Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Cheapest solution for targeted sequencing?

    Hi,

    We have 500-1000 genomic DNA samples and we are interested in a set of ~20 loci. What's the most affordable way to sequence the 20 loci for all the samples?

    Thanks,
    Shuli

  • #2
    If it's only 20 Loci I would do PCR and Amplicon sequencing. (Well, depends on the size of the Loci). You could use multipliex identifiers of any length which you incorporate into the amplification primer. With that amount of samples you could also think about a multiplex PCR amplifying 10 or even 20 PCR products in one reaction: that would lead to one PCR per sample targetted sequencing: I don't think anyone can do it cheaper...

    Comment


    • #3
      Originally posted by sulicon View Post
      Hi,

      We have 500-1000 genomic DNA samples and we are interested in a set of ~20 loci. What's the most affordable way to sequence the 20 loci for all the samples?

      Thanks,
      Shuli
      How long (bp) are those loci? If it is short enough, I'd say perform multiplex PCR using primers embedded with nextgen adaptors. In this case, sample prep cost may be significantly lower. You can multiplex many samples to control sequencing cost (sequencing reagents and materials), depending on the size of the loci. But the library prep may be too much a burden if you follow Illumina's gDNA library protocol for 500-1000 samples. On the other hand, if you can generate enough amplicons with Adaptors attached already, it will be a lot less work.

      I am dealing with a similar request from another client. If you wish to discuss a little more on this topic, you can send me a personal message.

      Rocksd

      Comment


      • #4
        Hi all,

        Stanford Genome Technology has published a 2nd generation "open source" capture technology using in solution oligonucleotides.

        We have an in silico design covering the CCDS genes (most of the exome) release and will have one covering the majority of the genome out soon (under review). You can download oligo sequences and create your own capture assays.





        More completely new third generation targeting technologies coming soon in a Nature journal. Be on the look out for it shortly.

        SGTC sequencing techies

        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