How to make association studies using haplotype (LD) blocks instead of SNPs?
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2.4 years ago
rimgubaev ▴ 270

Hello everyone! I wonder if someone suggests a tutorial or share one's own experience on the association studies using haplotype (LD) blocks not just SNPs. What I want is to find associations between the blocks and phenotype. I already understood how to find blocks in Haploview, however, it still does not clear to me how to add phenotype data as well as confounding factors (PCs with population structure, kinship matrix) and perform the association studies.

LD SNPs Haplotype GWAS • 618 views
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I think that these two papers answer to your questions in the methods section. Hope they are helpful!

https://www.nature.com/articles/s41398-017-0010-9#Sec2

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0212925#sec002

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Yes, they are, but the description is general and I need something more like a tutorial. To understand what are the programs, what are the inputs what are the outputs. Something with technical details.

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You just need to define the haploblocks and then provide a summary metric of each. It is the summary metric that would then be used in a regression model against your phenotype of interest.

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