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Thread: Ancestral and Derived reporting system

  1. #1
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    Ancestral and Derived reporting system

    I had asked this question on another forum but did not find a satisfactory answer , so I thought I would try here. When reporting a SNP result why is it important to give an ancestral value in addition to the derived value? What piece of information does one gain from knowing the ancestral value ? Why did the scientist involved decide upon this type of reporting system over say, for example, a simple positive or negative result?

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    Quote Originally Posted by Brunetmj View Post
    I had asked this question on another forum but did not find a satisfactory answer , so I thought I would try here. When reporting a SNP result why is it important to give an ancestral value in addition to the derived value? What piece of information does one gain from knowing the ancestral value ? Why did the scientist involved decide upon this type of reporting system over say, for example, a simple positive or negative result?
    I'd imagine it's because +/- isn't good enough as some positions can mutate to different values.
    Paternal: R1b-U152 >> L2 >> FGC10543 >> PR5365, Pietro Rocca, b. 1559, Agira, Sicily, Italy
    Maternal: H4a1-T152C!, Maria Coto, b. ~1864, Galicia, Spain
    Mother's Paternal: J1+ FGC4745/FGC4766+ PF5019+, Gerardo Caprio, b. 1879, Caposele, Avellino, Campania, Italy
    Father's Maternal: T2b-C150T, Francisca Santa Cruz, b.1916, Garganchon, Burgos, Spain
    Paternal Great (x3) Grandfather: R1b-U106 >> L48 >> CTS2509, Filippo Ensabella, b.~1836, Agira, Sicily, Italy

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    When a polymorphism (different alleles at a position) is first discovered, it is not known which allele is ancestral and which is derived. Only later testing (e.g., of an A00 man) can indicate that.

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    Quote Originally Posted by lgmayka View Post
    When a polymorphism (different alleles at a position) is first discovered, it is not known which allele is ancestral and which is derived. Only later testing (e.g., of an A00 man) can indicate that.
    Good point. Also, the reference sequences are sometimes changed, so what was ancestral in one sequence may be derived in another.
    Last edited by R.Rocca; 04-22-2014 at 08:14 PM.
    Paternal: R1b-U152 >> L2 >> FGC10543 >> PR5365, Pietro Rocca, b. 1559, Agira, Sicily, Italy
    Maternal: H4a1-T152C!, Maria Coto, b. ~1864, Galicia, Spain
    Mother's Paternal: J1+ FGC4745/FGC4766+ PF5019+, Gerardo Caprio, b. 1879, Caposele, Avellino, Campania, Italy
    Father's Maternal: T2b-C150T, Francisca Santa Cruz, b.1916, Garganchon, Burgos, Spain
    Paternal Great (x3) Grandfather: R1b-U106 >> L48 >> CTS2509, Filippo Ensabella, b.~1836, Agira, Sicily, Italy

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    reference sequences are sometimes changed, so what was ancestral in one sequence my be derived in another.
    Ok,well that makes sense.The point about new SNP's also makes sense. Of course I was thinking of well known SNP's when I asked the question but I do see the point.
    You guys are great , thank you. It is suprising hard to research that.

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    An example, ChrY:7,340,450 has two different derived allele values from the ancestral reference value of a 'c'.

    L513/DF1 has derived value of a 't' and an L969+ individual has a mutated to an 'a'. So if one tested positive for this position, the allele value must be reported to designate if one is either 'A-P262' or 'L513'.

    MJost
    148326, FGC-0FW1R, YSID6 & YF3272 R-DF13>FGC5494>*7448>*5496>*5521>*5511>*5539>*5538>* 5508>*5524
     
    Watterson USA GD1/67 & GD3/111, *5508+. GD1ís fatherís sister-23andme pred. 3rd Cous w/ 0.91% DNA shared-3 seg. Largest on Chr1 w/non-Euro admix affirms my NPE paternal Watterson line via aDNA & YDNA. A 2nd pred. 4th cous has same DKA b. 1840's Georgia and MDKA d 1703 IOM. 3rd Cousin FtDNA FF is from the Watterson Ala. *5538+ b. IOM w/ GD6/67 & GD8/111 -SGD3. FGC5539+ a Scot-Ross GD13/111 -SGD8

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    Quote Originally Posted by MJost View Post
    An example, ChrY:7,340,450 has two different derived allele values from the ancestral reference value of a 'c'.

    L513/DF1 has derived value of a 't' and an L969+ individual has a mutated to an 'a'. So if one tested positive for this position, the allele value must be reported to designate if one is either 'A-P262' or 'L513'.

    MJost
    Well I had to read that answer at least 6 times to understand , so to be sure, I did is the following summary of the answer to be sure I understood.

    Some Y chromsome positions can have more than one dervived value. Got it..
    What is not clear to me is how knowing the ancestral value C, helps determine which of the derived values it was?

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    Without knowing the ancestral value, you wouldn't be able to determine if the result indicated at that position was in a ancestral or derived state. One needs a control to measure against.

    Sure, for most people the +/- SNP results as shown by FTDNA's project pages serve just fine. However it skips the step of showing how the conclusion was made, and would require advanced users to utilize a lookup table on their own to determine what chromosomal location that arbitrary SNP name is referring to, what the ancestral value is, and the derived value that probably caused that SNP to show up as +. Why not err on the side of more information?

    And of course, as you indicated in your other discussion thread, it doesn't make much sense to exclude this information for newly discovered and unnamed SNPs, unless you want to cut third parties out of the discovery and documentation process.

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    [QUOTE]Without knowing the ancestral value, you wouldn't be able to determine if the result indicated at that position was in a ancestral or derived state. One needs a control to measure against./QUOTE]
    Does this suggest that the ancestral state is merely a control to measure the derived state like saying unmutated versus mutated? Or in the case of multiple derived states unmutated
    versus mutated and mutated? I don't know..I am missing something ..but I am sure I will eventually figure it out..What I lack in brilliance I make up in tenacity.

  16. #10
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    SNP markers often only exist in 2 forms - the ancestral and the mutated (derived) allele value. Y-DNA SNP markers are useful in tracing deep ancient paternal ancestry and Y-DNA SNP markers are used to define phylogenetic relationships in the Y-DNA phylogenetic tree. Each Y-DNA haplogroup and subclade in the phylogenetic tree is defined by an unique and specific set of Y-DNA SNP markers and their mutations. There is a researched ancestral reference sequence for the Y-chromosome that is also used in conjunction with ISOGG's placement on its Y-DNA phylogenetic tree and can be seen using the Human Y Chromosome Browser found at www.Ybrowse.ISOGG.org. DNA is made up of four bases: adenine (A), cytosine (C), thymine (T), and guanine (G). These value are called bases in genetics. In normal spiral DNA the bases form pairs between the two strands: A with T and C with G. If a position is ancestrally a 'c', any change to another value represents a mutation to one of the three remaining allele values of 'GATC' in Y-DNA.

    MJost

    MJost
    148326, FGC-0FW1R, YSID6 & YF3272 R-DF13>FGC5494>*7448>*5496>*5521>*5511>*5539>*5538>* 5508>*5524
     
    Watterson USA GD1/67 & GD3/111, *5508+. GD1ís fatherís sister-23andme pred. 3rd Cous w/ 0.91% DNA shared-3 seg. Largest on Chr1 w/non-Euro admix affirms my NPE paternal Watterson line via aDNA & YDNA. A 2nd pred. 4th cous has same DKA b. 1840's Georgia and MDKA d 1703 IOM. 3rd Cousin FtDNA FF is from the Watterson Ala. *5538+ b. IOM w/ GD6/67 & GD8/111 -SGD3. FGC5539+ a Scot-Ross GD13/111 -SGD8

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