What is the application of IBS in genetic analysis

This article introduces how IBS is used in genetic analysis, the content is very detailed, interested friends can refer to, hope to be helpful to you.

In genetics, there are two concepts, IBD and IBS, when describing the homologous relationship of alleles.

The full name of IBD is Identity By Descent, also known as blood homology, which means that the common alleles in two individuals come from a common ancestor; IBS full name Identity By Descent, also known as state homology, means that the common allele sequences in two individuals are the same.

In family data, IBD is widely used because of the typing data of parents, while IBS is usually used in natural populations. This article mainly introduces the application of IBS in data analysis.

IBS itself is only a qualitative concept, in order to quantify, put forward the concept of IBS state. For a SNP locus, the value of IBS state is the same number of allel in two individuals. For diploid organisms, the values of IBS include 0, 1 and 2, as shown in the following diagram.

Based on the results of SNP typing, we can calculate the IBS distance between samples. The formula for calculating IBS distance is as follows

Distance can measure the similarity between samples. According to IBS distance distance matrix, samples can be analyzed by MDS.

The following screenshot is from a literature in which the sample composition is explored through MDS analysis based on the IBS distance matrix between samples. The links to the literature are as follows

Https://www.ncbi.nlm.nih.gov/pubmed/21347369

Through MDS analysis, we can have a clear understanding of the composition of samples, and can also be used to eliminate samples that obviously deviate from the population.

In the actual data analysis, the IBS distance matrix can be calculated with the help of plink software, which is used as follows

Plink-file hapmap1-cluster-matrix-noweb

By default, a plink.mibs file is generated, which is a distance matrix that can be read in R language and then analyzed by MDS.

The code for MDS analysis in R language is as follows

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