Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • What does CNV has anything to do with SNP

    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?

  • #2
    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.

    Comment


    • #3
      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!

      Comment


      • #4
        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.

        --
        pg

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Strategies for Sequencing Challenging Samples
          by seqadmin


          Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
          03-22-2024, 06:39 AM
        • seqadmin
          Techniques and Challenges in Conservation Genomics
          by seqadmin



          The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

          Avian Conservation
          Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
          03-08-2024, 10:41 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, Yesterday, 06:37 PM
        0 responses
        11 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Yesterday, 06:07 PM
        0 responses
        10 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-22-2024, 10:03 AM
        0 responses
        51 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-21-2024, 07:32 AM
        0 responses
        68 views
        0 likes
        Last Post seqadmin  
        Working...
        X