1 / 53

Genetic Analysis Center

Genetic Analysis Center. Department of Biostatistics, University of Washington. Cathy Laurie David Levine Cecelia Laurie Sarah Nelson Stephanie Gogarten Adrienne Stilp Caitlin McHugh Matt Conomos Quenna Wong Jean Morrison Inae Hur Deepti Jain Tin Louie. Bruce Weir Ken Rice

idalee
Download Presentation

Genetic Analysis Center

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Genetic Analysis Center Department of Biostatistics, University of Washington Cathy Laurie David Levine Cecelia Laurie Sarah Nelson Stephanie Gogarten Adrienne Stilp Caitlin McHugh Matt Conomos QuennaWong Jean Morrison InaeHur Deepti Jain Tin Louie Bruce Weir Ken Rice Tim Thornton Sharon Browning Brian Browning Katie Kerr Adam Szpiro

  2. Figure 4

  3. SNP set A All autosomal SNPs with missing rate < 5% used to calculate PCs

  4. Identity By Descent • 34 sample pairs with KC > 1/32 • 10 PO from HapMap • 21 expected Dups • 1 unrelated (bottom right) • 2 unexpected Dups

  5. Deconvoluting relatedness, population structure and admixture • Estimate relatedness using KING-robust (robust to population structure, but not to admixture or departures from HWE) • Partition the sample into a mutually unrelated set and the remaining (relatives of the unrelated set) • Perform standard PCA on the set of unrelated individuals • Project PC values for the set of related individuals • Re-estimate relatedness using REAP-PC (uses PCs to provide unbiased kinship coefficients in the presence of population structure, admixture and HWE departures) • Repeat steps 2-5 to obtain final sets of PCs and kinship coefficients – to adjust for relatedness and ancestry in association tests Matt Conomos and Tim Thornton

More Related