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In genome-wide association studies (GWAS), what is the difference between imputing and typing? Are they the same?

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'Typing' is an SNV-typing. It is an explicit SNV detection using Affymetrix GeneChip arrays, Illumina BeadArray.

'Imputing' is an imputation. It is a statistical inferring from existing genotype data using haplotype estimation. It is useful because different genotyping arrays genotype a slightly different set of SNVs and they can't detect all variants as whole genome sequencing is still pricey.

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No, they are different altogether.

Typing in GWAS is genotyping individuals from a selected population to know say the genetic variation of SNP's (single nucleotide polymorphisms) among them via chips like Illumina Core-Exome etc.

Imputing is the statistical process of imputation of SNP's of an individual from a reference source like the HapMap reference panel. The process is a bit complex and typical tools like IMPUTE2/BEAGLE4/MINIMAC2 rely on HMM (Hidden Markov Models) to fill in the SNP's.

So, in essence within a GWAS study first, we genotype individuals (as it's cheaper than sequencing all SNP's) and get 300-500k SNP's via the chips as above, then impute the remaining variants using an established Human Genome Reference panel using the above software.

Edit:

An excellent resource for understanding imputation is Yun Li's 2009 paper.

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    $\begingroup$ Please add some references to your response. $\endgroup$ Dec 16, 2016 at 19:18
  • $\begingroup$ I have added one here, but I usually don't see references in the answers from most of the people in this forum !!! $\endgroup$
    – Shab86
    Dec 16, 2016 at 19:39

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