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  • ENT Fellow
    ENT Fellow
    • May 2013
    • 10

    Why is Chromosome 19 unreliable?

    Hi there,

    I'm doing low-coverage CNV-seq on illumine HiSeq 2500. I've been told that chromosome 19 is not trustworthy but am really struggling to find out why? Can anyone explain or throw me a reference I can read on this?

    Many thanks
  • GenoMax
    Senior Member
    • Feb 2008
    • 7142

    #2
    What kind of "not trustworthiness" are you referring to? It does appear that Chr19 has the highest number of alternate reference loci: http://www.ncbi.nlm.nih.gov/projects...urrent-regions

    Issues with chromosome 19: http://www.ncbi.nlm.nih.gov/projects...filters=chr:19

    Comment

    • ENT Fellow
      ENT Fellow
      • May 2013
      • 10

      #3
      Chromosome 19

      Many thanks for your reply.

      Well I was told that when analysing my data not to trust gains/losses that are in centromeric/telomeric regions (CNAs are overrepresented here) and to ignore Chr 19 as apparently these are not reliable. Is that a reflection of this high incidence of alternate reference loci you mentioned? Also why is this the case - is it a particularly repetitive chromosome?

      Comment

      • mastal
        Senior Member
        • Mar 2009
        • 666

        #4
        I have just been reading a comparative genomics paper, and apparently human chr 19 is particularly 'gene rich'.

        Comment

        • saraki
          Junior Member
          • Apr 2013
          • 5

          #5
          centromeric/telomeric regions tend to be highly repetitive regions which is why you might run into overrepresentation of CNAs. 19 does have a very high gene:bp length ratio ("gene rich") but I don't know why that would make it unreliable for CNAs?

          Comment

          • henry.wood
            Member
            • Apr 2010
            • 63

            #6
            I think the high number of alternate reference loci is a fairly plausible explanation. Looking at all the alternatives, for chr19, in total, they add up to about a quarter of the length of the chromosome. By comparison, for chr18 is is 0.7% and for chr20 it is 2%. It's not quite as simple as that, but it does suggest that there are a lot of different ways of arranging chr19. If you are doing copy number and using a pooled control sample - i.e. not the same person as the normal, there could be quite a difference in how well your test and control samples align to the main chr19 reference, which will make the apparent copy number of chr19 quite variable from person to person.

            Comment

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