Question

Genotype Imputation

5

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13.5 years ago

Zhshqzyc ▴ 520

Hi,

Is there any tutorial for genotype imputation? Suppose the poputation is chb+jpt.

I am newbie to this area. I want to know the general priciple. Examples and some programming code(if existing) will be welcome.

Thanks.

genotyping gwas • 7.0k views

ADD COMMENT • link updated 13.5 years ago by Larry_Parnell 16k • written 13.5 years ago by Zhshqzyc ▴ 520

Ram · Answer 1 · 2011-06-15

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13.5 years ago

Khader Shameer 18k

Imputation page at Wikipedia will be a nice start to understand the concept of "imputation".

From a genotyping perspective, it refers to the imputation SNPs that are not directly genotyped on your genotyping platform (for example: Illumina Human 660W-Quadv1_A) but are present on a reference panel such as the HapMap (for example: CEU, CHB or JPT populations; see HapMap tutorial).

I would like to point you to tutorials on how to use PLINK or MACH or IMPUTE for genotype imputation, these tools widely used for this type of analysis. This tutorials are not specific to your population of interest, but you can adapt them for your requirement.

Also please check the following review articles for a comprehensive overview of genotype imputation. Genotype Imputation: http://www.ncbi.nlm.nih.gov/pubmed/19706367 (PDF here) Current software for genotype imputation: http://www.ncbi.nlm.nih.gov/pubmed/19706367

ADD COMMENT • link 13.5 years ago by Khader Shameer 18k

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I want to know some algorithm. For example, the dataset has 100 snps then grow up to 500 snp. What is the priciple to insert missing genotype?

ADD REPLY • link 13.5 years ago by Zhshqzyc ▴ 520

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Didn't get you exact question. I found this article useful to understand various aspects of imputation. Other articles that I listed on GWAS in this post will also useful to understand the concept of GWAS and related methods.

ADD REPLY • link updated 5.2 years ago by Ram 44k • written 13.5 years ago by Khader Shameer 18k

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This is the only case of Human where we do imputation using a reference panel but in case of plant such as rice how should we go?
Where reference panel is not available.

ADD REPLY • link 11.7 years ago by kumar.vinod81 ▴ 340

score 1 · Answer 2 · 2011-06-15

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13.5 years ago

Larry_Parnell 16k

Because the CHB and JPT populations are so similar genetically at points of variation, you can impute in the combined CHB+JPT. Our colleagues ran MACH for a very CEU-like population.

Added on 9 Sep 2011: I would also look at this Primer in Nature Biotech on imputation methods and software.

ADD COMMENT • link 13.2 years ago by Larry_Parnell 16k