Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Hi and a hopefully not to dumb question

    Hi everyone,

    I've recently been "promoted" from the microarray analysis world now that the previous guy babysitting our dna sequencing projects has left for greener pastures.

    You all come very highly recommended, so I'm hoping you can help me go from asking lots of dumb questions to being able to contribute at least a bit.

    With the caveat that I'm not sure if this has been discussed ad nauseam and I whether I've got enough details to be clear, here's my little problem:

    We've got DNA sequencing for exome-capture run for about 40 cancer cell lines. I'm finding some very common differences from the reference genome that isn't in dbSNP or 1000 Genomes and I was wondering if anyone could help explain what it is and if there is a reasonable way to filter off these features.

    One example is A1BG with a T109G (ACC->CCC at position 325 [transcript ENST00000453054], reverse strand), chr19:58862835 T->G (hg19, chr19:63554647 for hg18). I have that mutation on 37/42 samples.

    The various QC metrics are good and the reads are nicely clustering around exonic regions as expected. I checked with a known gene (p53) and the resulting mutations also match up.

    The fact that it appears in so many samples and isn't in either dbSNP or 1000 genomes worries me a little bit. We have over 100 genes that have unknown mutations in over 30 samples, so I'd love to have a decent filter for them.
    Last edited by fpepin; 02-08-2011, 05:34 PM. Reason: typo

  • #2
    You might have a bigger chance of getting an answer by reposting the question in, for example, the bioinformatics forum...

    Comment


    • #3
      Ok.

      I thought about it afterward but then I started worrying about cross-posting.

      I'll move it there.

      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, 03-27-2024, 06:37 PM
      0 responses
      12 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-27-2024, 06:07 PM
      0 responses
      11 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      53 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