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Archiver > GENEALOGY-DNA > 2005-04 > 1114368864


From: "Lowe DNA" <>
Subject: RE: [DNA] A few more answers from Spencer Wells
Date: Sun, 24 Apr 2005 13:54:24 -0500
In-Reply-To: <200504240821.AA1694499132@usernet.com>


Max...

A couple of more questions..

(1.) Can FTDNA customers upload our full 37 markers and HVR1/HVR2 markers
to the IBM database or will be limited to 20 STR markers or so ?
If we upload 12 or 25 to the NGS database and then upgrade
to 27 markers will the upgrade copyover entail another fee ?

(2.) As new markers are discovered that are important, will FTDNA
roll them into your available test offerings ? How about new SNPS.

(3.) What are there Neanderthal lineages that can be tested; or,
is Spencer referring to remains from ancient burial remains ????

(4.) Have the IBM gurus given you any idea of the database design
or the search functionality by: Y-DNA/mtDNA, SNP, geographic location,
language group, frequency of distribution, or other parameters
that let us observe patterns ?

(5.) Have they spoken about opening up this database to folks
like us to perform group searches or will only academics be
allowed to browse, data mine this database..?

(5.) Will the improved IBM haplogroup predictor algorithm be
available for use by FTDNA as they are developed ?

Like the notice about non-medical information and the ban on
patenting findings. Gives me faith that this project will help
all of us...

Bill

-----Original Message-----
From: Max Blankfeld [mailto:]
Sent: Sunday, April 24, 2005 8:21 AM
To:
Subject: [DNA] A few more answers from Spencer Wells



List Members,

Here are a few more answers that Spencer Wells forwarded to me last night:
***********************************************************
We will primarily be collecting males from the indigenous populations around
the world, which will maximize the number of Y-chromosomes while providing
mtDNA as well. It is also easier to study X-chromosome variation in men,
since the X is only present in one copy and it is therefore easier to infer
haplotypes.

The populations will be chosen through a process of consultation with elders
and the people themselves. I have been in Australia for the past few days
getting this started, and am off to Singapore and India this week. We will
sample both ‘ethnically defined’ (by language, customs, etc.) and
‘geographically defined’ (i.e. if a group, such as the Kazaks of Central
Asia, are widespread then we will attempt to sample roughly on a grid)
groups.

Sampling from indigenous groups will be through blood draws, which will
yield hundreds of micrograms of DNA. This amount of DNA if far more than we
need for typing Y and mtDNA, and it will allow us to apply new markers to
the study of migratory patterns in the future. Particularly as the HapMap
data becomes available, new autosomal haplotype systems should provide great
resolution for questions that are unanswerable using Y and mtDNA (remember
that these only assess a tiny fraction of your complete genomic ancestry).
The DNA will be stored at the regional center that collected it, and will be
available for study in the future by all members of the scientific
community – effectively a virtual, global biobank. These studies will only
take place as collaborations, and the proposed genotyping must follow the
guidelines for the study – e.g. only markers that tell us about historical
or anthropological information. Also, the actual laboratory work will take
place at the regional center(s) – one of our project goals is to build
scientific capacity in the less developed countries (Brazil, South Africa,
India, etc.) where we have centers. No medical research will ever be
conducted using these samples, for reasons having to do with informed
consent and intellectual property. We will release all of the anonymous
data into the public domain as we analyze it. We feel that this information
is part of the ‘commons’ of our species – it belongs to everyone – and no
attempt will be made to patent it.

We will be testing every indigenous sample collected for Y and mtDNA. In
the case of the former, a multiplex PCR technique will be used to type AT
LEAST the 12 STR markers typed by Family Tree DNA. We will probably be
typing more – perhaps as many as 20 – in the initial screen. We will also
sequence HVR-1 in each individual. Initially, we will also SNP type every
Y-chromosome and mtDNA to confirm the haplogroup. Once we have a sufficient
database, we will probably be able to predict haplogroup affiliation with a
high degree of precision, allowing us to simply type the STRs for most
individuals. Over time new markers will be discovered – some perhaps by us,
to answer specific questions – but the key will always be having access to
the indigenous DNA samples to type these markers. These are the most
valuable asset of the project, and we don’t have to limit ourselves to any
particular markers – we’ll choose the best ones to answer the questions we
are investigating.

The maps shown on the website atlas at the moment demonstrate the routes
followed by the markers that will be reported in the public component at the
moment. Over time we will add more routes (= subhaplogroups) as the
information on them improves. Remember that this is a GLOBAL project of
enormous logistical complexity, and therefore that we may not show all of
the details of a well-studied region like Europe at this time. We will be
improving the level of detail over the coming years, and European users in
particular should see their routes become much more detailed. Purchasing a
participant’s kit is like purchasing a ‘subscription to your genome’, and
you will be able to check back every few months to see what has been updated
in your profile.

Finally, the data collected from the public part of the project will allow
us to add an enormous number of genotypes to the database, giving us the
power to answer some key questions. For instance, at the moment there is no
evidence for interbreeding with Neanderthals as modern humans migrated into
western Europe, but this is based on only 15-20,000 individuals who have
been genotyped. Will we find a rare Neanderthal lineage in the 234,000th
sample we type? Also, the public samples will allow us to assess patterns
of genetic variation in admixed populations. There are some interesting
studies we hope to do with the US census data, comparing Y and mtDNA
patterns to that database. So these samples really are part of the project,
not simply a way to raise funds - although that is a great aspect as well.
Most people I've spoken to love the fact that all of the net proceeds from
their kit - slightly more than 20% of the $99.95 price - get plowed back
into the research and Legacy project.

Spencer Wells
************************************************************

Max Blankfeld
VP Operations & Marketing
Family Tree DNA
History Unearthed Daily
http://www.familytreedna.com
713-868-1438




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