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  • Comparing genotyping chips to deep sequencing?

    Hi all,

    I'm looking for any literature that compares SNP genotyping chips (such as infinium or illumina genotyping platforms) to 'deep sequencing' datasets such as WGS or RNASeq (and the subsequent SNP calling using SAMTools or similar).

    I've seen a few human genome papers where the authors also include a SNP chip analysis (probably because it's so cheap compared to WGS), but I'm not sure of any specific studies or meta-studies.

    Thanks for any pointers,
    Dan.
    Homepage: Dan Bolser
    MetaBase the database of biological databases.

  • #2
    Some genome centers (e.g. WashU) use the SNP chip info as a quality check, sample identity check & also to determine if they have gone deep enough.

    I found this reference that did a direct comparison; I believe there are more
    Next-generation massively parallel sequencing technologies provide ultrahigh throughput at two orders of magnitude lower unit cost than capillary Sanger sequencing technology. One of the key applications of next-generation sequencing is studying genetic variation between individuals using whole-geno …

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    • #3
      Thanks very much for this link Kris. I'm looking to build a collection ;-)

      All the best,
      Dan.
      Homepage: Dan Bolser
      MetaBase the database of biological databases.

      Comment


      • #4
        You're welcome, but it's Lys-Glu-Ile-Thr-His not Lys-Arg-Ile-Ser :-)

        Comment


        • #5
          We did so in the U87MG Decoded paper. Ran Illumina 1M-Duo and compared to our SNP calls from WGS on the SOLiD.

          I think for these early studies it made sense, but we've reached the point where SNV calls from WGS are more accurate than the error rate of the SNP chips themselves. After that point, all we end up doing is saying, "Well, we did better than a SNP chip," which is kind of silly.
          Mendelian Disorder: A blogshare of random useful information for general public consumption. [Blog]
          Breakway: A Program to Identify Structural Variations in Genomic Data [Website] [Forum Post]
          Projects: U87MG whole genome sequence [Website] [Paper]

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          • #6
            Right, but there are different costs and requirements associated, so I'd like to know about the general characteristics so that the right choice can be made for the right study.

            Thanks for the link, I'm happy to pull in all such papers ;-)
            Homepage: Dan Bolser
            MetaBase the database of biological databases.

            Comment


            • #7
              Originally posted by krobison View Post
              You're welcome, but it's Lys-Glu-Ile-Thr-His not Lys-Arg-Ile-Ser :-)
              Met-Ile-Asn-Thr-Glu-Arg!

              I think I called you Kris a while back and for some reason it stuck.

              Cheers,
              Homepage: Dan Bolser
              MetaBase the database of biological databases.

              Comment

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