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This article shows you what is the basic knowledge of CNV analysis based on SNP chip, the content is concise and easy to understand, it can definitely brighten your eyes. I hope you can get something through the detailed introduction of this article.

There are many technical methods to detect CNV, and there are three common ones.

ACGH chip

SNP chip

NGS sequencing

This paper mainly introduces the principle of detecting CNV by SNP chip, which essentially determines the corresponding copy number based on the results of SNP typing in the chromosome region, as shown in the following diagram.

For each SNP locus, the two allel are represented by An and B respectively, A for ref allel and B for alt allel. In the above diagram, the red region represents a region of loss of heterozygosity LOH, which is a single copy, and there is only one allel for each locus typing, while the blue region represents a 3 copies and each locus has 3 allel. Through the results of locus typing, the copy number of the corresponding chromosome region can be determined. Before we understand this picture, let's explain the following two basic concepts.

The typing of SNP chip is determined by comparing the ratio of fluorescence signal strength of two kinds of allel corresponding to An allel. Similarly, in order to better describe CNV, the following two statistical values are defined.

1. LRR

The full name of LRR is log R ratio and the formula is as follows

R represents the sum of the fluorescence signal strength of An and B allel, observed is the actual value detected in the experimental sample, and exprected is the value fitted by the algorithm, which represents the detected value of the normal sample.

LRR is similar to Log2 ratio in aCGH chip, which characterizes the change of copy number relative to normal samples. This value is 0, which means that there is no exception in the number of copies. If it is two copies, it is greater than 0. It means that the number of copies increases, and if it is less than 0, the number of copies decreases.

2. BAF

The full name of BAF is B allel frequency, which represents the ratio of the signal strength of two allel. The formula is as follows

It can be seen from the above definition that the value range of BAF is 0-1, 0 means that only the fluorescence signal corresponding to A this allel is detected, the result of typing is AA, 1 means that only the fluorescence signal of B this allel is detected, the result of typing is BB; 0.5 means that the fluorescence signal intensity of An and B allel is equal, and the result of typing is AB.

It is worth mentioning that although there are only three typing results, the value of BAF can fluctuate in the range of 0-1, which should be due to the disturbance of fluorescence signal intensity.

It should be noted that the fluorescence signal intensity here is normalized. Through the two statistical values of BAF and LRR, the copy number of the corresponding region can be determined with the help of the algorithm, as shown below

There are a lot of software that can analyze CNV based on the data of SNP chip, such as PennCNV, QuantiSNP, which are widely used. With the help of high-density SNP chip, we can achieve higher resolution CNV detection, and detect copy number, LOH,UPD and other structural variation events.

What are the basic knowledge points in CNV analysis based on SNP chip? have you learned any knowledge or skills? If you want to learn more skills or enrich your knowledge reserve, you are welcome to follow the industry information channel.

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