Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • could known snp be disease causing variant?

    I am using exome seq to search for causative mutations in a family with Mendel type genetic disease.

    A mutation was found in all the patients while absent among normal people of the pedigree. function of the gene is strongly supporting the phenotype of the disease.

    however, the mutation has been reported in the 1000 genome project, although in a very low frequency(1 out of 1094). clinical features of the disease is very mild, only affecting skin pigment distribution.

    my questions are:
    Does this mutation worth further investigation?
    If does, what should I do?

    thanks for you attention.
    Last edited by gary; 03-05-2012, 10:33 PM.

  • #2
    You can run the statistics to see if there's a significant correlation. From what you write, I would assume there is. Normally, then, you would just start with the regular molecular biology experiments appropriate to this protein and then make a mouse (if appropriate to this gene, it's not for all of them). That's pretty much the normal flow of disease research.

    Comment


    • #3
      thanks for your valuable reply dpryan!

      The mutation was found in all the patients while absent among normal people of the pedigree. So I think it is clear that there is a significant correlation.

      My primary concern is that since the mutation has been reported in the 1000 genome database (absent in the dbSNP database), is it still worth further functional investigation?

      Are there any similar precedent studies I can learn from.

      Comment


      • #4
        I think the other issue is how do you know that 1000 Genomes individual doesn't in fact have the condition? I don't think the subjects are particularly well phenotyped. I think people need to start treading very carefully with the assumption 'because it's been seen before, it isn't pathogenic'. dbSNP has plenty of pathogenic mutations..

        Comment


        • #5
          thanks Bukowski

          Yes, that's what I'm thinking too.

          Is there a way I could get the detailed phenotype info of the 1000 Genomes individual who has the variant?

          Comment


          • #6
            I'm thinking 'no' from their not so helpful phenotype page: http://www.1000genomes.org/faq/can-i...mation-samples

            Comment


            • #7
              Originally posted by gary View Post
              The mutation was found in all the patients while absent among normal people of the pedigree. So I think it is clear that there is a significant correlation.
              You have not told us yet how many people you have in your statistics. I hope it is a reasonable sample size. (Have you calculated a p value with Fisher's test?)

              Comment

              Latest Articles

              Collapse

              • seqadmin
                Genetic Variation in Immunogenetics and Antibody Diversity
                by seqadmin



                The field of immunogenetics explores how genetic variations influence immune responses and susceptibility to disease. In a recent SEQanswers webinar, Oscar Rodriguez, Ph.D., Postdoctoral Researcher at the University of Louisville, and Ruben Martínez Barricarte, Ph.D., Assistant Professor of Medicine at Vanderbilt University, shared recent advancements in immunogenetics. This article discusses their research on genetic variation in antibody loci, antibody production processes,...
                11-06-2024, 07:24 PM
              • seqadmin
                Choosing Between NGS and qPCR
                by seqadmin



                Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...
                10-18-2024, 07:11 AM

              ad_right_rmr

              Collapse

              News

              Collapse

              Topics Statistics Last Post
              Started by seqadmin, 11-08-2024, 11:09 AM
              0 responses
              223 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 11-08-2024, 06:13 AM
              0 responses
              165 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 11-01-2024, 06:09 AM
              0 responses
              80 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 10-30-2024, 05:31 AM
              0 responses
              27 views
              0 likes
              Last Post seqadmin  
              Working...
              X