Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • how to calculate LOD scores for NGS results?

    Hi,
    I have NGS results (whole exomes, VCF files) for several family members with the same disease, and also the parents that are healthy.
    Is there an available algorithm to calcultae LOD scores for linkage of variants to the disease? I.e. I would like to have the LOD score for each variant.
    Or any other way to find the locus/loci associated with the disease.
    Because I'm not sure the responsible mutation is realy in the exome (maybe it is intronic, or a long indel, or in an uncovered exon, etc).

    Thanks!

  • #2
    Originally posted by Lilach View Post
    Hi,
    I have NGS results (whole exomes, VCF files) for several family members with the same disease, and also the parents that are healthy.
    Is there an available algorithm to calcultae LOD scores for linkage of variants to the disease? I.e. I would like to have the LOD score for each variant.
    Or any other way to find the locus/loci associated with the disease.
    Because I'm not sure the responsible mutation is realy in the exome (maybe it is intronic, or a long indel, or in an uncovered exon, etc).

    Thanks!
    I dont think LOD score would be useful in this regard since you would need a very extensive family unless you are studying a recessive disorder Besides with NGS you get so many data that would generate a lot of false positives. I would sugggest to look for homozygosity sharing regions or ibd larger regions which may content the causative mutation.
    Eitherway if you want to go with LOD score calculation try to get 1,000,000 random samples of SNPs distributed as evenly as posible in the exome and calculate LOD scores using Merlin. There may be additional setbacks such as linkage disequilibrium among samples, and that exomes are not ment to capture intron information and SNPs are more common intronic.

    Comment


    • #3
      Did you already look at identical variants in the affected individuals in the same family? Maybe they have the same mutation?

      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
      10 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      9 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      49 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      67 views
      0 likes
      Last Post seqadmin  
      Working...
      X