Lecture 16 Regulatory variation and eQTLs Chris

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Lecture 16 Regulatory variation and eQTLs Chris Cotsapas cotsapasbroadinstitute.org 6.0476.878HST.507 Computational Biology: Genomes, Networks, Evolution Module 4: Population Evolution Phylogeny L1516: Association mapping for

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Lecture 16 Regulatory variation and eQTLs Chris Cotsapas
cotsapas@broadinstitute.org 6.047/6.878/HST.507 Computational Biology: Genomes, Networks, Evolution<br>
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Module 4: Population / Evolution / Phylogeny L15/16: Association mapping for disease and molecular traits
Statistical genetics: disease mapping in populations (Mark Daly)
Quantitative traits and molecular variation: eQTLs, cQTLs
L17/18: Phylogenetics / Phylogenomics
Phylogenetics: Evolutionary models, Tree building, Phylo inference
Phylogenomics: gene/species trees, coalescent models, populations
L19/20: Human history, Missing heritability
Measuring natural selection in human populations
The missing heritability in genome-wide associations
And done! Last pset Nov 11 (no lab), In-class quiz on Nov 20
No lab 4! Then entire focus shifts to projects, Thanksgiving, Frontiers<br>
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Today: Regulatory variation and eQTLs Quantitative Trait Loci (QTLs), Regulatory Variation
Molecular phenotypes as QTs: expression, chromatin…
Discretization: a GWAS for each gene. Cis-/Trans-eQTLs
Underlying regulatory variation: eQTLs, GWAS, cis-eQTL
Finding trans-eQTLs (distal from gene that varies)
Challenges: Power, structure, sample size
Cross-phenotype analysis: trans QTLs affect many genes
Identifying underlying regulatory mechanisms
Cis-eQTLs: TSS-distance, cell type specificity
eQTLs vs. GWAS: Expression as intermediate trait
Population differences, emerging efforts
Shared associations, SNP-gene pairs, allelic direction
Confound: environment, preparation, batch, ancestry<br>