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Epigenetic Studies in ALSPAC

Epigenetic Studies in ALSPAC. Caroline Relton CAiTE Symposium 12 th January 2010. Objectives. Define DNA methylation variation due to DNA source and extraction method Quantify changes in DNA methylation over time

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Epigenetic Studies in ALSPAC

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  1. Epigenetic Studies in ALSPAC Caroline Relton CAiTE Symposium 12th January 2010

  2. Objectives • Define DNA methylation variation due to DNA source and extraction method • Quantify changes in DNA methylation over time • Validate differential DNA methylation at selected target loci in serial DNA samples • Undertake pilot MeDIP-sequencing of the entire methylome • Quantify differential DNA methylation in pre- and post-menopausal women • Apply a Mendelian randomisation approach to strengthen evidence for a causal relationship between environmental exposures, DNA methylation and childhood outcomes • Develop bioinformatic and statistical approaches for handling DNA methylation data

  3. Define DNA methylation variation due to DNA source and extraction method Average beta (Me/unMe) Avg Beta, Phenol 114 probes more methylated in guanidine extracted DNA (> 1.5-fold) Buffy coat White cells Whole blood Avg Beta, Guanidine

  4. Quantify changes in DNA methylation over time • SequenomEpiTyper • 6 amplicons • 12-21 CpG sites per amplicon • Birth and 7y DNA • N=90 • Correlation is much lower than that observed in adults at 2 time points • Additional samples are being analysed Highest intra-probe correlations B = bootstrapped

  5. Validate differential DNA methylation at selected target loci Methylation at birth and body composition in childhood SNP-dependent locus associated with insulin resistance Methylation at CpGvs rs231840 BMI Fat mass Lean mass Methylation (%) Change in outcome / 1% in methylation Genotype (rs231840)

  6. Undertake pilot MeDIP-sequencing of the entire methylome • High vs normal BMI • Aged 0y, 7y and 15y • N=10 per group • MeDIP-seq pilot • Illumina 27K array Quantitative comparison of genome-wide DNA methylation mapping technologies ChristophBock, EleniM Tomazou, ArieB Brinkman, FabianMüller, FemkeSimmer, HongcangGu, Natalie Jäger, Andreas Gnirke, HendrikG Stunnenberg & Alexander Meissner Nature Biotechnology : 28: 1106–1114 (2010)

  7. Quantify differential DNA methylation in pre- and post-menopausal women Pregnancy vs +17y • 1032 CpG sites differ +/- 5% Average methylation for 5 largest methylation shifts in each direction with SD error bars Avg beta Post MP Avg beta Pre MP Pre vs Post menopause • 199 CpG sites differ +/- 5%

  8. CVD CVD CVD CVD CpG CpG CpG CpG BMI BMI BMI Apply a Mendelian randomisation approach ADH1B Reverse causation Alcohol CpG HNSCC Confounded Socio-economic position Nutritional status Smoking On causal pathway Alternative non-epigenetic pathway Independent and both causal

  9. Develop bioinformatic and statistical approaches Defining where in the genome to look for differential methylation • In silicotools • CGI Explorer • Data mining tools • Transcription factor binding sites • Gene expression data • Whole methylome analysis • MeDIP-seq • Genome-wide site-specific analysis • Illumina 450k array • Targeted approaches • IlluminaVeraCode Analysing DNA methylation data • Large data sets • Highly correlated • Non-normal distribution • Outlier effects • Temporal variation • Tissue specificity • Differences in DNA source and method used • Illumina • Sequenom • Pyrosequencing • Relationship between genotype and epigenotype

  10. Grant submissions and future plans • Grants awarded • WT/MRC Strategic Award (GDS) • WT ALSPAC Mums (DAL) • MRC Fellowship (LZ) • Grant submitted • NIH Conduct problem trajectories (EB) • NIH Obesity and epigenetics (CR) • MRC ALSPAC Mums (DAL) • BBSRC BBR (GDS) • Grants in preparation • MRC Obesity and epigenetics (CR) • NIH methylation trajectories in development and ageing (CR) • Future directions • Prostate cancer (RM) • Insulin resistance/T2D (CR) • Air pollution and respiratory phenotypes (JH, PV, PE) • UV exposure (JT, AS) • Geneticalepigenomics (GDS) • Other longitudinal studies (MCS, NSHD (1946), Bto20, IMS, APCAPS, Barshi)

  11. Acknowledgements • George DS • Debbie L • Sue R • Wendy M • BeateStP • Tom G • Adrian S • Jon T • Luisa Z • Nic T • Kate T • Kate N • Hannah Elliott • Alix Groom

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