Whole-genome prediction of complex traits using kernel methods

  • View
    426

  • Download
    1

Embed Size (px)

DESCRIPTION

Presented at my Ph.D. thesis defense. University of Wisconsin-Madison.

Text of Whole-genome prediction of complex traits using kernel methods

  • 1. Whole-genome prediction of complex traits using kernel methods Gota Morota May 12, 2014 1 / 31

2. Outline Part 1: Kernel-based whole-genome prediction method Part 2: Application to dairy cattle and wheat data Part 3: Application to dairy cow health traits Part 4: Application to broiler chicken data using genome annotation Part 5: Ph.D.-wide Conclusions 2 / 31 3. Quantitative genetics related individuals 3 / 31 4. Prediction of complex traits from genotypes 1) GWAS-based prediction select inuential markers rst and then predict single marker regression (2001) marker assisted BLUP (MABLUP, 1989) 2) Whole-genome prediction use all available markers simultaneously Whole-genome marker regression Kernel-based regression 4 / 31 5. How to parameterize response variable y ? 1. prediction of additive genetic effects y = E + a + 2. prediction of total genetic effects parametrically y = E + a + d + a a + a d + d d g + 3. prediction of total genetic effects non-parametrically y = E + g + 5 / 31 6. Whole-genome marker regressions 50K SNP panel (n