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Author Topic: National Geographic and Family Tree DNA Announce Geno 2.0  (Read 29306 times)
Heber
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« on: July 25, 2012, 07:25:03 PM »

This is an exciting new product from National Genographic and FTDNa and a far cry from the 12 marker test I did in 2005 with and estimated 12,000 Y DNA SNPs.

"National Geographic is entering the next phase of their Genographic Project in partnership with  Family Tree DNA and the genetic genealogy community. Continuing to move toward their goal of mapping the pattern of human genetics, they are introducing the new GenoChip 2.0. This chip is specifically designed for ancestry testing and includes SNPs from autosomal DNA, X-DNA, Y-DNA and mtDNA. The design of the new chip was a collaborative effort between Eran Elhaik of Johns Hopkins, Spencer Wells of National Geographic, Family Tree DNA and Illumina.  The testing will be done at FTDNA in Houston....
The Geno 2.0 test will be offered for $199.95 with free shipping within the US on the National Geographic site and will only require a cheek swab. All resulting data will be downloadable. They will begin accepting pre-orders today for a fall shipping date (10/30/12). In the future, orders will  also be accepted through the Family Tree DNA website....

Y-DNA SNPs
 
The chip includes just over 12,000 Y-DNA SNPs. Ten thousand of these are completely unique and have “never been published before”.  First, they created probes for all of the 862 Y-SNPs from the current YCC 2010 Tree. Next, they contacted research centers all over the world and asked them to provide a list of all the Y-SNPs that they had data mined or discovered, including the L SNPs and Z SNPs and “private Hammer” SNPs, and created probes for those. Y-SNPs discovered by citizen scientists were also included....."

http://www.yourgeneticgenealogist.com/2012/07/national-geographic-and-family-tree-dna.html

http://www.thegeneticgenealogist.com/2012/07/25/the-genographic-project-announces-geno-2-0/
« Last Edit: July 25, 2012, 08:27:22 PM by Heber » Logged

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eochaidh
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« Reply #1 on: July 25, 2012, 07:29:54 PM »

This is pretty amazing for the price.
« Last Edit: July 25, 2012, 07:30:05 PM by eochaidh » Logged

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df.reynolds
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« Reply #2 on: July 25, 2012, 11:16:24 PM »

IMPORTANT NOTE: If you are an existing FTDNA customer, please do not pre-order through National Geographic at this time. There is no advantage to doing so, it will likely cost you more, and at this point, it is not at all clear what will happen if you do so -- you may end up with some test results under your current kit, and the Geno 2.0 results underneath a different kit number. Please give FTDNA a chance to clarify what current customers should do to make sure we don't end up with an IT nightmare.

Geno 2.0
https://genographic.nationalgeographic.com/about/

* Does not include STRs -- does not replace Y37/Y67/Y111 tests
* Does not predict family relationships -- does not replace Family Finder
* Is not a full mitochrondial sequence -- does not replace FMS
* Contains no medical information (avoid wrath of Big Brother)

* If pre-ordered from National Geographic, will ship no later than 30 Oct, but expected to go out in early September
* 6-8 weeks for results, no waiting list expected
* FTDNA customers will have the option to test an existing sample at an upgrade price. Link will appear on the myFTDNA page if the kit is eligible (late summer, early fall)

* Does replace the current Deep Clade tests
* No cost to transfer results from National Geographic to FTDNA
* 12,000 Y SNPs
* 3,352 mtDNA SNPs (if you see 32,000 referenced, they are referring to the number of probes necessary to accurately sample 3,352 mtDNA SNPs)
* Some 130,000 autosomal and X-chromosomal Ancestry Informative Markers, derived from roughly 450 populations around the globe
* Focus is deep ancestry, not finding relatives
* Raw data will be available for download
* Reference population data will be downloadable
* 400 WTY and 500 Y Samples were tested as proof of concept -- 5,291 new nodes found to add to the haplotree

Per Thomas Krahn:
* Cutoff on Y SNPs was rough Nov 2011; new DF, L, Z SNPs found after that won't be included [but will be in a future custom chip update]
* Not all "known" Y-SNPs will be available -- "not all SNPs can be typed on a chip"
* Spencer Wells has a paper pending; once that is published, information on markers being tested will be available via Thomas's db. [this fall for the paper??]

Question: Custom Illumina chip was vetted by running against 400 pre-existing WTY samples, finding over 5,000 new nodes to add to the haplotree. Will customers be able to order an "upgrade" for their sample and obtain this data, sooner than later? (Since it already exists.)

Blogs which discuss Geno 2.0:
http://www.yourgeneticgenealogist.com/
http://genealem-geneticgenealogy.blogspot.com/
http://legalgenealogist.com/blog/2012/07/25/geno-2-0-launches/
http://www.thegeneticgenealogist.com/
http://blogs.discovermagazine.com/gnxp/2012/07/the-genographic-project-onto-the-autosome/#more-17526
http://dna-explained.com/2012/07/25/national-geographic-geno-2-0-announcement-the-human-story/
« Last Edit: July 26, 2012, 07:38:51 PM by df.reynolds » Logged
eochaidh
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« Reply #3 on: July 25, 2012, 11:41:29 PM »

Well, I guess it's not as good as I thought, but I don't really care about finding relations or recent ancestry. Not that I wouldn't like to know who my mystery, female 2nd cousin is on 23andMe, but I know where my family is from on all counts. Unless some exotic person was an NPE in Ireland, Scotland, Quebec or France. That would have already showed up on my autosomal population results, though, I guess. I have a high Caucasus score, so perhaps an Armenian guy or gal.

If this stuff can help find when and from where people came to The Isles back in the Bronze Age, I'd be pleased. I'm probably being an idiot again  :)
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secherbernard
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« Reply #4 on: July 26, 2012, 03:31:33 AM »

* 400 WTY and 500 Y Samples were tested as proof of concept -- 5,291 new nodes found to add to the haplotree
How to know if my WTY sample was tested as proof of concept, and then how to get the results ?
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mtDNA: U6a7a1
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df.reynolds
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« Reply #5 on: July 26, 2012, 05:24:52 AM »

* 400 WTY and 500 Y Samples were tested as proof of concept -- 5,291 new nodes found to add to the haplotree
How to know if my WTY sample was tested as proof of concept, and then how to get the results ?

I am trying to find that out from FTDNA, and will certainly pass along whatever information I might find out.

--david
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secherbernard
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« Reply #6 on: July 26, 2012, 06:31:24 AM »

I am trying to find that out from FTDNA, and will certainly pass along whatever information I might find out.

--david
Thanks David! My WTY id is GRC014326
« Last Edit: July 26, 2012, 06:31:36 AM by secherbernard » Logged

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mtDNA: U6a7a1
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Ysearch of my maternal uncle: CEC59

Wayne Kauffman
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« Reply #7 on: July 26, 2012, 06:37:51 AM »

due to the number of offered SNPs there is a reasonable chance that one will be able to identify a SNP, say M365.xx, which help define your paternal line within a genealogical time frame.  In other words multiple occurrences of a SNP (L176.1, L172.2,......) will be identified and some of these will end up being private to a specific line and of great genealogical value.  There also means there will be some value in having cousins tested to zero in on the age of specific SNP(s) that appear to be private to your lineage.
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secherbernard
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« Reply #8 on: July 26, 2012, 09:00:24 AM »

I imagine that the next updated FTDNA Y-DNA haplotree will have the same SNPs that those present on this GEno2.0 chip.
« Last Edit: July 26, 2012, 09:01:15 AM by secherbernard » Logged

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mtDNA: U6a7a1
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Ysearch of my maternal uncle: CEC59

gtc
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« Reply #9 on: July 26, 2012, 09:59:25 AM »

I imagine that the next updated FTDNA Y-DNA haplotree will have the same SNPs that those present on this GEno2.0 chip.

To date, FTDNA has based its tree on the few and far between peer-reviewed papers authored by the YCC ... which is why it is always so far behind the real world action.
« Last Edit: July 26, 2012, 09:59:39 AM by gtc » Logged

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Mike Walsh
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« Reply #10 on: July 26, 2012, 10:57:40 AM »

I imagine that the next updated FTDNA Y-DNA haplotree will have the same SNPs that those present on this GEno2.0 chip.

To date, FTDNA has based its tree on the few and far between peer-reviewed papers authored by the YCC ... which is why it is always so far behind the real world action.

Maybe Richard R knows the answer to this.  

One of the nice things about the paper he and several hobbyists and Thomas Krahn wrote is that it is published and I think qualifies as a peer-reviewed paper. Therefore, FTDNA does not have to wait on YCC which seems to be tied into the University of Arizona. Not sure I get all of the relationships, but YCC is so slow its practically useless.... at least for our purposes.
« Last Edit: July 26, 2012, 10:58:43 AM by Mikewww » Logged

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gtc
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« Reply #11 on: July 26, 2012, 11:20:38 AM »

I imagine that the next updated FTDNA Y-DNA haplotree will have the same SNPs that those present on this GEno2.0 chip.

To date, FTDNA has based its tree on the few and far between peer-reviewed papers authored by the YCC ... which is why it is always so far behind the real world action.

Maybe Richard R knows the answer to this.  

One of the nice things about the paper he and several hobbyists and Thomas Krahn wrote is that it is published and I think qualifies as a peer-reviewed paper. Therefore, FTDNA does not have to wait on YCC which seems to be tied into the University of Arizona. Not sure I get all of the relationships, but YCC is so slow its practically useless.... at least for our purposes.

The YCC thing is pretty circular, given that Michael Hammer is a member of every part of YCC and he's also FTDNA's chief scientist and member of their Scientific Advisory Board.

http://ycc.biosci.arizona.edu/contributors.html
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gtc
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« Reply #12 on: July 26, 2012, 11:51:25 AM »

One of the nice things about the paper he and several hobbyists and Thomas Krahn wrote is that it is published and I think qualifies as a peer-reviewed paper.

Given that the authors are not themselves academics -- and of course that's the thrust of the paper's raison d'etre-- then I think it will not excite much interest among the academic community.

It's moot what Dr Michael Hammer, in particular, thinks about any of this work, given his status at FTDNA. It would be interesting to ask him directly.
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Y-DNA: R1b-Z12* (R1b1a2a1a1a3b2b1a1a1) GGG-GF Ireland (roots reportedly Anglo-Norman)
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Richard Rocca
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« Reply #13 on: July 26, 2012, 12:13:20 PM »


Maybe Richard R knows the answer to this.  

One of the nice things about the paper he and several hobbyists and Thomas Krahn wrote is that it is published and I think qualifies as a peer-reviewed paper. Therefore, FTDNA does not have to wait on YCC which seems to be tied into the University of Arizona. Not sure I get all of the relationships, but YCC is so slow its practically useless.... at least for our purposes.

Mike, I can only assume that FTDNA needs some stability in its nomenclature. We get confused by the constant renaming of haplogroups, so you can imaging the casual DNA customer that logs into his or her FTDNA homepage once or twice a year.

Regarding the paper, it was indeed peer reviewed.
« Last Edit: July 26, 2012, 12:54:56 PM by Richard Rocca » Logged

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DaveinCA
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« Reply #14 on: July 26, 2012, 12:19:13 PM »

For those of us associated with well-defined haplogroups such as M222, how is Geno 2.0 relevant?  Will there be SNPs under M222?  20% of M222s have DYS391=10 and the densities are highest for them in the historic Breifne region.  Will WTY or 1000 Genomes Project or more STRs or something else be the key to subdivide groups like M222 to the Breifne group and beyond (i.e. still narrower)?
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Heber
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« Reply #15 on: July 26, 2012, 02:07:59 PM »

For those of us associated with well-defined haplogroups such as M222, how is Geno 2.0 relevant?  Will there be SNPs under M222?  20% of M222s have DYS391=10 and the densities are highest for them in the historic Breifne region.  Will WTY or 1000 Genomes Project or more STRs or something else be the key to subdivide groups like M222 to the Breifne group and beyond (i.e. still narrower)?

From Richards post above, I expect many of the new SNPs discovered since Nov 2011 are not included in this version but will be included in a future chip update. Spencer Wells paper expected in the fall should give further detail on the structure of the Tree and SNP coverage. This does not replace genealogy products such as FF and recent relative matching but looks like a good base platform for deep ancestry analysis. I look forward to seeing if we can use it to map to the Gaelic Clan structure. I hope the design is flexible enough to support the rapid rate of new SNP discovery.


"Per Thomas Krahn:
* Cutoff on Y SNPs was rough Nov 2011; new DF, L, Z SNPs found after that won't be included [but will be in a future custom chip update]
* Not all "known" Y-SNPs will be available -- "not all SNPs can be typed on a chip"
* Spencer Wells has a paper pending; once that is published, information on markers being tested will be available via Thomas's db. [this fall for the paper??]"
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Heber


 
R1b1a2a1a1b4  L459+ L21+ DF21+ DF13+ U198- U106- P66- P314.2- M37- M222- L96- L513- L48- L44- L4- L226- L2- L196- L195- L193- L192.1- L176.2- L165- L159.2- L148- L144- L130- L1-
Paternal L21* DF21


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df.reynolds
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« Reply #16 on: July 26, 2012, 07:37:47 PM »

Please see this blog entry for Bennett Greenspan's answers to some of the questions about Geno 2.0.

http://dna-explained.com/2012/07/26/geno-2-0-qa-with-bennett-greenspan/

-david
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Peter M
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« Reply #17 on: July 26, 2012, 07:48:58 PM »

For those of us associated with well-defined haplogroups such as M222, how is Geno 2.0 relevant?  Will there be SNPs under M222?  20% of M222s have DYS391=10 and the densities are highest for them in the historic Breifne region.  Will WTY or 1000 Genomes Project or more STRs or something else be the key to subdivide groups like M222 to the Breifne group and beyond (i.e. still narrower)?
Bennett's Blog quoted by David gives the answer:

By way of example, in haplogroup R-M222 – the new Geno chip includes discoveries of at least three unique SNP’s downstream of R-M222.
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DaveinCA
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« Reply #18 on: July 26, 2012, 07:51:25 PM »

3 SNPs under M222 on the chip!  :^)
I wonder whether they will be separately available to test at FTDNA.
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Heber
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« Reply #19 on: July 27, 2012, 08:14:40 AM »

Please see this blog entry for Bennett Greenspan's answers to some of the questions about Geno 2.0.

http://dna-explained.com/2012/07/26/geno-2-0-qa-with-bennett-greenspan/

-david

From Bennet Greenspan's answers:

"Q:  Can I purchase the Geno 2.0 kit elsewhere?

A:  The Geno 2.0 product can only be purchased through the National Geographic Society.  This product cannot be ordered from Family Tree DNA..  

Q:  Will there be a way to move my Geno 2.0 results to the Family Tree DNA database?

A: As with the original National Geographic product, we plan to have a link on the Geno 2.0 personal page to allow people to upload their results.  With the Geno 2.0 deep SNP results, they will be able to enter their Family Tree DNA account number, if they have an existing account at Family Tree DNA, and their deep SNP results will be included with their other tests results on their personal page.

Q:  Does Family Tree DNA plan to offer a test that will be more extensive then the new Genographic test for the Y chromosome?

A:  No. The most extensive test for obtaining YDNA SNP data is available on the Geno 2.0 chip and Family Tree DNA has no plans to compete with its partner.  STR results will not be supplied by Geno 2.0 and all regular genealogical marker tests should be ordered through Family Tree DNA.  These two tests go hand in hand.

By way of example, in haplogroup R-M222 – the new Geno chip includes discoveries of at least three unique SNP’s downstream of R-M222.

These 10,000 new SNPs will provide, for almost everyone, one or two additional clades (subhaplogroups) down the tree from where they are located today.  For some people, these will reach into a genealogical timeframe, connecting their SNPs and their STR data.  The STR tests will then be used to further augment the Geno 2.0 SNP tests for genealogical comparisons within families."

David, what is the recommendation for testing. Test on Genographic using the $30  for Genographic 1.0 subscribers or wait for a FTDNA offer. It is not clear from Benett's reply if FTDNA will offer this test.

Roberta's blog on the announcement is really very good.

http://dna-explained.com/2012/07/25/national-geographic-geno-2-0-announcement-the-human-story/
« Last Edit: July 27, 2012, 09:30:38 AM by Heber » Logged

Heber


 
R1b1a2a1a1b4  L459+ L21+ DF21+ DF13+ U198- U106- P66- P314.2- M37- M222- L96- L513- L48- L44- L4- L226- L2- L196- L195- L193- L192.1- L176.2- L165- L159.2- L148- L144- L130- L1-
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Mike Walsh
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« Reply #20 on: July 27, 2012, 10:58:03 AM »

For those of us associated with well-defined haplogroups such as M222, how is Geno 2.0 relevant?  Will there be SNPs under M222?  20% of M222s have DYS391=10 and the densities are highest for them in the historic Breifne region.  Will WTY or 1000 Genomes Project or more STRs or something else be the key to subdivide groups like M222 to the Breifne group and beyond (i.e. still narrower)?

From Richards post above, I expect many of the new SNPs discovered since Nov 2011 are not included in this version but will be included in a future chip update. Spencer Wells paper expected in the fall should give further detail on the structure of the Tree and SNP coverage. This does not replace genealogy products such as FF and recent relative matching but looks like a good base platform for deep ancestry analysis. I look forward to seeing if we can use it to map to the Gaelic Clan structure. I hope the design is flexible enough to support the rapid rate of new SNP discovery.


"Per Thomas Krahn:
* Cutoff on Y SNPs was rough Nov 2011; new DF, L, Z SNPs found after that won't be included [but will be in a future custom chip update]
* Not all "known" Y-SNPs will be available -- "not all SNPs can be typed on a chip"
* Spencer Wells has a paper pending; once that is published, information on markers being tested will be available via Thomas's db. [this fall for the paper??]"

Does this put DF27 in or out?
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df.reynolds
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« Reply #21 on: July 27, 2012, 07:47:54 PM »


David, what is the recommendation for testing. Test on Genographic using the $30  for Genographic 1.0 subscribers or wait for a FTDNA offer. It is not clear from Benett's reply if FTDNA will offer this test.

Roberta's blog on the announcement is really very good.

http://dna-explained.com/2012/07/25/national-geographic-geno-2-0-announcement-the-human-story/


Well, from what Bennett said, it sound like FTDNA would not be offering Geno 2.0 as an upgrade anytime soon. My own personal decision is go ahead and order Geno 2.0 from Nat Geo, taking advantage of the $30  for v1.0 customers.

-david
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Richard Rocca
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« Reply #22 on: July 27, 2012, 09:33:55 PM »


David, what is the recommendation for testing. Test on Genographic using the $30  for Genographic 1.0 subscribers or wait for a FTDNA offer. It is not clear from Benett's reply if FTDNA will offer this test.

Roberta's blog on the announcement is really very good.

http://dna-explained.com/2012/07/25/national-geographic-geno-2-0-announcement-the-human-story/


Well, from what Bennett said, it sound like FTDNA would not be offering Geno 2.0 as an upgrade anytime soon. My own personal decision is go ahead and order Geno 2.0 from Nat Geo, taking advantage of the $30  for v1.0 customers.

-david

David, how can I order v1.0? I am both a Nat Geo and FTDNA customer. Thanks.
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df.reynolds
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« Reply #23 on: July 27, 2012, 09:49:49 PM »


David, what is the recommendation for testing. Test on Genographic using the $30  for Genographic 1.0 subscribers or wait for a FTDNA offer. It is not clear from Benett's reply if FTDNA will offer this test.

Roberta's blog on the announcement is really very good.

http://dna-explained.com/2012/07/25/national-geographic-geno-2-0-announcement-the-human-story/


Well, from what Bennett said, it sound like FTDNA would not be offering Geno 2.0 as an upgrade anytime soon. My own personal decision is go ahead and order Geno 2.0 from Nat Geo, taking advantage of the $30  for v1.0 customers.

-david

David, how can I order v1.0? I am both a Nat Geo and FTDNA customer. Thanks.

Richard, this is the info I found on the web--I plan on ordering Monday (I need to find my v1.0 order information this weekend...).

Quote
We are offering first-phase Genographic participants a limited-time  of $30 on the Geno 2.0 kit. For a limited-time only, first-phase Genographic participants can purchase a Geno 2.0 kit for $169.95 (includes free shipping within the US). To receive this , you will need to have purchased the first generation Genographic Project Participation Kit. Participants who who did not purchase the first generation kit, but received the kit as a gift are not eligible for this . Please call our customer service line at 1-800-437-5521 to receive the . This  does not apply to online orders.

EDIT: The above reads a little funny, because apparently the board s/w is eating the word "d-i-s-c-o-u-n-t" every place it appears.
--david
« Last Edit: July 27, 2012, 09:52:01 PM by df.reynolds » Logged
secherbernard
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« Reply #24 on: July 28, 2012, 02:51:58 PM »

A french guy who wanted to buy the Geno 2.0 test on the genographic project site, got the following message:
Quote
This item cannot be shipped to France.
What is the problem ?
« Last Edit: July 28, 2012, 02:55:04 PM by secherbernard » Logged

YDNA: R-DF13+ L69+ DYS464X: cccc.3
mtDNA: U6a7a1
mtDNA of my father: U5a2c
YDNA of my maternal uncle: I1*
Ysearch and Mitosearch: UE9BU
Ysearch of my maternal uncle: CEC59

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