Thomas Krahn

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From: Thomas Krahn thomas@familytreedna.com
To: CarolVass@comcast.net
Subject: Re: seeking clarification on DYS463=24
Date: Fri Apr 6 14:03:22 2007

Dear Carol,

I'm very sorry for the confusion that you're in with DYS463 and we're also unhappy with the situation.
Unfortunately this has historical reasons why there are so many nomenclature problems with DYS463.

The newest standard for reporting DYS463 according NIST and ISFG publications includes the two differing repeat units. This is exactly what Family Tree DNA, SMGF and DNA-Fingerprint report when the labs release their results.
Relative Genetics and DNA Heritage seem to report a repeat count that is 2 units shorter than we do. Probably they want to stick to the old reporting method which didn't count the terminal 2 AAGGA units, because they where thought to be invariant. Just recently somebody found out, that the chimp DNA sequence had only one AAGGA unit. That's why this was now included in the new NIST & ISFG standards. See: http://www.cstl.nist.gov/div831/strbase/pub_pres/ISFG_YSTRupdate_FSI2006.pdf

Only the DNA-Fingerprint Ymatch database and the SMGF database in native mode support the newest standard for counting the repeats of DYS643.

Ysearch uses the short counting method, because this database contained mainly allele reports from DNAH and Relative Genetics because Family Tree DNA didn't test DYS463 those days.
So we decided to keep this nomenclature for Ysearch and we will make a complete upgrade of the whole database by +2 units one day.

The programmer of the SMGF database wanted to make it easier for FTDNA customers to enter their alleles into the search mask, so he programmed an automatic conversion routine. The time when he did this, Family Tree DNA didn't report any DYS463 results, so he assumed that the Ysearch standard was relevant. We don't have any influence on the SMGF database, so we can't change this on our end. I'd guess that SMGF will want to change this in their next release.

So here's the summary:
If you have a DYS463 result from Family Tree DNA, DNA-Fingerprint or from the SMGF foundation (directly!)
For:
Ymatch >> enter the exact value
SMGF >> Use the Family Tree DNA conversion mask and enter the DYS463 value -2
Ysearch >> subtract 2 units

For results from DNAH or RG do the reverse.

I hope this helps,

Thomas

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What's New

I have run a new calculation of the age of our cluster using a set of 181 37-marker haplotypes and a second set of 81 67-marker haplotypes.

These result is 993 years and 966 years respectively ... certainly about the time of Brian Boru!

A further run omitting the variable markers, 385, 389, 459, 464 and CDY resulted in a time of 1086 years with an error of ±20%.

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