicians when seeking to support children without an autism spectrum disorder (ASD), but who nevertheless have elevated levels of autistic traits.

Secondly we described a SCI by gender by verbal IQ (VIQ) interaction. VIQ was protective against social communication impairment for females across the full range of abilities but not for males. Above average VIQ did not offer extra protection for males, and there was some suggestion that high VIQ may even operate as a risk factor for social communication impairment in males. This striking and original finding has the potential to elucidate the development of Asperger's syndrome, which is associated with high VIQ and a large male to female ratio (9:1).

We propose to use further data from ALSPAC to replicate and elucidate these findings. Specificly we aim to investigate the following:

Continuities and changes in the associations between SCI and functional impairment.

We aim to replicate our analyses of SCDC and SDQ data from middle childhood, using data collected when participants were c.11 years old. This will enable us to take a longitudinal, developmental perspective, examining continuities and changes in the way in which SCI serves as a risk factor for maladaption in childhood. Such research will in turn offer insights for clinicians and teachers seeking to better understand and treat behavioural, social and emotional maladaption in middle and later childhood.

Gender, IQ and autistic traits

We aim to further investigate the finding that VIQ is protective against social communication impairment across the range of abilities for females but not males. Firstly this will involve testing the replicability of this gender by VIQ interaction using a measure of social communication impairment taken in later childhood. Secondly we aim to use WISC-III subtest data to investigate which specific components of VIQ are driving the not-linear trend we observed. This will offer insight into the neurocognitive mechanisms involved in the development of high-functioning ASD and Asperger's syndrome in males. Thirdly we aim to test whether a distinct sub-group exists on the autistic spectrum comprising males who have both high VIQ and high social communication impairments. This will involve consideration of whether this group is stable over time, and whether they have a distinct pattern of cognitive, social and emotional strengths and vulnerabilities compared to other groups in the sample (high VIQ, high SCI females; high VIQ, low SCI males; low VIQ, high SCI males). We propose to include measures of neurodevelopment (attention, face and voice emotion recognition) relevant to the clinical syndrome of autism.

Our proposed investigation will be useful to clinicians diagnosing high-functioning ASDs, and will potentially help to reduce heterogeneity in studies aiming to identify the aetiology of ASDs.

REFERENCES

Constantino JN. How Continua Converge in Nature: Cognition, Competence and Autistic Syndromes.J Am Acad Child Adolesc Psychioatry. 2009;48: 97-8.

Constantino JN, Todd RD. Autistic traits in the general population: a twin study. Arch Gen Psychiatry. 2003;60:524-530.

Goodman R, Ford T, Simmons H, Gatward R, Meltzer H. Using the Strengths and Difficulties Questionnaire (SDQ) to screen for child psychiatric disorders in a community sample. Int Rev Psychiatry. 2003;15:166-172.

Skuse DH, Mandy WPL, Scourfield J. Measuring autistic traits: heritability, reliability and validity of the Social and Communication Disorders Checklist. Br J Psychiatry. 2005;187:568Y572.

Skuse DH, Mandy WPL, Steer CD et al. Social Communication Competence and Functional Adaption in a General Population of Children: Preliminary Evidence for Sex-by-Verbal IQ Differential Risk. 2009;48: 128-37.

Date proposal received: 
Monday, 1 June, 2009
Date proposal approved: 
Monday, 1 June, 2009
Keywords: 
Autism
Primary keyword: 

B966 - Genome-wide association meta-analysis of heart rate - 24/05/2009

B number: 
B966
Principal applicant name: 
Dr Dave Evans (University of Bristol, UK)
Co-applicants: 
Prof George Davey Smith (University of Bristol, UK), Dr Ruth Loos (Not used 0, Not used 0)
Title of project: 
Genome-wide association meta-analysis of heart rate
Proposal summary: 

Mean heart rate at eleven years of age will be correlated against genome-wide imputed snp data on 1500 ALSPAC children. The summary level association statistics will be provided to Ruth Loos (Cambridge) who is chairing a consortium, aiming to meta-analyse the results of several cohorts with the heart rate measure. We also request that the heart rate measures and DNA be made available for follow up single SNP genotyping for genome-wide significant SNPs from the meta-analysis.

Date proposal received: 
Sunday, 24 May, 2009
Date proposal approved: 
Sunday, 24 May, 2009
Keywords: 
Genetics
Primary keyword: 

B831 - Erasmus student projects - 21/05/2009

B number: 
B831
Principal applicant name: 
Dr Pauline Emmett (University of Bristol, UK)
Co-applicants: 
Prof Christina Campoy (University of Granada, Spain, Europe), Dr Maria Jos? Piqueras Benavides (University of Granada, Spain, Europe), Dr Lucrezia Algar Berrondo (University of Granada, Spain, Europe)
Title of project: 
Erasmus student projects.
Proposal summary: 

1. Omega-3 fatty acids in childhood diets

Provision of a balanced diet is important in relation to the growth and development of children. Some specific aspects of diet have been shown to relate to cognitive development: for example, the consumption of oily fish in pregnancy was associated with better eyesight in 3-year olds (Williams et al 2001) and better cognition in 7-year olds in ALSPAC (Hibbeln et al 2007). The possible active factor in fish is its high content of omega-3 fatty acids.

Diet diary information was collected on the children at age 3 and age 7 by ALSPAC and this has been evaluated for nutrient and energy content. However the diary could also provide information on omega-3 and omega-6 fatty acids if the nutrient database was extended to cover these nutrients.

This project will entail working to extend the database to cover omega-3 and omega-6 fatty acids in all foods eaten at 3 and 7 years. Then combining this data with the information already available on these children to assess their intake of these nutrients. Outcomes, measured in ALSPAC, would then be investigated in the light of the intake of these fatty acids by the children.

This would provide a self-contained project with a data collection and handling element and a statistical and nutritional analysis element. The student would acquire practical skills in Nutritional Epidemiology that would be extremely beneficial to future work. These skills would include the use of international tables of nutrient content of foods, the assessment of misreporting and the handling of energy adjustment in dietary datasets. The latter two are very important issues that are difficult to deal with and have important affects on the meaningful interpretation of results in the field of nutrition.

2. Early nutrition

Correct feeding practices are important in relation to the growth and development of infants. When feeding formula the infant has less control over intake than when being breast fed as illustrated by a study from ALSPAC of infant diets at 4 months in relation to growth [Ong 2006]. Another European wide study has found that formula was often incorrectly made up by parents (CHOP personal communication) with possible consequences for obesity development.

Diet diary information was collected on 900 infants aged 4 months by ALSPAC. At the same time mothers were asked how they made up the formula in terms of number of scoops of powder used. This data needs to be extracted from the records. It could then be used in conjunction with the diet diary information already available and the records of growth in these children to investigate the affect of incorrect procedures on outcome.

This would provide a self-contained project with a data collection and handling part and a statistical and nutritional analysis part. A project report would be prepared with a possibility of submission for publication in a peer-reviewed journal at a later date.

3. Adolescent nutrition

The period of adolescence is a critical for the growth and development of an individual. It is also a time when children may take control of their diet from their parents and make important decisions about what foods they eat. This may impact on their growth with some tending towards obesity and other cutting down on particular foods e.g. avoiding dairy products or becoming vegetarian or cutting out many foods and becoming anorexic. Thus it is an important time to study the diet and nutrition of children.

Food frequency questionnaires were completed by children and their parents, in ALSPAC, when the children were aged 12 years. These have not yet been analysed. This data needs to be prepared for analysis using nutritional information about foods likely to have been eaten and portion sizes appropriate to 12-year-old children. Nutrient intakes can then be calculated and linked to outcomes such as low or high weight.

This project would give direct experience of how to analyse food frequency data, the handling of large datasets, the use of statistical packages and simple statistical analysis. A project report would be prepared that would input into further research.

ALSPAC website: http://www.bristol.ac.uk/alspac/

Emmett P. Dietary assessment in the Avon Longitudinal Study of Parents and Children. European Journal of Clinical Nutrition. 2009;63:S38-S44

Ong KK, Emmett PM, Noble S, Ness A, Dunger D, ALSPAC Study Team. Dietary energy intake at the age of 4 months predicts postnatal weight gain and childhood body mass index. Pediatrics 2006; 117:e503-508.

Date proposal received: 
Thursday, 21 May, 2009
Date proposal approved: 
Thursday, 21 May, 2009
Keywords: 
Diet
Primary keyword: 

B823 - Gene x gene and gene x environment interactions underlying speech language and reading development - extended analysis - 20/05/2009

B number: 
B823
Principal applicant name: 
Dr Silvia Paracchini (Wellcome Trust Centre for Human Genetics, UK)
Co-applicants: 
Title of project: 
Gene x gene and gene x environment interactions underlying speech, language and reading development - extended analysis.
Proposal summary: 

The present proposal is a a follow up of our current B598 project, which aims to investigate the gene x gene and gene x environment interactions at the basis of dyslexia and related disorders. Preliminary data from the analysis conducted so far are encouraging. We were able to replicate in the ALSPAC sample some associations of genetic markers we have idetified in our selected samples for dyslexia and SLI (Paracchini et al, 2008 , Newbury et al, submitted). The B598 has been designed as a short 2-years pilot study and we would now like to take forward and extend its format while the aims remain the same.

Aims of the project are:

1) To replicate in the ALSPAC sample previously reported genetic association at the basis of dyslexia and SLI

2) To investigate whether the effect of dyslexia and SLI susceptibility variants can be modulated by different genetic factors (gene x gene interactions).

3) To investigate the role of environmental factors in modulating the effect of genes that contribute to measures of reading, speech and language (gene x environment interactions).

4) To test whether shared genetic or environmental factors can explain co-morbidity between dyslexia and SLI and whether it is possible to identify a correlation between genetic/environment background and specific sub-groups of phenotypes.

We would like to expand the current analysis by genotyping additional SNP, genotyping the mother cohort and possibly the fathers. We will also expand, consequentially, the statistical analysis.

We would like to include in the analysis additional genes that have been implicated in SLI, dyslexia and ADHD as well as interesting gene implicated in regulating cognitive function. We are also cunducting an extensice functional characterisation of the KIAA0319, focusing in particular on the identification of interacting proteins. We have identify and verified several protein interacting with KIAA0319 and we would like to include these in our analysis. We are in the process of testing for association SNPs within these genes and we planning to include in ALSPAC only significantly associated SNPs. Therefore at this stage we cannot speficy any rs number for these genes.

For some genes we are planning to investigate parent-of-origin effect. Therefore we would like to include in this proposal the genotypic analysis of the available parents.

Details of resources requested:

- Biological materials

We have enough DNA for the children cohort to carry out this project. we will perform the genetic analysis here at the Wellcome trust Centre for Human genetics using the I-plex sequenom system. We are planning to analyse in the parents only specific SNPs and, if possible, we would like to genotype these through the K-Biosciences service.

-Existing data

We would like to include in this project the analysis of genes already genotyped in the ALSPAC sample by different research groups. In some case we would like to use the existing genotypic data (providing the quality is good) and in other cases we would to genotype additional markers.

- Phenotypic measures

We would like to include in this project all the outcomes that we have already accessed through the our previous project DTA (B566) and the ones we will finalise for the B598 project. I anticipate that we might add some specific extra measures but the the basic "concepts" will be the same.

- Data linking

We would like the genotypic data to be linked to the database including the genotypes generated in our previous projects. If possible we would like to use the same old codes otherwise we are happy to get a new code as long as all the genotypes will be included.

-Statistical analysis

We would like to choose the option of performing the staitical analysis in our laboratory.

Details of funding

This project will be part of my next fellowship applications. I am planning to apply to the Wellcome Trust, MRC, Royal Society and European Council aiming to a project starting date in Oct 2010. I will submit to ALSPAC copies of my application for your approval before submitting to funding bodies.

Date proposal received: 
Wednesday, 20 May, 2009
Date proposal approved: 
Wednesday, 20 May, 2009
Keywords: 
Genetics, Speech & Language
Primary keyword: 

B821 - The role of lipid level variation in childhood health Mendelian Randomisation from the top 10 available lipid loci - 15/05/2009

B number: 
B821
Principal applicant name: 
Dr Nic Timpson (University of Bristol, UK)
Co-applicants: 
Prof George Davey Smith (University of Bristol, UK), Prof Naveed Sattar (University of Glasgow, UK)
Title of project: 
The role of lipid level variation in childhood health: Mendelian Randomisation from the top 10 available lipid loci.
Proposal summary: 

Lipids are essential biological molecules with diverse functions in the body such as, energy storage, membrane structure and cell signalling. The major lipid components in blood are Cholesterol (C) and Triglycerides (TG), only a small percentage of circulating cholesterol is exogenous (dietary), the majority is derived from endogenous synthesis in the liver(1).

In the past screens for rare monogenic forms of dyslipidemia have successfully identified many important genes for lipoprotein metabolism(2). It is only since more recent technical developments that the GWAS has become feasible and we have been able to identify genes that are involved with more common human diseases. Using high-density genotyping arrays the GWAS approach is used to statistically associate SNP markers from across the genome with a range of quantitative traits in large samples of unrelated individuals. Over the last 2 years results from several independent analyses like these have identified greater than 30 genetic loci that influence blood lipid concentrations, many of which had not been previously been implicated in lipid or lipoprotein metabolism(3-11). The novel results from these analyses are currently being investigated further and replicated in larger and more diverse cohorts, a broader knowledge of the common genetic variation that influences plasma lipid and lipoprotein levels will improve our understanding of the metabolic processes and disease mechanisms and aid the classification, diagnosis and treatment of CVD.

In this study we aim to genotype the top 10 lipid related loci derived from large population based genomewide association studies (8). We aim to replicate the associations known between common genetic variation and blood lipid concentrations in ALSPAC children (data on serological measurements available at age 9) and to explore the relationship between both this variation lipid variation and health related outcomes through the application of Mendelian randomisation approaches.

Whilst de novo association between common genetic variation and circulating lipid levels at age 9 has been noted within the limited number of ALSPAC children with genomewide data (unpublished work by PhD Student Chris Boustred), the major lipid loci previously recognised by large meta-analyses of genomewide associaiton studies for lipids have also been confirmed within the ALSPAC cohort. Thus, for the purposes of applying the Mendelian randomisation approach to the ALSPAC cohort re. lipid levels and their causal relationships with health outcomes, we aim to take the top 10 loci from Katherisan et al (8)(see below), the most recent pooling of large data sets (adult) concerning common genetic variability and circulating lipid levels.

Top 10 SNPs to be genotyped in ALSPAC (chosen on the basis of effect size in meta-samples, min size n=19,648):

LDL - rs6544713 (ABCG8)

LDL - rs4420638 (APOE-APOC1-APOC4-APOC2)

LDL - rs6511720 (LDLR)

LDL - rs12740374 (CELSR2-PSRC1-SORT1)

HDL - rs1800691 (HNF4A)

HDL - rs173539 (CETP)

HDL - rs12678919 (LPL)

TG - rs7679 (PLTP)

TG - rs964184 (APOA1-APOC3-APOA4-APOA5)

TG - rs12678919 (LPL)

We enclose a quotation for this work detailing the specifics of the genotyping from KBioscience.

References:

1. Hegele, R.A. Plasma lipoproteins: genetic influences and clinical implications. Nat Rev Genet 10, 109-121(2009).

2. Mansah, G A, M.J. The Atlas of Heart Disease and Stroke (WHO, Geneva, 2004).

3. Insull, W. The pathology of atherosclerosis: plaque development and plaque responses to medical treatment. Am. J. Med 122, S3-S14(2009).

2. Goldstein, J.L. & Brown, M.S. MOLECULAR MEDICINE: The Cholesterol Quartet. Science 292, 1310-1312(2001).

3. Aulchenko, Y.S. et al. Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. Nat Genet advanced online publication, (2008).

4. Diabetes Genetics Initiative of Broad Institute of Harvard and MIT, L.U. et al. Genome-Wide Association Analysis Identifies Loci for Type 2 Diabetes and Triglyceride Levels. Science 316, 1331-1336(2007).

5. Kathiresan, S. et al. A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study. BMC Med Genet 8 Suppl 1, S17(2007).

6. Kathiresan, S. et al. Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans. Nat Genet 40, 189-197(2008).

7. Kathiresan, S. et al. Polymorphisms associated with cholesterol and risk of cardiovascular events. N Engl J Med 358, 1240-9(2008).

8. Kathiresan, S. et al. Common variants at 30 loci contribute to polygenic dyslipidemia. Nat Genet 41, 56-65(2009).

9. Sabatti, C. et al. Genome-wide association analysis of metabolic traits in a birth cohort from a founder population. Nat Genet advanced online publication, (2008).

10. Sandhu, M.S. et al. LDL-cholesterol concentrations: a genome-wide association study. The Lancet 371, 483-491

11. Willer, C.J. et al. Newly identified loci that influence lipid concentrations and risk of coronary artery disease. Nat Genet 40, 161-169(2008).

12. ENOS, W.F., HOLMES, R.H. & BEYER, J. Coronary disease among United States soldiers killed in action in Korea; preliminary report. J Am Med Assoc 152, 1090-1093(1953).

13. Stary, H.C. The sequence of cell and matrix changes in atherosclerotic lesions of coronary arteries in the first forty years of life. Eur. Heart J 11 Suppl E, 3-19(1990).

14. Strong, J.P. et al. Prevalence and extent of atherosclerosis in adolescents and young adults: implications for prevention from the Pathobiological Determinants of Atherosclerosis in Youth Study. JAMA 281, 727-735(1999).

Date proposal received: 
Friday, 15 May, 2009
Date proposal approved: 
Friday, 15 May, 2009
Keywords: 
Genetics, Mendelian Randomization
Primary keyword: 

B822 - Replication Study of Associations between rs2891168 and Blood Pressure in Childhood and Adolescence - 13/05/2009

B number: 
B822
Principal applicant name: 
Dr Paul Leeson (University of Oxford, UK)
Co-applicants: 
Prof Hugh Watkins (University of Oxford, UK), Prof Keith Channon (University of Oxford, UK), Prof Peter Whincup (University of London, UK), Prof Derek Cook (University of London, UK), Professor Aroon Hingorani (University College London, UK), Prof John Deanfield (University College London, UK)
Title of project: 
Replication Study of Associations between rs2891168 and Blood Pressure in Childhood and Adolescence.
Proposal summary: 

A susceptibility locus on chromosome 9p21 has become the most consistently reproduced genetic risk marker for myocardial infarction1, 2. The locus has also now been associated with an increased risk of aneurysm formation via different underlying pathological processes, in distinct vascular beds; the abdominal aorta and intracranial arteries3. Together these observations point towards an underlying biological mechanism that operates at the level of the arterial wall4.

We have completed a comprehensive vascular phenotype study in around 2500 individuals to study the impact of genotype on the arterial wall in young people and compared the findings to those with established coronary artery disease. As well as associations with vascular phenotypes we have demonstrated an unexpected association between blood pressure and genotype in young people (based on a sample of 1354 adolescents from the Ten Towns Study) (see below). While unexpected, the direction of effect fits with our observations of vascular phenotype in young subjects. Other studies in older subjects have not demonstrated associations between this genotype and conventional risk factors, including blood pressure.

We wish to undertake a collaborative project to establish whether we can replicate this finding in a second cohort of young people of similar age. At the same time the lack of association with other risk factors during childhood could be verified. Our analysis has been based on the rs2891168 SNP (which effectively tags the 9p21 risk haplotype4) and we propose the joint analysis with ALSPAC be based on the same SNP or the most closely associated proxy SNP within the available ALSPAC genome wide association study dataset of 2000 subjects. We propose that we study associations with blood pressure levels at both age 11 and during adolescence (as performed for the Ten Towns Study) and with other risk factors at these time points.

This collaboration would provide a unique opportunity to present data from two different populations on the association between this specific genetic locus and risk factors during childhood. Furthermore, the collaboration with ALSPAC provides the possibility for rapid analysis based on existing data for both blood pressure and genome-wide association.

Adolescence

AA

AG

GG

p

Number of male (%)

199 (55)

350 (55)

193 (55)

0.9

Median age in years (range)

15 (13-16)

15 (13-16)

15 (13-16)

0.7

Systolic blood pressure in mmHg

122.6 (14.1)

120.9 (13.2)

120.4 (13.2)

0.03

Diastolic blood pressure in mmHg

67.8 (7.8)

66.8 (7.2)

66.5 (7.1)

0.02

Aged 10-11 years

AA

AG

GG

p

Systolic blood pressure in mmHg

113.3 (11.2)

112.4 (11.1)

111.9 (10.8)

0.1

Diastolic blood pressure in mmHg

66.1 (6.8)

65.5 (7.0)

65.0 (6.9)

0.03

Values expressed as mean (SD) unless otherwise stated. p represents the significance level of an ANOVA.

1. Samani NJ, Erdmann J, Hall AS, et al. Genomewide association analysis of coronary artery disease. N Engl J Med. Aug 2 2007;357(5):443-453.

2. McPherson R, Pertsemlidis A, Kavaslar N, et al. A common allele on chromosome 9 associated with coronary heart disease. Science. Jun 8 2007;316(5830):1488-1491.

3. Helgadottir A, Thorleifsson G, Magnusson KP, et al. The same sequence variant on 9p21 associates with myocardial infarction, abdominal aortic aneurysm and intracranial aneurysm. Nat Genet. Feb 2008;40(2):217-224.

4. Broadbent HM, Peden JF, Lorkowski S, et al. Susceptibility to coronary artery disease and diabetes is encoded by distinct, tightly linked SNPs in the ANRIL locus on chromosome 9p. Hum Mol Genet. Mar 15 2008;17(6):806-814.

Date proposal received: 
Wednesday, 13 May, 2009
Date proposal approved: 
Wednesday, 13 May, 2009
Keywords: 
Blood Pressure, Genetics
Primary keyword: 

B817 - The contribution of mixed dishes to fruit vegetable intake in children MSc project 2009 - 07/05/2009

B number: 
B817
Principal applicant name: 
Dr Pauline Emmett (University of Bristol, UK)
Co-applicants: 
Dr Jane Thomas (University of Hull, UK), Dr Emma Copeland (King's College London, UK)
Title of project: 
The contribution of mixed dishes to fruit & vegetable intake in children (MSc project 2009).
Proposal summary: 

There are many dishes that people eat regularly in Britain that have fruit or vegetables incorporated within them. These include fruit pies and crumbles, traditional stews/ casseroles/spaghetti bolognese/ pizza/ curry and even beef burgers. Fruit and vegetables eaten in this way are not included in the normal fruit and vegetable (F & V) categories which usually cover only separately described fruits and vegetables. Therefore when assessing dietary intake using these usual F & V food groups fruits and vegetables eaten in mixed dishes are usually not included. It may be that a substantial proportion of some people's intakes of F & V are taken in this way so that omitting them could be giving misleading results.

This research would assess the likely percentage of F & V within the mixed dishes eaten by the children in ALSPAC at 7,10 & 13 years. Computer programs will be prepared by the student that combine all the foods within percentage bands of F & V content so that a percentage of each food can be calculated and new food groups produced for mixed dishes. The programs will be run against the diet diary data, collected at 7, 10 & 13 years, by Pauline Emmett and the new food group files produced returned to the student. Kate Northstone will act as data buddy for this project and the data will be incorporated into ALSPAC food group datasets for future analysis.

The student will investgate the contribution of F & V from mixed dishes to total intake and assess what impact not including this data has on overall intake in each age group and within groups defined by maternal education.

This project has potential to be developed into a publishable paper. The student could be encouraged to take this as far as possible within the time constraints.

Date proposal received: 
Thursday, 7 May, 2009
Date proposal approved: 
Thursday, 7 May, 2009
Keywords: 
Diet
Primary keyword: 

B819 - Identification of genetic factors determining human head circumference - 06/05/2009

B number: 
B819
Principal applicant name: 
Dr Andrew Jackson (MRC Human Genetics Unit, UK)
Co-applicants: 
Dr Nic Timpson (University of Bristol, UK), Prof Alan Wright (MRC Human Genetics Unit, UK)
Title of project: 
Identification of genetic factors determining human head circumference.
Proposal summary: 

The mammalian brain has undergone significant expansion in its evolution to man, and is over 3 times bigger than our closest primate relatives (1). The longterm research interests of the Jackson laboratory are in brain size. Head circumference is highly correlated with brain size, and is used clinically as a proxy measurement for brain volume. To date our major work has been in the identification and functional analysis of genes causing marked reduction in head circumference/brain size (Primary Microcephaly/Seckel syndrome,ref. 2-6). Several genes have been identified, all of which have centrosomal functions (6-8). Two of these, ASPM and MCPH1 have been found to undergo significant adaptive evolution in primates (9,10). However, to date, variants in these genes have not been found to be associated with normal population variation in head circumference/brain size (11).

Following on from the identification of Mendelian genes for these disorders of extreme reduction in head circumference (-4 to -10sd), it is now of interest to identify the factors responsible for variation in head circumference and brain size in the general population.

Within the Human Genetics Unit, head circumference has been measured as a QTL in ongoing GWAS studies in Croatia and Orkneys. To increase the power of these studies we now plan to perform metaanalyses in conjunction with other cohorts to identify SNPs associated with determining head circumference in the general population. The ALSPAC cohort provides an ideal cohort to combine with our studies, particularly given that genotyping has been performed on the same 317 platform, and the availability of a larger cohort for replication/confirmation, of positive hits. (If required, such validation work through genotyping of candidate SNPs would be performed by Nic Timpson on the ALSPAC cohort for within cohort replication/confirmation)

Once identified, and validated, such genes contributing to variation in head cirucmference, will be functionally characterised at the cellular level and in model organisms, using approaches already established in ongoing work in the lab to characterise the MCPH1 and PCNT genes. Such work, will address whether such variants are acting in developmental pathways already implicated by mendelian genetics in brain size determination.

1. Ponting, C. & Jackson, A.P. Evolution of primary microcephaly genes and the enlargement of primate brains. Curr Opin Genet Dev 15, 241-8 (2005).

2. Griffith, E. et al. Mutations in pericentrin cause Seckel syndrome with defective ATR-dependent DNA damage signaling. Nat Genet 40, 232-6 (2008).

3. Brunk, K. et al. Microcephalin coordinates mitosis in the syncytial Drosophila embryo. J Cell Sci 120, 3578-88 (2007).

4. Alderton, G.K. et al. Regulation of mitotic entry by microcephalin and its overlap with ATR signalling. Nat Cell Biol 8, 725-33 (2006).

5. Trimborn, M. et al. Mutations in Microcephalin Cause Aberrant Regulation of Chromosome Condensation. Am J Hum Genet 75, 261-266 (2004).

6. Jackson, A.P. et al. Identification of microcephalin, a protein implicated in determining the size of the human brain. Am J Hum Genet 71, 136-42 (2002).

7. Bond, J. et al. Protein-Truncating Mutations in ASPM Cause Variable Reduction in Brain Size. Am J Hum Genet 73, 1170-7 (2003).

8. Bond, J. et al. A centrosomal mechanism involving CDK5RAP2 and CENPJ controls brain size. Nat Genet 37, 353-5 (2005).

9. Evans, P.D. et al. Adaptive evolution of ASPM, a major determinant of cerebral cortical size in humans. Hum Mol Genet 13, 489-94 (2004).

10. Evans, P.D., Anderson, J.R., Vallender, E.J., Choi, S.S. & Lahn, B.T. Reconstructing the evolutionary history of microcephalin, a gene controlling human brain size. Hum Mol Genet 13, 1139-45 (2004).

11. Timpson, N., Heron, J., Smith, G.D. & Enard, W. Comment on papers by Evans et al. and Mekel-Bobrov et al. on Evidence for Positive Selection of MCPH1 and ASPM. Science 317, 1036; author reply 1036 (2007).

Date proposal received: 
Wednesday, 6 May, 2009
Date proposal approved: 
Wednesday, 6 May, 2009
Keywords: 
Face Shape , Genetics
Primary keyword: 

B820 - Replication of GWAS for Maternal and Fetal Genotype Associations with Birthweight - 05/05/2009

B number: 
B820
Principal applicant name: 
Prof William J Lowe (Northwestern University, USA)
Co-applicants: 
Dr Nic Timpson (University of Bristol, UK), Prof George Davey Smith (University of Bristol, UK), Dr Rachel Freathy (Peninsula Medical School, University of Plymouth, UK)
Title of project: 
Replication of GWAS for Maternal and Fetal Genotype Associations with Birthweight.
Proposal summary: 

Fetal growth is determined by interactions between fetal genes and the maternal uterine environment. We are performing a genome wide association study (GWAS) to address the hypothesis that gene-environment interactions in the context of the maternal-fetal unit impact fetal size at birth and maternal metabolism. This is being accomplished using Caucasian, Hispanic, and Afro-Caribbean DNA samples collected from mothers and offspring as part of the NIH-funded Hyperglycemia and Adverse Pregnancy Outcome (HAPO) Study. HAPO is a multicenter, international study in which high quality phenotypic data related to fetal growth and maternal glucose metabolism was collected from 25,000 pregnant women of varied racial backgrounds using standardized protocols that were uniform across centers. A major strength of HAPO is the large number of subjects available for replication. In addition to the samples analyzed in the initial GWAS, there are additional cohorts of Caucasian, Asian and Israeli Arab/Bedouin and Jewish mothers and babies which are available for replication of the initial GWAS findings. Importantly, phenotype data related to fetal growth and maternal metabolism was collected from these mothers and babies using standardized protocols that were uniform across centers and identical to those used to phenotype subjects in the initial GWAS. In this initial replication study, we intend to focus efforts on a phenotype for which: (i) there are not other ongoing, large GWAS efforts and (ii) there are large replication cohorts from the same ethnic background available. Thus, this study aims to replicate the contribution of maternal SNPs to offspring birth weight and the contribution of fetal SNPs before and after correction for maternal genotype to offspring birth weight. Importantly, our proposal takes advantage of one of the unique strengths of HAPO, access to GWAS data from both mothers and their offspring, and we will be able to consider the contribution of both offspring and maternal genetic variation to the regulation of birth weight. We intend to use a two-stage replication approach by including an additional large cohort of Caucasian subjects from the UK who were recruited under the auspices of the Exeter Family Study of Childhood Health (EFSOCH) and ALSPAC. This project has the following specific aims.

1. To perform a two stage replication of the GWAS results from maternal SNP vs. offspring birth weight associations. We will take 115 SNPs into 2,556 Stage 1 maternal replication samples and a further 15 SNPs into 11,000 Stage 2 maternal replication samples and perform a joint analysis on greater than 15,000 mothers.

2. To perform a two stage replication of the GWAS results from fetal SNPs vs. offspring birth weight associations, including analyses corrected for maternal genotype. We will take 115 SNPs into 2,669 Stage 1 offspring replication samples and a further 15 SNPs into 11,000 Stage 2 offspring replication samples and perform a joint analysis on greater than 15,000 offspring.

The first aim of our study is to investigate, genome-wide, the association between maternal genotype and offspring birth weight. This aim does not overlap with current aims of the EGG consortium.

Since we are also interested in the association between fetal genotype and offspring birth weight, there is some overlap between our proposed analyses and the current GWAS meta-analysis (including 1500 ALSPAC offspring) being carried out by the EGG consortium. However, our proposed analysis is distinct from these efforts because we will adjust for maternal genotype at the genome-wide stage and follow up hits based on those data. To our knowledge, other than in HAPO, there are no existing genome-wide association studies with both maternal and fetal genotype data on large numbers of subjects. It is important to point out that whereas the proposal amendment for B768 asks for the genotyping of top hits from a fetal-only genome-wide study in EGG to test in replication samples whether these top hit are independent of maternal genotype, our proposal is to follow up hits from a genome-wide study that is already adjusted for maternal genotype.

Another feature of HAPO that is distinct from the current EGG collaboration is that genome-wide data are available on different ethnic groups: Afro-Caribbean and Hispanic, in addition to European. This may lead to the prioritisation of different top hits for follow-up, as was seen with the recent discovery of the KCNQ1 gene for type 2 diabetes (Unoki et al and Yasuda st al, 2008 Nat Genet).

Recent successes from genome-wide association studies have highlighted the need for collaboration between centers to provide sufficient power to detect modest effects of common genetic variants. For early growth traits, efforts are already underway in the EGG consortium to ahieve this for fetal genotype vs. birth weight. We acknowledge that the current combined genome-wide fetal genotype sample in EGG exceeds our own fetal genotype sample, and that the contribution of HAPO may be better placed in the wider consortium in regard to this aim. Like ALSPAC, the HAPO group is keen to participate, where possible, in the EGG consortium and the emerging EAGLE consortium once we have examined our own genome-wide data.

In Stage 1 of the planned replication study, we will genotype 115 offspring SNPs for size at birth in 2,669 additional Caucasian subjects from the HAPO study as well as 115 maternal SNPs for size at birth in 2556 Caucasian HAPO mothers. The genotypes from the Stage 1 replication study will be analyzed together with the genotypes from the 1500 mothers and offspring analyzed in the original GWAS. From these analyses, we will identify the 15 most significant offspring SNPs for birth weight and 15 most significant maternal SNPs for offspring birth weight. These will then be typed in the ALSPAC mothers and offspring. Thus, from ALSPAC, we will need offspring birth weight data and additional data that will need to be controlled for in the analyses (gestational age of the neonate at the time of delivery, neonatal gender, parity, maternal age, BMI, and blood pressure). We will also need genotype data. As noted, the SNPs to be genotyped will be determined from analysis of the GWAS and Stage 1 replication study. We are planning that the ALSPAC samples will be genotyped at Kbiosciences. We will pay for the genotyping using the resources of the grant from the NIH.

Date proposal received: 
Tuesday, 5 May, 2009
Date proposal approved: 
Tuesday, 5 May, 2009
Keywords: 
Birth Outcomes, GWAS
Primary keyword: 

B815 - DIUS Shopping List - 28/04/2009

B number: 
B815
Principal applicant name: 
Ms Lynn Molloy (University of Bristol, UK)
Co-applicants: 
Ms Kerry Humphries (University of Bristol, UK)
Title of project: 
DIUS Shopping List.
Proposal summary: 

ALSPAC proposes to use the funding from DCSF (£30,000 in the first year and £55,000 in the second year) towards increasing participation in the ALSPAC study.

In June 2009, ALSPAC executive commissioned the Social Marketing Department at University of West of England to conduct research into how ALSPAC could increase participation in the study. A literature search was carried out which revealed that recruiting and retaining 16-18 year olds in longitudinal cohort studies is a common problem. This is because it is a difficult time for them with hugely conflicting demands over their time and energies. They tend to be very busy and prefer not to adhere to strict timetables or commit to long-term research projects. This has been evident in our recent participation rates for clinic and questionnaires which shows a marked difference from even a year ago. The literature review confirms that although retention is challenging, it can be done, as long as there is an in depth understanding of what moves and motivates young people.

Focus groups were held with participants from the ALSPAC study to try and find out more about what motivates them and what would keep them engaged in the project. Those interviewed were 17 or 18 years old and were from a diverse range of social and study participation backgrounds. Of particular interest were the participants who had completely disengaged from the study. The interviews were analysed and the findings were used to develop strategies that could increase participation. A plan has been devised to implement these strategies over the next two years. This coincides with the remainder of the DCSF funding data collection, Focus at 17 and the 18 year questionnaire.

Findings from these initiatives will be disseminated amongst the research community and hold many benefits for other longitudinal cohort studies, e.g. LSYPE. As previously mentioned, attrition is a major problem in all longitudinal studies, especially amongst young people, and if ALSPAC can show that certain strategies are successful in retaining young people in the study then these techniques can be transferred to LSYPE and other research projects. The DCSF have invested a considerable amount of money into the development of the ALSPAC data set, and through data linkage ALSPAC will continue to collect further education data from the National Pupil Database. The proposed engagement initiatives will enable future data collection to add outcome data to the resource. This significant data set will enable the DCSF to continue to track the young people and their educational achievements and aspirations which could inform their policy making.

ALSPAC intend to fully evaluate each of the initiatives described below with a view to assessing which was the most successful in terms of increasing the participation rate and why. Firstly, we will undertake background research to examine the effectiveness andefficiencyof similar initiatives elsewhere and learn from the most successful of these. Secondly, we will clearly identify the aims and objectives of each initiative and judge the outcome of the activity against these aims and objectives. We will regularly run focus groups and other participatory activities to sound out our participants views on the various activities we are running and if appropriate adapt the activity accordingly.

We believe that the following initiatives are those most likely to improve participation in the study over the next two years.

Year One (November 2009 - March 2010)

  1. New Media techniques

In the first year the focus will be on using marketing and new media techniques in order to 'reach out' to the young people in the cohort. The social marketing report highlighted very strongly that "the internet is a social crutch of huge importance" to the cohort members. They communicate primarily through social networking sites such as Facebook. To maintain contact and credibility with the teenagers, it is essential that ALSPAC fully engages with this online world. In addition to straightforward communication, we need to build online communities which will maintain cohort loyalty, particularly now that the members are dispersing geographically as they get jobs or go to college. ALSPAC already has a presence on Facebook and YouTube, but to make the most of the enormous potential of the internet we need specialist help to develop, execute and monitor a long-term online strategy. This work would include establishing and moderating networks and forums, orchestrating 'viral' and 'buzz' marketing, and creating unique games. Marketing research stressed the importance of these techniques within this age group. It would also include constant monitoring of the ever-changing online world and how the age group inhabits it. Facebook leads the field at the moment - but in a few months it may fall out of fashion. ALSPAC need to stay one step ahead and to keep the cohort members engaged. Specialist youth/digital marketers will ensure that ALSPAC always puts across the right messages in the right media. One idea is to use 'key peers' to engage with the cohort. The key peers will be the 'popular' young people who have lots of influence over a wide range of other young people including those who are disengaged in the study. They will be commissioned to provide content for the ALSPAC facebook site, to comment on ALSPAC on their Facebook page, as well as upload photos of ALSPAC events. Through the use of age appropriate materials and the involvement of influential peers we aim to encourage their 'friends' on Facebook to become interested in what ALSPAC is all about and to get them re-engaged.

  1. Targeted Messages

In order that ALSPAC reaches out to the whole cohort it is important to target the young people as three separate groups; the engaged, recently dropped off, the disengaged. The report made it very clear that involving these three groups in the study would require three different strategies. For example, the young people who were engaged with the study wanted to find out more about the 'Science', whereas the recently dropped off and disengaged could be motivated by incentives. We would like to commission specialist help in assisting us with formulating targeted messages to each of these groups and the way in which this message should be delivered. Funding is also necessary in order to give these incentives; they are likely to range from vouchers for Amazon.co.uk to offering custom 'fitness testing' sessions based on ALSPAC scientific expertise. This would make sure that the three separate groups were catered for.

Year Two (April 2010 - March 2011)

1. Club Membership

The focus for the funding in the second year will be on introducing 'club membership' to all those originally eligible for the study as they turn 18 years of age. This is something that all of the young people taking part in the focus groups were very enthusiastic about. The idea behind this is to keep all of the YPs engaged in the study and to give ALSPAC more of a presence in their everyday lives. It would be similar to an NUS card but will be free to join. The young people will be given a membership card which will entitle them to discounts on various items that could include: nationwide shops/cinemas, a free bus/rail card etc and entry to ALSPAC events (e.g. CV writing, fitness assessment, parties and comedy nights) and competitions. More importantly, it will sustain a link between ALSPAC and them. ALSPAC will be able to keep them updated with what they are doing and what clinics/questionnaires are currently running. For instance, using their membership card, they will be able to use their 'username' to access online questionnaires etc. Evidence has shown that questionnaires are becoming less popular than they were; especially with boys. Short online questionnaires are one way in which to address this problem and if it can be linked in with a membership scheme where there will be incentives to fill out the questionnaire then this will hopefully keep the young people on board with the study. The DCSF funding will go towards setting this up and the ongoing development of the scheme.

Costs

These initiatives will cost £30,000 in Year 1 and £55,000 in Year 2. The costs are broken down below:

Year 1

  • New media techniques - £10,000
  • Specialist expertise - £5,000
  • Incentives - £15,000

Year 2

  • Club membership - £45,000
  • Continuing new media techniques - £10,000

Summary

ALSPAC is at a critical phase of its development. There is serious concern that as the study participants enter young adulthood they will desert the study. We are very encouraged by the findings of this recent work we have undertaken as it shows that attrition is not inevitable and that with further funding there are strategies that can be put in place to increase participation. These initiatives are likely to attract particpants across the social spectrum which has major advantages in terms of representiveness of the study.

Date proposal received: 
Tuesday, 28 April, 2009
Date proposal approved: 
Tuesday, 28 April, 2009
Keywords: 
Cross Cohort Study
Primary keyword: 

B814 - Children born prematurely compared to children born full term in terms of contrast sensitivity contour interaction and circle deformation visual acuity stereoscopic vision and accommodation at age seven data from the ALSP - 23/04/2009

B number: 
B814
Principal applicant name: 
Miss Nicola Jackson (University of Bristol, UK)
Co-applicants: 
Miss Cathy E M Williams (University of Bristol, UK), Dr Kate Northstone (University of Bristol, UK)
Title of project: 
Children born prematurely compared to children born full term in terms of contrast sensitivity, contour interaction and circle deformation, visual acuity, stereoscopic vision and accommodation at age seven: data from the ALSPAC Study.
Proposal summary: 

(No outline received).

Date proposal received: 
Thursday, 23 April, 2009
Date proposal approved: 
Thursday, 23 April, 2009
Keywords: 
Birth Outcomes
Primary keyword: 

B812 - The Geography of Fast Food and Childhood Obesity - 23/04/2009

B number: 
B812
Principal applicant name: 
Dr Lorna Taylor (University of Leeds, UK)
Co-applicants: 
Prof Graham Clarke (University of Leeds, UK), Prof Janet Cade (University of Leeds, UK), Dr Kimberley Edwards (University of Leeds, UK)
Title of project: 
The Geography of Fast Food and Childhood Obesity.
Proposal summary: 

Background

Obesity in children, and adults, is a rapidly growing problem in the UK and worldwide and has been increasing at accelerating rates in more recent years. It is associated with a number of co-morbidities in childhood and with increased risk of adult disease, particularly cardiovascular disease, hypertension and type 2 diabetes. Obesity related diseases account for a substantial proportion of costs of health care resources worldwide (WHO, 2004). The Select Committee Report on Obesity (2004) estimated that the total cost of treating obesity in the UK was £3.3-3.7 billion in 2002, increasing to £7 billion by 2020, and the latest estimates (Foresight report, 2007) put it at £45.5 billion by 2050.

A dietary risk factor for obesity is a high consumption of high fat, salt and sugar (HFSS) foods, and in particular "fast foods" (energy dense, nutrient poor, foods) (Reidpath et al, 2002; Mendoza et al, 2007; Procter, 2007a). The popularity of fast foods has increased over recent years and consumption by children has risen 300% over the last twenty years (St-Onge et al, 2003). It has been shown that on days when children eat fast food, then their energy and fat intake is likely to be higher, and fruit and vegetable intake lower, than normal (Bowman et al, 2004). Also children who eat fast food frequently consume more total energy, more energy per gram of food, more total fat, more total carbohydrate, more added sugars, and less fibre, less milk, fewer fruit and vegetables than children who eat fast food infrequently (Bowman et al, 2004; Speiser et al, 2005). Accordingly, it may not be the consumption of fast food, per se, that leads to obesity (as both lean and obese people consume fast food), but the fact that overweight consumers of fast food are less likely to adjust their daily energy intake to take account of an energy dense fast food meal than their lean counterparts (Ebbeling et al, 2004). This "passive over-consumption" is due to the weak innate ability of humans to identify energy dense foods and thus do not correspondingly reduce the amount of food eaten to achieve energy balance (Prentice & Jebb, 2003).

Household income has been shown to be a significant predictor of obesity (inverse relationship) (Strauss & Knight, 1999; Stamatakis et al, 2005), as has deprivation (Kinra et al, 2000; Kinra et al, 2005) and low socio-economic status (SES) (Parsons et al, 1999; Hardy et al, 2000; Okasha et al, 2003; Monden et al, 2006). The increased prevalence of obesity from more deprived backgrounds could be due to a multitude of factors: dietary differences are often apparent; lack of opportunity / funds for activities, so TV viewing is the primary leisure activity by default; constraints on calories per pound, which focuses purchases on energy dense foods. Also the association between SES and obesity may be due to SES acting as a proxy for the effect of multiple adverse circumstances, which are then manifesting as obesity in the long term (Power & Parsons, 2000). For example, it has been shown that there is a higher density of fast food outlets in poorer areas, which may (partially) explain the phenomenon (Reidpath et al, 2002). Obesity and deprivation may be connected due to the routine consumption of a high energy dense, low cost diet (Drewnoski, 2003). Energy dense diets are associated with lower diet quality and lower costs, and vice versa (Cade et al, 1999; Darmon et al 2004; Andrieu et al, 2006; Drewnoski et al, 2007). Research shows that low income households are associated with a high energy dense diet (Mendoza et al, 2006).

There is a large literature contending that the environment, particularly that of our place of residence or school/work, impacts on health related behaviour and therefore health outcomes (Macintyre et al, 2002; Mohan et al, 2005). This increased interest in the effect of place on health seems to stem from the publication of the Black Report some twenty-five years ago (Black et al, 1980). Since then many authors have shown that deprivation is related to mortality as well as to specific health outcomes. An important debate within health geography is that of whether the environment has compositional or contextual effects on health. That is, the issue of whether individual or area effects on health predominate. Accordingly, the compositional school of thought is that individuals have risks of ill health, therefore an area's ill health is reflective of that of the individuals who live (or work, as appropriate) there. For example, do obese people congregate in similar locations? Conversely, the contextual theory is that living (or working) in an area imposes ill health on that area's residents. For example, do certain attributes of places cause its inhabitants to become obese? This study seeks to address the question of fast food and obesity from both contextual (the physical environment of fast food outlets) and compositional (individual consumption) perspectives

Objectives and hypothesis of project

To describe, measure and map obesity, fast food outlet density and fast food consumption in Bristol, UK(and Leeds,UK)

To investigate the relationship between density of outlets and area measures of deprivation, and to examine whether there is a dose-response relationship between deprivation and outlet density (e.g. as deprivation rises, outlet density rises).

To assess the relationship between obesity and energy dense, low nutrient ("fast") foods: availability and consumption.

To consider the policy implications of the results.

Hypothesis: Fast food outlet density and consumption will be related to the patterns of obesity. Families with the lowest incomes will be more influenced by or susceptible to these factors than higher income households.

Methods

Stage 1 - Describing and mapping obesity

The first stage in the study of spatial variations in obesity will be to build a geographic information system (GIS). The GIS will contain all the census data for Bristol/Avon Region at 'output area' (the new small area census unit), as well as the Index of Deprivation (Communities and Local Government, 2004) at 'super output area' level. This will allow us to identify areas of both low and high social deprivation. The GIS will also contain obesity data from the ALSPAC dataset.

Spatial microsimulation modelling will then be used for estimating or predicting small area levels of obesity. Specifically, we will build on the SimObesity model (a deterministic, re-weighting, spatial microsimulation model developed in the School of Geography, University of Leeds), which combines individual micro-data from national level surveys, such as the Health Survey for England (HSE), which only have location data at the scale of large areas, with census statistics for lower Super Output Areas (SOAs) to create synthetic micro-data estimates for SOAs in Leeds. The new, synthesised, micro dataset includes all the attributes from both the survey and the census datasets. The key benefits of using spatial microsimulation are: to add more attributes to the population under analysis by adding census data to the survey data thereby creating a richer dataset; to get data to a smaller geographical scale in order to identify 'hot spots' of problem areas; and it is cheaper and quicker than commissioning a survey of the local area. There is significant experience of spatial microsimulation modelling in the University of Leeds (Clarke, 1996; Ballas et al, 2005; Procter, 2007b).

Significant clusters of obesity (from both children and adults) will be identified using Spatial Scan Statistics (such as SaTScan, Kulldorff, 1997). Temporal (serial cross sectional) as well as geographic analysis will be undertaken.

Stage 2 - Relationship between fast food and obesity

Once the patterns and spatial/temporal variations of obesity have been understood, the next exercise is to consider the relationship with fast food consumption. There are two components to this analysis.

Firstly we wish to examine the relationship between fast food outlet density and obesity. This stage of the project will involve sourcing (e.g. from the council or yellow pages) the location of fast food restaurants in the study area and transposing this data into a GIS. Ground truthing of the data will also be required (i.e. physically checking the locations exist). Then fast food outlet density for output areas can be calculated and the relationship with obesity considered. The association with an area measure of deprivation will also be considered.

The next stage is to take this further, and to consider the relationship between actual fast food consumption and obesity. This Fast Food consumption data regarding diet is available from the ALSPAC cohort and will be added to the previously described GIS model. This data may be used to simulate fastfood consumption in children in other geographical areas using spatial microsimulation modelling.

Analysis of these data will involve the use of multi-level modelling and geographically weighted regression, in order that the special properties of spatial data (e.g. spatial autocorrelation) can be accounted for.

Stage 3 - Policy implications

The final stage in the project will be to consider how the results from the previous two stages can be utilised to influence policy and to help slow down the rising rates of obesity. The spatial microsimulation model will be used to undertake "what if" scenario analysis to theoretically evaluate the potential impact of policy/intervention suggestions on the prevalence of obesity in say 5, 10 or 20 years time, which is cheaper and much quicker than running a pilot study. Further, we will work with key local stakeholders (from both public and private sector, as both have a responsibility to endorse public health (Stafford et al, 2007)) to enable suggestions to be rated for validity, relevance and potential for change. This is important, as small individual programmes are unlikely to make a difference to the obesity epidemic. For maximum benefit an obesity prevention policy needs to take a coordinated, multi-component, multi-sectoral public health approach and overall policy unity and coherence is required, with buy-in of all stakeholders.

How will the research be useful and to whom

This research will be useful to the PCTs for health planning as it will identify any hot spots of problem areas of obesity. It will also elucidate further on the impact of aspects of the environment and diet on obesity and whether these issues can be addressed using public health policies, and if so, the likely future impact of such changes.

Interdisciplinary nature of the research

This project is clearly interdisciplinary. It combines the quantitative geographic techniques (such as spatial microsimulation, GIS) with those from medical research, using data from local studies as well as national cross sectional surveys. Training will be given for use of the spatial techniques (e.g. SimObesity, ArcGIS, geographically weighted regression). There is extensive experience of using these techniques within the University of Leeds, plus some external courses are available.

Timetable

Year 1/2: Develop literature review; gather information for mapping; learn techniques; carry out stage 1

Year 3/4: Carry out stage 2

Year 5/6: Carry out stage 3 and write up thesis

References

Andrieu, E., N. Darmon, et al. (2006). "Low-cost diets: more energy, fewer nutrients." European Journal of Clinical Nutrition 60(3): 434-6.

Black D, Morris J, Smith C, Townsend P (1980). Inequalities in health: report of a Research Working Group. London: Department of Health and Social Security

Bowman SA, Gortmaker SL, Ebbeling CB, Pereira MA, Ludwig DS (2004). Effects of fast-food consumption on energy intake and diet quality among children in a national household survey. Pediatrics, 113: 112-118

Communities and Local Government. The English Indices of Deprivation 2004. http://www.communities.gov.uk/index.asp?id=1128449 Accessed September 2007

Darmon, N., A. Briend, et al. (2004). "Energy-dense diets are associated with lower diet costs: a community study of French adults." Public Health Nutrition 7(1): 21-7.

Drewnowski, A. (2003). "The role of energy density." Lipids 38(2): 109-15.

Drewnowski, A., P. Monsivais, et al. (2007). "Low-energy-density diets are associated with higher diet quality and higher diet costs in French adults." Journal of the American Dietetic Association 107(6): 1028-32.

Ebbeling CB, Sinclair KB, Pereira MA, Garcia-Lago E, Feldman HA, Ludwig DS (2004). Compensation for energy intake from fast food among overweight and lean adolescents. The Journal of the American Medical Association, 291 (23): 2828-2833

Foresight Report (2007). Tackling Obesities: future choices http://www.foresight.gov.uk/Obesity/obesity_final/20.pdf Accessed October 2007

Hardy R, Wadsworth M, Kuh D (2000). The influence of childhood weight and socioeconomic status on change in adult body mass index in a British national birth cohort. International Journal of Obesity, 24 (6): 725-34

Kinra S, Nelder RP, Lewendon GJ (2000). Deprivation and childhood obesity: a cross sectional study of 20,973 children in Plymouth, United Kingdom. Journal of Epidemiology & Community Health, 54 (6): 456-460

Kinra S, Baumer JH, Davey Smith G (2005). Early growth and childhood obesity: a historical cohort study. Archives of Disease in Childhood, 90 (11): 1122-1127

Kulldorff M (1997). A spatial scan statistic. Communications in Statistics: Theory and Methods, 26: 1481-1496

Macintyre S, Ellaway A, Cummins S (2002). Place effects on health: how can we conceptualise, operationalise and measure them? Social Science and Medicine, 55: 125-39

Mendoza, J. A., A. Drewnowski, et al. (2006). "Dietary energy density is associated with selected predictors of obesity in U.S. Children." Journal of Nutrition 136(5): 1318-22.

Mendoza, J. A., A. Drewnowski, et al. (2007). "Dietary energy density is associated with obesity and the metabolic syndrome in U.S. adults." Diabetes Care 30(4): 974-9.

Mohan J, Twigg L, Barnard S, Jones K (2005). Social capital, geography and health: a small-area analysis for England. Social Science and Medicine, 60: 1267-1283

Monden CWS, van Lenthe FJ, Mackenbach JP (2006). A simultaneous analysis of neighbourhood and childhood socio-economic environment with self-assessed health and health-related behaviours. Health and Place, 12(4): 394-403

Okasha M, McCarron P, McEwen J, Durnin J, Davey Smith G (2003). Childhood social class and adulthood obesity: findings from the Glasgow Alumni Cohort. Journal of Epidemiology and Community Health, 57: 508-9

Parsons TJ, Power C, Logan S, Summerbell CD (1999). Childhood predictors of adult obesity: a systematic review. International Journal of Obesity, 23 (Suppl. 8): S1-107

Prentice AM & Jebb SA (2003). Fast foods, energy density and obesity: a possible mechanistic link. Obesity Reviews, 4 (4): 187-194

Reidpath DD, Burns C, Garrard J, Mahoney M, Townsend M (2002). An ecological study of the relationship between social and environmental determinants of obesity. Health and Place, 8: 141-145

Rudolf MCJ, Cole TJ, Krom AJ, Sahota, P, Walker J (1999). Growth of primary school children: a validation of the 1990 standards and their use in growth monitoring. Archives Disease in Childhood 83: 298-301

Rudolf MCJ, Levine R, Feltbower RG, Connor A, Robinson M (2006). The Trends project: development of a methodology to reliably monitor the obesity epidemic in childhood. Archives of Disease in Childhood; 91: 309-311

Select Committee on Health - Third Report (Obesity) (2004). Health Committee Publications, http://www.parliament.thestationeryoffice.co.uk/pa/cm200304/cmselect/cmh... Accessed December 2005

Speiser PW, Rudolf MC, Anhalt H, Camacho-Hubner C, Chiarelli F, Eliakim A, Freemark M, Gruters A, Hershkovitz E, Iughetti L, Krude H, Latzer Y, Lustig RH, Pescovitz OH, Pinhas-Hamiel O, Rogol AD, Shalitin S, Sultan C, Stein D, Vardi P, Werther GA, Zadik Z, Zuckerman-Levin N, Hochberg Z; Obesity Consensus Working Group (2005). Childhood Obesity, The Journal of Clinical Endocrinology and Metabolism, 90 (3):1871-87

Stamatakis E, Primatesta P, Chinn S, Rona R, Falascheti E (2005). Overweight and obesity trends from 1974 to 2003 in English children: what is the role of socioeconomic factors? Archives of Disease in Childhood, 90: 999-1004

St-Onge MP, Keller KL, Heymsfield SB (2003). Changes in childhood food consumption patterns: a cause for concern in light of increasing body weights. The American Journal of Clinical Nutrition, 78 (6): 1068-1073

Strauss RS & Knight J (1999). Influence of the home environment on the development of obesity in children. Pediatrics, 103 (6): e85

World Health Organisation (2004). Report of a WHO Consultation on Obesity: preventing and managing the global epidemic. WHO Technical Report Series; 894. Geneva. http://www.who.int/nutrition/publications/obesity/en/index.html (accessed Oct 2007).

Date proposal received: 
Thursday, 23 April, 2009
Date proposal approved: 
Thursday, 23 April, 2009
Keywords: 
Diet, Obesity
Primary keyword: 

B816 - Foetal and maternal genetic modifiers of the effects of prenatal tobacco exposure - 20/04/2009

B number: 
B816
Principal applicant name: 
Dr Thomas S Price (King's College London, UK)
Co-applicants: 
Prof Barbara Maughan (King's College London, UK), Sara Jaffee (King's College London, UK), Dr Alina Rodriguez (King's College London, UK)
Title of project: 
Foetal and maternal genetic modifiers of the effects of prenatal tobacco exposure.
Proposal summary: 

1. SUMMARY

Maternal smoking during pregnancy is a well-established and preventable risk factor for low birthweight and its sequelae of poor physical, cognitive and behavioural development, excess morbidity, and increased rates of both perinatal and adult mortality. Preliminary findings from genetic epidemiology studies suggest that the degree to which prenatal tobacco exposure depresses birthweight may be moderated by foetal and maternal genotype. The advent of affordable genomewide genotyping presents an opportunity for systematic investigation of this phenomenon. We propose to prioritize candidate polymorphisms using genomewide genotype data from three studies for which data is available on prenatal tobacco exposure and perinatal outcomes. We will use this information to prioritize approximately 50 single nucleotide polymorphisms (SNPs) to be genotyped in 3,500 mother-child dyads participating in ALSPAC. We will use these data to test hypotheses about the moderating effects of maternal and foetal genotype on the effects of prenatal tobacco exposure to reduce birthweight, shorten gestation, and alter postnatal physical, cognitive, and behavioural development.

2. BACKGROUND

Maternal smoking during pregnancy is a well-established and preventable risk factor for low birthweight (less than 2,500g) and its sequelae of poor physical, cognitive and behavioral development, excess morbidity, and increased rates of both perinatal and adult mortality (Kramer, 2003). The primary causes of low birthweight are preterm birth and intrauterine growth restriction (IUGR). The consequences of IUGR include both short-term and long-term morbidity and permanent deficits in growth and neurocognitive development (Kramer, 2003). Epidemiological studies have shown that maternal smoking is associated with both short gestation and IUGR (Kramer, 2003). Mothers who quit smoking while pregnant have longer gestations and heavier newborns than those who continue to smoke (Lumley, Oliver, Chamberlain, & Oakley, 1998). This fact is recognized in public policy: in the UK, formal smoking cessation programs are recommended as part of antenatal care to prevent low birthweight (Health Development Agency, 2004).

Preliminary findings from studies in genetic epidemiology, including my own research, suggest that the degree to which prenatal tobacco exposure depresses birthweight may be moderated by foetal and maternal genotype (e.g. Infante-Rivard, Weinberg, & Guiguet, 2006, T. S. Price, Grosser, Plomin, & Jaffee, 2008). The combination of affordable experimental methods for high-throughput genotyping and the availability of richly phenotyped birth cohorts for whom information is available on prenatal environmental exposures and perinatal outcomes provides an opportunity for systematic investigation of this phenomenon. I propose to study the issue using a two-phase experimental design. Phase 1 will address the issue broadly, in three large cohorts, by studying the impact on intrauterine growth of all common genetic variation. Phase 2 will address the issue deeply, in an independent sample, by looking at the downstream effects of selected polymorphisms on long-term features of postnatal development.

3. METHODS

3.1 Overview

Phase 1. Genomewide association studies to detect interactions between maternal and child genotype and maternal smoking during pregnancy on intrauterine growth. I have negotiated access to three studies with genomewide genotype data and information on prenatal environmental exposures and perinatal outcomes. Two of these studies are birth cohorts with genomewide genotype information on the children: the Twins Early Development Study (TEDS, PI R. Plomin; Trouton, Spinath, & Plomin, 2002) and the 1966 North Finnish Birth Cohort (NFBC, PI: M.-R. Jarvelin; Rantakallio, 1969). The third has genotype data from parent-child trios and siblings (IMAGE, PI: P. Asherson; Kuntsi, Neale, Chen, Faraone, & Asherson, 2006). In total, these samples comprise more than 9,000 families for whom information will be available on genomewide genotype, environmental risk exposure and perinatal outcomes. Hypotheses of genotype*environment interaction and haplotype*environment interaction will be tested genomewide in each study population. Untyped polymorphisms will be imputed using standard techniques (Marchini, Howie, Myers, McVean, & Donnelly, 2007) to ensure that the genotype set is consistent across studies and facilitate meta-analysis.

Phase 2. Replication and extension. Approximately 50 single nucleotide polymorphisms (SNPs) prioritized in the initial stage - located in the 5 genomic regions providing the best evidence of genotype-environment interaction - will be typed in an independent sample of approximately 3,500 mother-child dyads participating in the Avon Longitudinal Study of Parents and Children (ALSPAC, PI: G. Davey-Smith; Golding, Pembrey, & Jones, 2001). These data will be used to test hypotheses of genotype-environment interaction and haplotype-environment interaction on intrauterine growth and on postnatal phenotypes associated with maternal smoking during pregnancy including Attention-Deficit Hyperactivity Disorder (ADHD), cognitive ability, and height. The availability of prospective information on environmental exposure in this sample will allow hypotheses to be tested about dose-related effects and the impact of timing for mothers who quit smoking during pregnancy.

3.2 Data collection.

We propose to genotype approximately 3,500 mothers and their children participating in the ALSPAC study for approximately 50 single nucleotide polymorphisms prioritized in the first phase of the study. We will choose the 1,500 or so families in which the mother reported smoking throughout the pregnancy, an equal number of families in which the mother reported not smoking at any time during the pregnancy, plus the 500 or so families in which the mother reported smoking early in the pregnancy and subsequently quitting. The intention is to select the five regions providing the best evidence of genotype-environment interaction in phase 1, and fine map the immediate regions of linkage disequilibrium (as defined using resequencing data for Caucasian populations) in ALSPAC so as to be able to test hypotheses of haplotype-environment interaction in phase 2. Although haplotype block length is enormously variable, we anticipate an average of 10 non-redundant SNPs per region will suffice based on estimates of haplotype block length in Caucasian populations (Li & Chen, 2008).

3.3 Existing data required

Concept

Specific Measure

Person

Source

Time Point(s)

Demographic variables (age, sex, ethnicity, marital status, family structure, SES, education, employment, income etc.)

Family

Questionnaire

Antenatal

Pregnancy health variables (nulliparity, pre-eclampsia, IUGR, gestational diabetes etc.)

Mother

Questionnaire, medical records

Antenatal

Parental anthropometrics (height weight)

Mother, Father

Questionnaire

Antenatal

Pregnancy exposure variables (tobacco, alcohol and drug use; chemical exposure; diet; nutrient supplementation; stress; life events; partner cruelty; lack of social support)

Mother

Questionnaire

Antenatal

Birth/delivery variables (weight/length, placental weight, gestational age, Caesarian), perinatal health

Child

Questionnaire, medical records

Birth/perinatal period

Childhood head injury

Child

Questionnaire

Birth - 4 years

Childhood temperament

Carey

Child

Questionnaire

6-24 months

Childhood behaviour

SDQ

Child

Questionnaire

42 - 157 months

ADHD

Child

Questionnaire

166 months

Antisocial behaviour

Child

Questionnaire

169 months - 198 months

Psychotic symptoms

Child

Questionnaire

140 months - 198 months

Adolescent substance use (tobacco, alcohol, drugs)

Child

Questionnaire

157 months - 198 months

Language development

McCarthy

Child

Questionnaire

24 months

Cognitive ability

WISC

Child

Clinic test

8-10 years

Scholastic achievement

Child

Questionnaire

166 months

Anthropometrics (Height, weight)

Child

Questionnaire

Birth - 157 months

Parental antisocial behaviour (antisocial behaviour as children or adults; contact with police; criminal convictions)

Mother, father

Questionnaire

Antenatal - 145 months

Childhood postnatal experiences (maternal depression and anxiety, parental discipline)

Mother

Questionnaire

Birth - 145 months

Parental postnatal substance use (tobacco, alcohol, drugs)

Mother, father

Questionnaire

Birth - 145 months

3.4 Data Analysis.

Phase 1. Missing genotype data (including polymorphisms genotyped in at least one but less than three of the datasets) will be imputed using published methods (Marchini et al., 2007). Hypotheses about effects on birthweight (corrected for gestational age) will be tested using linear models incorporating terms for prenatal tobacco exposure, foetal genotype, interaction between foetal genotype and prenatal tobacco exposure plus relevant covariates (including significant principal components of the genetic data to guard against spurious associations due to population admixture (A. L. Price et al., 2006), demographics, pregnancy and antenatal health variables, and parental physical and behavioural characteristics). Meta-analysis will be performed to synthesize the results from the three studies. SNPs to be genotyped in phase 2 will be chosen based on the regions that show the greatest evidence of association in phase 1. Where significant results are found for foetal genotype, post hoc analyses of the influence of maternal genotype and parent-of-origin effects will be tested in the IMAGE sample.

Phase 2. Hypotheses about effects on birthweight, head circumference, and crownheel length (all corrected for gestational age) will be tested using linear models incorporating terms for prenatal tobacco exposure, maternal genotype, foetal genotype, interaction between maternal genotype and prenatal tobacco exposure, interaction between foetal genotype and prenatal tobacco exposure, and the three-way interaction between foetal and maternal genotype and prenatal tobacco exposure, plus relevant covariates (including demographics, pregnancy and antenatal health variables, and parental physical and behavioural characteristics). Analyses will be stratified by ethnicity to guard against spurious associations due to population admixture. Should statistically significant results be found, post hoc hypotheses about trajectories of postnatal physical, behavioural, and cognitive development will be tested using growth curve models and growth mixture models; in addition, mediation analyses will be conducted to test whether postnatal development is conditionally independent of genotype and prenatal tobacco exposure after controlling for any effects on birthweight and gestational age. Hypotheses about the effects of prenatal tobacco exposure will test for heterogeneity of the effects with respect to mode of exposure (maternal smoking/maternal exposure to second hand smoke), dose, and timing of smoking cessation. A parallel set of analyses will be conducted using paternal tobacco exposure as the environment of interest in order to validate the inference of intrauterine effects. Analyses will be conducted to assess the possible influence of attrition in the sample on the outcomes of interest. If necessary, informative missingness will be explicitly modelled.

3.5 Statistical Power

Phase 1. Based on the most accurate information available, we anticipate that information on genomewide genotype, prenatal environmental exposures, and perinatal outcomes will be available for children from 4,000 families enrolled in TEDS, 4,763 families participating in NFBC, and 304 families from IMAGE. We expect that the numbers of children born to mothers who reported smoking during pregnancy in these three samples will be, respectively, 568, 700, and 63. For the purposes of the power analysis let us assume a total population of N = 9,067, exposure prevalence of 14.7%, population SD of birthweight = 400g, marginal effect of maternal smoking -200g, and no marginal effect of genotype. We will use alpha = 10-6 so that if we test 2-sided hypotheses of GxE in relation to 10-6 SNPs we expect on average 1 false positive by chance. Under these assumptions we will have 80% power to detect GxE accounting for 0.356% of the variance in birthweight and 50% power to detect GxE accounting for 0.261% of the variance.

Under an additive model of inheritance, 0.261%-0.356% of the variance corresponds to GxE accounting for a difference of 102-119 g between groups differing by an allele count of 1 and with different smoking status, assuming a minor allele frequency of 20%, or 136-159 g assuming a minor allele frequency of 10%. Under a dominant model of inheritance, 0.380%-0.521% of the variance corresponds to GxE accounting for a difference of 120-141 g between groups differing in whether or not they carry a risk allele and with different smoking status, assuming a minor allele frequency of 20%, or 147-172 g assuming a minor allele frequency of 10%.In other words, for common SNPs there is good power to detect a GxE whose coefficient is similar in magnitude to the marginal environmental effect. Effect sizes of this magnitude are by no means implausible, as recent candidate gene studies have demonstrated (e.g. Sasaki et al., 2008, T. S. Price et al., 2008), but there are likely to be relatively few variants in the genome that could account for interactive effects of this size. It is for this reason that we intend to follow up only a handful of the best hits.

Phase 2. Assuming that genotype data is available for 3,000 individuals, with 50% exposure to prenatal smoking throughout pregnancy, a population SD for birthweight of 400g, a marginal effect of maternal smoking of -200g, and using 2-tailed hypotheses for each of the three phenotypes of birthweight, head circumference, and crownheel length and a conservative significance threshold of alpha = 3.3e-4 (0.05 after Bonferroni correction for 50 x3 = 150 hypothesis tests), we estimate that for the effect sizes giving 50% power in the phase 1 we expect 69% power to replicate in phase 2, and for the kinds of effect size giving 80% power in phase 1 we expect at least 88% power to replicate in phase 2.

3.6 Work already completed

We recently investigated the relations between maternal smoking, foetal genotype, and foetal growth in a dizygotic twin pairs participating in TEDS (T. S. Price et al., 2008). Maternal smoking retarded growth by 118g in twins born to mothers who reported smoking less than 10 cigarettes per day and by 185g in twins born to heavier smokers, allowing for the effects of twin sex, birth order, gestational age, and maternal and familial characteristics. We selected 497 twin pairs, whose mothers smoked, for a molecular genetic study. In this subsample, a functional SNP in the NQO1 gene (Pro187Ser; rs1800566) was significantly associated with foetal growth within families assuming a dose-related model of effects (p=0.0028). These results provide the first demonstration that foetal genotype for a xenobiotic metabolizing enzyme influences intrauterine growth under conditions of smoke exposure independently of maternal genotype.

4. REFERENCES

Golding, J., Pembrey, M., & Jones, R. (2001). ALSPAC--the Avon Longitudinal Study of Parents and Children. I. Study methodology. Paediatr Perinat Epidemiol, 15(1), 74-87.

Health Development Agency. (2004). The evidence of effectiveness of public health interventions - and the implications.

Infante-Rivard, C., Weinberg, C. R., & Guiguet, M. (2006). Xenobiotic-metabolizing genes and small-for-gestational-age births - Interaction with maternal smoking. Epidemiology, 17(1), 38-46.

Kramer, M. S. (2003). The epidemiology of adverse pregnancy outcomes: An overview. Journal of Nutrition, 133(5), 1592S-1596S.

Kuntsi, J., Neale, B. M., Chen, W., Faraone, S. V., & Asherson, P. (2006). The IMAGE project: methodological issues for the molecular genetic analysis of ADHD. Behav Brain Funct, 2, 27-27.

Li, J., & Chen, Y. (2008). Generating samples for association studies based on HapMap data. BMC Bioinformatics, 9, 44-44.

Lumley, J., Oliver, S., Chamberlain, C., & Oakley, L. (1998). Interventions for promoting smoking cessation during pregnancy. Cochrane Database of Systematic Reviews(3), Art. No.: CD001055. DOI: 001010.001002/14651858.CD14001055.pub14651852.

Marchini, J., Howie, B., Myers, S., McVean, G., & Donnelly, P. (2007). A new multipoint method for genome-wide association studies by imputation of genotypes. Nat Genet, 39(7), 906-913.

Price, A. L., Patterson, N. J., Plenge, R. M., Weinblatt, M. E., Shadick, N. A., & Reich, D. (2006). Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet, 38(8), 904-909.

Price, T. S., Grosser, T., Plomin, R., & Jaffee, S. R. (2008, Nov 11-15). Fetal genotype for the xenobiotic metabolizing enzyme NQO1 influences intrauterine growth among infants whose mothers smoked during pregnancy. Paper presented at the American Society for Human Genetics, Philadelphia, PA.

Rantakallio, P. (1969). Groups at risk in low birth weight infants and perinatal mortality. Acta Paediatr Scand, 193.

Sasaki, S., Sata, F., Katoh, S., Saijo, Y., Nakajima, S., Washino, N., et al. (2008). Adverse birth outcomes associated with maternal smoking and polymorphisms in the N-nitrosamine-metabolizing enzyme genes NQO1 and CYP2E1. American Journal of Epidemiology, 167(6), 6.

Trouton, A., Spinath, F. M., & Plomin, R. (2002). Twins Early Development Study (TEDS): A multivariate, longitudinal genetic investigation of language, cognition and behavior problems in childhood. Twin Research, 5(5), 444-448.

Date proposal received: 
Monday, 20 April, 2009
Date proposal approved: 
Monday, 20 April, 2009
Keywords: 
Smoking
Primary keyword: 

B813 - The assessment of loci associated with varying levels of IL6 through the use of Genome Wide Association Studies - 20/04/2009

B number: 
B813
Principal applicant name: 
Prof Tim Frayling (Peninsula Medical School, University of Plymouth, UK)
Co-applicants: 
Dr Andrew R Wood (Peninsula Medical School, University of Plymouth, UK), Dr Michael N Weedon (Peninsula Medical School, University of Plymouth, UK), Dr Nic Timpson (University of Bristol, UK), Prof George Davey Smith (University of Bristol, UK), Dr Luigi Ferrucci (National Institute on Ageing, USA), Dr Stefania Bandinelli (National Institute on Ageing, USA)
Title of project: 
The assessment of loci associated with varying levels of IL6 through the use of Genome Wide Association Studies.
Proposal summary: 

Interleukin-6 (IL6) is a key pro-inflammatory cytokine involved in the acute-phase response and is associated with a number of diseases, including Type 2 Diabetes.

We plan to do an IL6 genome-wide association study meta-analysis of 1410 ALSPAC individuals with 1210 individuals from the InCHIANTI study. We will require IL6 levels, age and gender adjusted results and combine using an inverse variance approach. We will perform genome-wide analyses and also cis-effect analyses for variants in or near (+/- 300kb) the genes coding for IL6 or IL6R - encoding for the IL6 receptor. IL6R SNPs have been previously associated with IL6 levels and can act as positive controls (Melzer et. al 2008).

Having meta-analysed this data, we then plan to replicate our initial findings using ~5000 additional children with IL6 measured from the ALSPAC study in order to determine loci that are robustly associated with varying levels of IL6. Potentially, this may involve ~10 top hits (or candidate hits) from the meta-analysis, although the exact number of SNPs we will follow up will depend on the false discovery rate/QQ plot statistics.

Note also that the InCHIANTI study has been approached by another GWAS consortium looking at IL6 levels (based around the Sardinia study) with a view to replicating their results. In the event that the GWAS meta-analysis of ALSPAC and InCHIANTI does not produce any stand out results, we would suggest that the best next step will be to join ALSPAC and InCHIANTI into an expanded IL6 GWAS consortium. Although making the relative contribution of ALSPAC and INCHIANTI smaller, it will increase power substantially and help identify variants that influence IL6 levels, something that could be useful for Mendelian Randomisation studies.

Date proposal received: 
Monday, 20 April, 2009
Date proposal approved: 
Monday, 20 April, 2009
Keywords: 
Mendelian Randomisation
Primary keyword: 

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