Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Questions about whole-exome sequencing on NextSeq 500

    Hi everyone,

    My lab is looking into performing whole-exome sequencing on a small sample of human subjects on the NextSeq 500. I am responsible for researching the budget involved in such an endeavor and, as a newbie to this subject, would like to seek your advice on the number/type of sample prep/reagent kits to achieve our sequencing goals.

    We would like to whole-exome sequence 4-8 (depending on total costs) human subjects at >100x coverage, pair-ended read using the Nextera Rapid Capture Exome Kit and, ideally, the High Output 300 cycle NextSeq Kit.

    So, if we use 1 Nextera Rapid Capture Exome Kit (8rxn x 6plex), which according to documentation at 6plex can sequence 6 exome samples using NextSeq 500 High-Output kit, and 1 NextSeq Kit, High Output (300 cycle), can I whole-exome sequence up to 6 unique human subjects at >100x coverage with pair-ended read?

    edit: As a follow up question, I'm assuming that 1 Nextera Rapid Capture Exome Kit (8rxn x 6plex) can support sequencing of up to 48 exome samples, by the 8 reaction x 6 plex criteria? I apologize for my ignorance, thank you very much for your help.

    Thank you for your help.
    Last edited by newtoseq; 11-02-2014, 08:10 PM.

  • #2
    Are you locked in to the NextSeq platform, or do you have the possibility of using something else?

    Comment


    • #3
      Originally posted by Brian Bushnell View Post
      Are you locked in to the NextSeq platform, or do you have the possibility of using something else?
      Hi Brian, at this point, we are currently only looking at using the NextSeq 500. Thank you.

      Comment


      • #4
        I encourage you to look at this thread.

        But that aside... I can't help you with the economics. In fact, I think human resequencing is one area where NextSeq might possibly be useful, though it highly depends on the price. Unless NextSeq is vastly cheaper than HiSeq per bp, it's a bad idea, since the error rate is currently so high. Particularly for exome capture, where the coverage is even more highly variable than usual for Illumina, forcing you to call variants at very low coverage.

        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
        67 views
        0 likes
        Last Post seqadmin  
        Working...
        X