What does CNV has anything to do with SNP

[yuhao]

In SNP genotyping array data, we use the singal intensity at each SNP to infer CNV by using Hidden Markov Model, what does CNV region has anything to do with SNP detected?I am so confused about this! Can anyone give me some help?

[krobison]

Posting the same question twice is not recommended.

The simplest answer to your question is to imagine the signal coming off an A/B heterozygous SNP at different copy number states. If they are 1:1, then the two should have the same signal. If one were at double the copy number, then it is 2:1 and the signal should follow. The overall signal should also be informative; 1:0 should look different than 2:0 and 2:1 should look different from 4:2

The HMM enables the weak, noisy signal of multiple locations to be combined; you wouldn't trust a CNV call from a single element.

[yuhao]

hi, thank krobison!
I still don't understand some points here. so choose all the SNP detected and labelled 1, 2, ...., so then we construct a hidden markov model with transition probability and emission probability, and then we infer the hidden states from the the sequence of observed Ratio and BAF signal. But all the we get now is a sequence of hidden states(each hidden state is the copy number 0,1,2,3,4 stats of just a single nucleotide), for example ,if we can sequence of hidden states, 2,2,2,4, what does it mean? It means that at the fourth SNP, the copy number is 4, so it is AAAA,AAAB,AABB,ABBB,BBBB, so we know that there is a copy number variation at the locus the fourth SNP, but then what????What are other copy number variation regions?How do we determine the breakpoints of any copy number variation region?I was confused--what we get is just something on a single locus where a SNP lives!

[gprakhar]

Hello,

I guess, SNP information from CNV regions can help in genotyping.
That is, information about the Copy number variation in the different alleles of the sample.

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pg