GENEALOGY-DNA-L Archives

Archiver > GENEALOGY-DNA > 2009-12 > 1260130910


From: "Roberta Estes" <>
Subject: Re: [DNA] real relatedness or fluff and fairytales?
Date: Sun, 6 Dec 2009 15:21:50 -0500
References: <587770.27617.qm@web24502.mail.ird.yahoo.com> <953242.47354.qm@web24503.mail.ird.yahoo.com> <91E96C076B6F44FD94D81A3E9CFFB6A3@RESTES2007><ea3bd9560912060951n54f72c7ci4366cdcdd746e2b4@mail.gmail.com><4B1C032E.8060206@familytreedna.com>
In-Reply-To: <4B1C032E.8060206@familytreedna.com>


Thank you Thomas and every one else who replied to this thread. I think the
essence of this is that we're sampling, not sequencing, which is why the two
criteria are used, in their most simple format.

Roberta

-----Original Message-----
From:
[mailto:] On Behalf Of Thomas Krahn
Sent: Sunday, December 06, 2009 2:17 PM
To:
Subject: Re: [DNA] real relatedness or fluff and fairytales?

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
>>
>>
>>
>>



-------------------------------
To unsubscribe from the list, please send an email to
with the word 'unsubscribe' without the
quotes in the subject and the body of the message

This thread: