Genetic Variation Impacting Methylome and Transcriptome in Primary Immune Cells of Multiple Sclerosis Patients
Tomi Pastinen, MD, PhD
Wednesday, October 22, 2014
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Chapters
Introduction
Non-coding regulatory variants and disease susceptibility
Multiple Sclerosis Loci vs. Allelic Expression or Expression QTL Mapping (AEM, eQTL)
Genome-wide perturbation of immune-cell regulators in MS
Strategy to dissect known loci and complete map of immunogenetic alterations in MS
Open chromatin: ATAC-seq. – identifying candidate regulatory elements
Direct interrogation of function by allele specific assays: depth, depth, depth
Strategy to dissect known loci and complete map of immunogenetic alterations in MS
ImmunoSeq. (v3) design on Roche SeqCap EZ Developer Target Enrichment System
In silico assessment of ImmunoSeq.
Accuracy and sensitivity in ImmunoSeq v.3 production
Rare non-coding variants increase allelic variance in gene expression (CD8+, GERP++>2)
Rare variants and highly differentially expressed genes
On-going work applying ImmunoSeq. v3
Pilot studies on ImmunoSeq. v3
Strategy to dissect known loci and complete map of immunogenetic alterations in MS
Capture Methylome Immune V1 (Roche SeqCap Epi Developer Enrichment System)
On-going applications of ImmuneV1
Applications of ImmuneV1 Capture Methylome in Disease Studies
Application – Genotyping
Capture Methylome: Allele-specific methylation (ASM)
Capture Methylome– ASM (continued)
ASM is enriched at cis-rSNPs
Integrative analyses with allele-specificity
Allelic correlation: linking functional elements to altered gene expression
Summary
Acknowledgements
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