Haplotypes for association studies: estimation from genotypes and tagging

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Outline

Background

SNP and Genotypes

IL18R1 Genotypes, 2 Samples

SNP - Visual Genotype

SNP - Ordered Visual Genotype

Slide 8

Haplotypes: Definition

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Haplotypes: Why the fuss?

Haplotypes: Inference

Haplotypes: ML methods

IL18R1 Haplotypes Inferred by SNPHAP

Haplotypes: Bayesian methods

IL18R1 Haplotypes inferred by Phase

Slide 17

Slide 18

Slide 19

5 htSNP for >5% Haplotypes?

1 set of 5 3 sets of size 4

Finding htSNP: The Problem

Finding htSNP: Brute force

BEST - algorithm for htSNP

IL18R1 - by eye?

Repeat Masked SNP Flanks

Slide 28

BEST - benefits

Slide 30

Author: Ross Lazarus

Homepage: https://innateimmunity.net/