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Archiver > GENEALOGY-DNA > 2009-12 > 1260234601
From: "john" <>
Subject: Re: [DNA] real relatedness or fluff and fairytales?
Date: Mon, 7 Dec 2009 17:10:01 -0800
References: <53b3.7f3773a.384ef538@aol.com>
Thanks for the lesson Ann. I checked my results with my father and noticed
one of those white lines you
were talking about in cromosome #3 I checked and my son has the same white
line in the same place.
with me. I did not have one when compared to my mother. Now what?????
----- Original Message -----
From: <>
To: <>
Sent: Monday, December 07, 2009 4:18 PM
Subject: Re: [DNA] real relatedness or fluff and fairytales?
> The centromeres are SNP "deserts", but 23andMe requires a certain
> threshold
> of cM and SNPs before identifying a haploblock. Currently at least one
> haploblock must contain 700 SNPs and 7 cM. That eliminates most of the
> artifacts
> around the centromeres.
>
> One "wrong SNP" call (i.e. opposite homozygotes) is allowed if it is
> surrounded by hundreds of SNPs in a long continuous run.
>
> For a calibration of error rates, I looked for Mendelian inconsistencies
> in
> two parent-child trios from my own family study.These would be SNPs where
> the parent is say "AA" and the child is "GG". Here is the tally (out of
> 561,848 SNPs)
>
> Mother and son: 13
> Father and son: 34 (6 in a cluster)
>
> Mother and son: 17
> Father and son: 25 (5 in a cluster)
>
> The SNPs that show up in a cluster could signify a microdeletion, where
> one
> chromosome is missing some bases. If 23andMe sees just one allele, it gets
> called as homozygous.
>
> For 23andMe customers with parent-child data, you can look at the table
> view in Ancestry Labs to see if any chromosome has more than one segment.
> If
> the microdeletion is big enough, it will also be visible as a small white
> area
> in the Family Inheritance view.
>
>
>
>
>
> In a message dated 12/6/2009 11:17:33 AM Pacific Standard Time,
> writes:
>
>> 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".
>
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