GENEALOGY-DNA-L Archives

Archiver > GENEALOGY-DNA > 2003-04 > 1050967804


From: Charles <>
Subject: Re: FW: [DNA] DNAPrint Test: Validation Studies
Date: Mon, 21 Apr 2003 19:31:27 -0400
References: <NGBBJJHDALCHOBFBBMPIKELNCJAA.tfrudakis@dnaprint.com> <3EA47C18.FF614AFF@yahoo.com>


OOPS. Darn typos. I meant to say this area is NOW a melting pot.
The older I get the more typos I make. Glad I had others proof
read my manuals. :-)

Charles


Charles wrote:
>
> Tony,
>
> Sounds like Dr. Mark Shriver lucked out with those younger self
> designated European students who volunteered and hat he didn't get any
> significant "pure blooded" PA Germans, aka PA Dutch, from this area of
> PA, in those tested. But since they were students they were probably
> very much younger than me too. I am almost 60 and have what is
> considered a "pure-blood PA German Pedigree Chart". There are less and
> less of us each decade. The dialect is disappearing fast as is the
> culture. In my children's generation, age 36ish, all PA German charts
> are harder to find. And my grandchildren are all Heinz 57 varieties
> blended. :-) Many other population groups have moved into this area in
> the last 40 years. In our school district when I graduated we were all
> European (several hundred in the class), with only 2 African-Americans,
> no Hispanics, and no Asians. It was that way for as long as I can
> remember. Not anymore. This area is not a melting pot with the current
> generation, of college age. But I don't think anyone had any prior
> knowledge to eliminate the PA German sub-group, or even thought of
> asking the question, "Are you a PA German, aka PA Dutchman", prior to
> this point. I think this East Asian content in PA Germans such as I and
> Zach's wife is a surprise to all. JMHO.
>
> Charles
>
> TONY N FRUDAKIS wrote:
> >
> > Charles,
> >
> > Just because the chances of systematic bias are unacceptible. In retrospect
> > we may have been right. The inbreeding coefficient among PA dutch would be
> > greater than expected for a more diverse population of Europeans...meaning
> > that the population would be more homogeneous than desired. THis is not a
> > bad thing, but for developing a test like ours it could interject bias. If
> > East Asian admixture is common among the PA dutch, and we used them to
> > calculate our allele frequencies, every other European tested would show a
> > result artificially biased towards European and away from East Asian. The
> > goal is to use a good sample from the population, of all the extant
> > variability.
> >
> > Tony Frudakis, Ph.D.
> > DNAPrint genomics, Inc.
> >
> > -----Original Message-----
> > From: Charles [mailto:]
> > Sent: Monday, April 21, 2003 5:33 PM
> > To:
> > Subject: Re: FW: [DNA] DNAPrint Test: Validation Studies
> >
> > Tony,
> >
> > Just curious, why would you not have picked the PA Germans, aka the PA
> > Dutch. I don't think anyone prior to your DNAPrint test would have
> > surmised that some of us may be harboring ancient "East" Asian content,
> > such as for my test and for Zach's wife. Going into your DNAPrint test I
> > think most PA Germans would think they were 100% European. What advance
> > knowledge did you have which would rule out the PA Germans, aka PA
> > Dutch.
> >
> > Also, again, do you consider Mongolia, which is north of and abuts
> > China, as East Asian for your definition of your East Asian population
> > group. It seems logical to me that Mongolia would be included. It
> > certainly would make sense as to how "East" Asian genetic content got
> > into Europe. It certainly didn't get there in large numbers via modern
> > Chinese, Korean, or Japanese immigration such that it would show up in
> > the PA German stock. I think they definitely should be included. As you
> > know, I have suggested changing the graphic map for the Group
> > delineations. You said you were going to look into in one email. I just
> > wanted to see if you agree with those points. If Cambodia and Vietnam
> > are in then I think definitely Mongolia should be too. And according to
> > the reference source I found the other day, Mongolia is defined as part
> > of East Asia.
> >
> > Charles
> >
> > TONY N FRUDAKIS wrote:
> > >
> > > Charles,
> > >
> > > You are correct in my view - the test is reaching farther back than you
> > are
> > > interested to learn about, but the 3.0 version is expected to be able to
> > > provide you the information you seek. In the future, we will advertise
> > the
> > > 3.0 version as the test of choice for genealogical aims, and the 2.0 test
> > > as a journey farther back in time than 3.0 for those with more deep
> > > anthropological interests. Nonetheless, you have to admit, you learned
> > > something about your tree that I bet you didnt know before, even if it is
> > > not exactly what you were seeking to learn...
> > >
> > > It would indeed be interesting to see how a collection of PA Dutch type on
> > a
> > > population level scale. For what it is worth, the Europeans we used as a
> > > parental group came from PA - a collection of "white" students at PSU (as
> > I
> > > mentioned previously, about half of Europeans tested are 100% pure
> > > IndoEuropean, and admixture within this parental group would balance out,
> > so
> > > there is no bias expected towards or away from any one type of admixture).
> > > For example, we would not have used PA Dutch as a parental group of fear
> > > that a certain type of admixture may be systematic within this group, as
> > it
> > > appears is possible from your and other results recently.
> > >
> > > Ill be monitoring, but to be honest the volume of emails clogs my system
> > > making it difficult for me to conduct day to day business. I may assign
> > the
> > > monitoring to someone else here, and respond from time to time to certain
> > > posts... but Ill keep going as currently for a couple days more at least.
> > >
> > > Tony Frudakis, Ph.D.
> > > DNAPrint genomics, Inc.
> > >
> > > -----Original Message-----
> > > From: Charles [mailto:]
> > > Sent: Monday, April 21, 2003 4:19 PM
> > > To:
> > > Subject: Re: FW: [DNA] DNAPrint Test: Validation Studies
> > >
> > > Tony,
> > >
> > > If my 21% East Asian admixture as reported by my DNAPrint test results
> > > is indeed accurate, then in my case, it must be picking it up East Asian
> > > AIM's in my genome from fairly old sources, say significantly beyond
> > > more than 500 years ago, and it must be fairly widespread within the PA
> > > German people, at least in my area where all my PA German ancestors for
> > > the last 250 years lived roughly within 25 miles of each other. My 30
> > > years of genealogical research into my PA German lineage, and that of
> > > others in this area, pretty much reaches a dead-end, once you cross the
> > > big pond to Europe, on most lines about 500 years ago. The records are
> > > just not there in Europe on most of my lines prior to 1500, and for
> > > people in my area. The records in this area for significant numbers of
> > > PA Germans in my area start about 1740. The much older sources for the
> > > East Asian AIMs may be of anthropological interest but are not of much
> > > use to me for genealogical purposes.
> > >
> > > I am still trying to get more so-called "pure-blooded PA Germans by self
> > > designation" tested to see if a significant East Asian content exists in
> > > most PA Germans in this area, near the county line border of Lehigh and
> > > Berks Counties, PA. Here is my picture so you can see my phenotype,
> > > clearly Caucasian European.
> > >
> > > http://www.kerchner.com/cfk.htm
> > >
> > > I look forward to hearing more about your version 3.0 test. How much
> > > more of a recent time frame will those AIM markers target to evaluate?
> > > Will it be more useful for genealogical work?
> > >
> > > Also, Tony, please don't leave the list in the future as you mentioned.
> > > At least stay and monitor it if your are just too busy to respond.
> > >
> > > Charles
> > >
> > > TONY N FRUDAKIS wrote:
> > > >
> > > > OK, I cannot send the file as an attachment. If anyone wants to see the
> > > > file described below, please email me at and Ill
> > > send
> > > > it to you directly.
> > > >
> > > > Tony Frudakis, Ph.D.
> > > > DNAPrint genomics, Inc.
> > > >
> > > > -----Original Message-----
> > > > From: TONY N FRUDAKIS [mailto:]
> > > > Sent: Monday, April 21, 2003 4:05 PM
> > > > To:
> > > > Subject: RE: [DNA] DNAPrint Test: Validation Studies
> > > >
> > > > Also I have to say that the Chandler implication that our validation
> > data
> > > is
> > > > just a few advertising jingo's and pretty pictures is enormously unfair
> > to
> > > > our effort. We have spent millions developing this test and validating
> > > it.
> > > > Never before in the history of mankind has it been possible to detect
> > > > minority admixture from the DNA, and our validation data shows that the
> > > > detection of minority (and majority) admixture is sensible within the
> > > > context of pedigree analysis, that it usually correlates with self
> > > reported
> > > > mixture (though not always because, it appears, such knowledge is not
> > > always
> > > > complete or accurate) and that it is impervious to numerous trivial
> > > > environmental variables, such as input DNA quantity (which any
> > laboratory
> > > > scientist would want to see, because such things can happen quite easily
> > > for
> > > > a poorly developed test). To merely whisk the data away with a swipe of
> > > the
> > > > hand is horribly unfair to the test.
> > > >
> > > > Let me share the attached figure, which is part of the remainder of the
> > > data
> > > > that we do not normally communicate to keep the document simple (I dont
> > > know
> > > > how attachments are handled by the server but I will try). This figure
> > > > shows that when the markers useful for resolving Native American and
> > East
> > > > Asian ancestry are deleted from the analysis, the program has trouble
> > with
> > > > the confidence and in this dimension of the plot, and only this
> > dimension,
> > > > the confidence contours are dramatically skewed (basically the algorithm
> > > is
> > > > saying its not sure where the sample falls on the Native American/East
> > > Asian
> > > > axis because there are no good markers for resolving these ancestries in
> > > the
> > > > analysis). If this does not convince you the sequences are accurate
> > > > reporters and that the algorithm works, then I am at a loss.
> > > >
> > > > I think people need to reevaluate their expectations on what will be
> > > > possible to take from DNA. What many of you want is a 3.0 version of our
> > > > test, for finer resolution, not so far back in time as our current test.
> > > > Let me say that we want this too, but it is enormously expensive.
> > Simply
> > > > put, nothing like this has ever existed before, and it will certainly
> > get
> > > > better in the future, but let us appreciate the information the current
> > > > version provides to us as well because it means something.
> > > >
> > > > Tony.
> > > >
> > > > -----Original Message-----
> > > > From: David Faux [mailto:]
> > > > Sent: Monday, April 21, 2003 2:40 PM
> > > > To:
> > > > Subject: Re: [DNA] DNAPrint Test: Validation Studies
> > > >
> > > > Well, on this point we agree John. My conclusion in an e-mail to Drs.
> > > > Thomas and Frudakis, after reading the Validation Study, was that I was
> > of
> > > > the opinion that the test was properly validated for forensic purposes
> > > > (actually it seems to be an excellent tool for that market) - but the
> > > > evidence was not compelling for those of us who wish to use the results
> > > for
> > > > genealogical purposes. This is not to say that the test is not useful
> > for
> > > > genealogists, clearly it is, but for me, to be thoroughly convinced, for
> > > > example the East Asian sample sizes (10 Chinese and 10 Japanese) would
> > > need
> > > > to be larger. I offered them a detailed critique, page by page. I
> > hope
> > > > others with an interest in the DNAPrint test will also offer their
> > > opinions
> > > > to the List. David.
> > > >
> > > > "John F. Chandler" <> wrote:
> > > > It appears to be aimed entirely at crime lab customers. Certainly, a
> > > > crime lab would want to know what happens if they send in a sample
> > > > containing blood from two individuals or contamination from a mouse,
> > > > but those things have no bearing on the validity of the test for the
> > > > hobby market. They did show some three-generation test results and
> > > > mumbled about the surprising difference between two siblings being
> > > > within a standard deviation (without saying how big the standard
> > > > deviation actually is). On the other hand, they made no comment
> > > > about the surprising admixture of NA in a Filipino or East Asian
> > > > in some Europeans. As a whole, I'd say it makes a good advertising
> > > > blurb for selling the product to crime labs, but that's about all.
> > > >
> > > > John Chandler
> > > >
> > > > ==============================
> > > > To join Ancestry.com and access our 1.2 billion online genealogy
> > records,
> > > go
> > > > to:
> > > > http://www.ancestry.com/rd/redir.asp?targetid=571&sourceid=1237
> > > >
> > > > Dr. David K. Faux, 4028 Larwin Ave., Cypress, CA, 90630, USA
> > > >
> > > >
> > > >
> > > >
> > > > ---------------------------------
> > > > Do you Yahoo!?
> > > > The New Yahoo! Search - Faster. Easier. Bingo.
> > > >
> > > > ==============================
> > > > To join Ancestry.com and access our 1.2 billion online genealogy
> > records,
> > > go
> > > > to:
> > > > http://www.ancestry.com/rd/redir.asp?targetid=571&sourceid=1237
> > > >
> > > > ==============================
> > > > To join Ancestry.com and access our 1.2 billion online genealogy
> > records,
> > > go to:
> > > > http://www.ancestry.com/rd/redir.asp?targetid=571&sourceid=1237
> > >
> > > ==============================
> > > To join Ancestry.com and access our 1.2 billion online genealogy records,
> > go
> > > to:
> > > http://www.ancestry.com/rd/redir.asp?targetid=571&sourceid=1237
> > >
> > > ==============================
> > > To join Ancestry.com and access our 1.2 billion online genealogy records,
> > go to:
> > > http://www.ancestry.com/rd/redir.asp?targetid=571&sourceid=1237
> >
> > ==============================
> > To join Ancestry.com and access our 1.2 billion online genealogy records, go
> > to:
> > http://www.ancestry.com/rd/redir.asp?targetid=571&sourceid=1237
> >
> > ==============================
> > To join Ancestry.com and access our 1.2 billion online genealogy records, go to:
> > http://www.ancestry.com/rd/redir.asp?targetid=571&sourceid=1237
>
> ==============================
> To join Ancestry.com and access our 1.2 billion online genealogy records, go to:
> http://www.ancestry.com/rd/redir.asp?targetid=571&sourceid=1237


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