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Archiver > GENEALOGY-DNA > 2009-12 > 1260127022


From: Thomas Krahn <>
Subject: Re: [DNA] real relatedness or fluff and fairytales?
Date: Sun, 06 Dec 2009 13:17:02 -0600
References: <587770.27617.qm@web24502.mail.ird.yahoo.com> <953242.47354.qm@web24503.mail.ird.yahoo.com> <91E96C076B6F44FD94D81A3E9CFFB6A3@RESTES2007><ea3bd9560912060951n54f72c7ci4366cdcdd746e2b4@mail.gmail.com>
In-Reply-To: <ea3bd9560912060951n54f72c7ci4366cdcdd746e2b4@mail.gmail.com>


Note that 23andMe also ignores the centromere regions completely.
This makes the calculations easy for them but may introduce some severe
length misinterpretations when a haploblock stretches over the
centromeric region.

Also there is apparently a threshold for "wrong SNP" calls. If you
compare a parent-child result closely you will find a couple of SNPs
that don't share any of the alleles. 23andMe simply considers them as
typing errors or mutations and ignores them. This is in my opinion very
dangerous (especially in highly conserved regions). The correct way to
handle this would be to at least list the inconsistencies and if
possible give a reason why they are ignored. So for now I recommend to
not simply trust the display of a continuous haploblock in the 23andMe
chromosome browser. You should definitely verify the raw SNP calls.

Another phenomenon that cannot be understood from a simple SNP chip
result are large scale re-arrangements of large chromosome stretches. We
know already from the Y chromosome that we have a significant number of
people who have duplications, inversions or deletions in palindromic
regions of the chromosome. This of course affects the length and the
pattern of haploblocks and this will definitely affect the "half
identical regions".

So generally speaking the the relative finder is an extremely simplified
tool to detect a possible related person. An experienced DNA genealogist
will certainly want to have a deeper look into the real raw results
before he blindly accepts the relative finder output.

I hope this helps,

Thomas



>
> On Sun, Dec 6, 2009 at 8:49 AM, Roberta Estes <> wrote:
>
>
>> I find this just a hair confusing, so I'll ask what is probably a stupid
>> question.
>>
>> Since there are two criteria to be fulfilled, both the 7cM and the 700
>> SNPS,
>> I'm presuming that SNPs take up a different amount of space, or there
>> wouldn't be two criteria, just one. But my understanding of a SNP is that
>> it is just one occurrence of a, t, c or g. So unless there is an insertion
>> or a deletion, how can different groupings of SNPs be of different lengths.
>> Don't a, c, t and g take up the same amount of space?
>>
>> Roberta
>>
>>
>>
>>


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