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Old 07-25-2012, 03:29 PM   #1
KerryOdair
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Default National Geographic and Family Tree DNA Announce Geno 2.0

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.

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.

Link for details:
http://www.yourgeneticgenealogist.co...-tree-dna.html


Link for National Geographic
https://genographic.nationalgeograph...about-project/
https://genographic.nationalgeograph...sting-results/

Are there discounts available for first-phase participants who want to purchase a Geno 2.0 kit?

We are offering first-phase Genographic participants a limited-time discount 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 discount, 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 discount. Please call our customer service line at 1-800-437-5521 to receive the discount. This discount does not apply to online orders.
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Old 07-26-2012, 03:08 AM   #2
Geoffreyion
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Oh that's really superb! Great job done by the National Geographic as well as the Family Tree DNA. I truly appreciate their hard labour in designing chip for testing ancestry. The information is explained in simple clear terms. I didn't go through the links but soon I will visit to get a interesting view.
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Old 07-26-2012, 10:20 AM   #3
KerryOdair
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More information from Yahoo newbie list. Some of this may be duplicated but just trying to get information to our members about this product and how it affects their testing.

Here is another excellent post from the R-L21 forum from David Reynolds:

beginquote:

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/201...-2-0-launches/
http://www.thegeneticgenealogist.com/
http://blogs.discovermagazine.com/gn...me/#more-17526
http://dna-explained.com/2012/07/25/...e-human-story/

endquote

Some interpretation of the above:

1) I think the FMS mtDNA will become the WTY equivalent where new mutations could be discovered and the Geno 2.0 will test 95 % of the known mtDNA mutations that are currently known. Since the mtDNA structure is only 16,000 base pairs, there are probably not a whole bunch more mutations to be found since 3,300 have been found to date. So all those who tested FMS mtDNA as well as those with HVR1 and HVR2 testing will have their mutations included.

2) I looks like November, 2011 was the cutoff for adding any new content to the custom plate being used. So some of the exciting newly discovered Y-SNPs, DF13, DF63, etc. probably did not make it this round but will be in Geno 2.5. With 10,000 new Y-SNPs from around 1,000 submissions (probably 10M base pairs from the 454 scanner) - there is going to be a lot of new raw data to absorb and understand.

3) I am confused on where the 12,000 Y-SNPs come from. The draft tree of the FTDNA haplotree is only 2,000 Y-SNPs. The must have data mined a lot from the Roche 454 scanner (thought to be the new WTY scanner). The 454 may now be dedicated for research for Geno 2.0 and Geno 2.5 now. Each of the four beta tests with 10M base pairs (vs. 400K with WTY) were yielding 100s of new SNPs per submission. The above implies that they may have behind the scenes used the 454 scanner to re-scan all 400 previous WTYs - what a deal for those people. You can probably assume that the other 500 were very geographically diverse in order to meet Nat Geo desire to properly address the world's haplotree vs. the bias of WTY testing.

--- In [email protected], "wheatons_surname_project" <[email protected]> wrote:

Robert,

This is the best analysis yet of the usefulness of the new product. And I agree with your recommendation to test a brother (if you have one) for the y info---really should be discounted for women.

I do think this a very shrewd business move on FTDNA's part. Eliminates the medical and identity issues, works to FTDNA's strengths and ties into the power of National Geographic. This is really good news for those of us that would like to see FTDNA remain a big player for the long term.

Like computers DNA testing has a higher price tag at the beginning and then 3 years down the road it's almost obsolete with the new tests coming along---but that's just the price we pay for incredibly rapid acceleration of the field.

Thanks again for your review,
Kelly

--- In [email protected], "Robert" <[email protected]> wrote:

Here is my speculative summary of what I have read to date:

1) The exciting news is that it will extremely great for Y-SNP research. It will include 12,000 Y-SNPs - including about all that have primers from FTDNA. Unfortunately, the Scottish DNA SNPs will probably not get included. It will include a lot of redundant SNPs, SNPs where position not clear and a lot very old SNPs 2,000 to 20,000 years old. It will surely include all 60 or so R-L21 SNPs that we know about which now available at $29 per SNP. Obviously, the deep clade test will bite the dust and no longer be ordered for now. Unfortunately, many women will order this test (they really should not) as the Y-chromosome will be empty. Women should sponsor their brothers, sons, husbands, male cousins, etc. to get the most out of this test. Y-STR testing is not part of this new test and will continue to be ordered as today.

2) It includes most of the mtDNA markers. I am sure that it will approach the scope of the full mtDNA test - so it is questionable at this point in time if the current mtDNA tests will provide enough added value to make the extra expense worthwhile. Both males and females have mtDNA, so no issues for this test.

3) The autosomal part is strictly for ethnic / geographic research. It is not a replacement for any Family Finder type test where large segments are compared. This part of the test only includes "Ancestry Informative Markers" (AIMs) which are SNPs that show substantial differences in allele frequency across population groups. Approximately 75,000 AIMs were chosen from approximately 450 populations around the world. You also get this already with Family Finder but that is a very small portion of the Family Finder test.

This will bring hundreds of new people to our haplogroup forums who will ask for assistance to interpret the results - so these forums will be swamped with data and requests to analyze the data. We will have to learn how to collect all this new data - my recommendation is to wait for FTDNA's offering as it will include putting the results into their database vs. just downloading the data from Net Geo and where does that go from there ? FTDNA will probably offer a upload your Nat Geo data for a small fee at some point in time since FTDNA is the lab where these tests are run.

These are additional remarks from rootsweb on the new chip with some additional information by various people.


The FF product looks at 750,000 locations to do the cousin matches. The new Geno 2.0 product has 130,000 SNPs, but they are focused on specific areas of ancient ancestry. 130,000 is not enough to do the FF type of matching, so both of these tests are useful for different purposes.

Dear Reberta,
Dwight and others,Perhaps John Olson will allow data from the new test to be uploaded to GEDmatch for matching purposes, particularly if the data has already been phased before it is uploaded. However, if someone has already done Family Finder or 23andMe and uploaded that data to GEDmatch I don't think that the new Geno 2.0 test will add very much to the value of Family Finder or 23andMe in terms of generating matches. The average coverage for 23andMe's v3 chip is 131.7 SNPs per cM. The SNP average coverage for Family Finder is 104.7 SNPs per cM. The SNP average coverage for the new Geno 2.0 test will be 20.6 SNPs per cM (assuming 146,000 autosomal SNPs are on the chip and assuming 7098 cMs are in the entire genome). The exome is apparently excluded from the new Geno 2.0 test, so that will exclude coverage of about 5% of the genome. It is clear that the coverage with the new Geno 2.0 test will not be as good as is the case with 23andMe and with Family Finder, but in any case it will be still possible to use the Geno 2.0 test data to find people who are related to us in a genealogical time frame if people's data is compared to look for HIRs like GEDmatch does. If the Genographic Project and/or FTDNA would phase all of the new Geno 2.0 test data using a program such as Beagle then I think that there would be value to comparing the phased Geno 2.0 test data with the Family Finder dataset. I think that this is something that we should encourage FTDNA and the Genographic Project to do.
Sincerely,
Tim Janzen

FTDNA will be offering this as an upgrade to existing customers in the fall. NGS is launching now to build up operating capital and public interest. I have a sneaky hunch that the deep clade price increase last spring was FTDNA's method of doing the same thing.
Vince T.

I agree that the chip could have some level of utility for (close) cousin matching. It would depend on the SNP properties -- how they're distributed over the chromosomes, the amount of linkage disequilibrium, the minor allele frequencies in the relevant population, and so forth. The higher SNP densities in FF and RF may include lots of redundancies: if you have a particular allele for one SNP, you are highly likely to have a particular allele for the neighboring SNP (the definition of linkage disequilibrium). Back in the days when DNAPrint was in business, Tony Frudakis estimated that ~100 autosomal SNPs were as good as the 13 CODIS STR markers for paternity testing. STR markers shine because each marker has multiple possible alleles. Paternity testing is special, though, because matching is "obligatory": if an allele is found in a child, it MUST have come from one of the parents.

The question would be how easy it is to achieve a false positive result, e.g. if a 20 cM match between two parties harbors some differences within it that would be unmasked by more SNP coverage. In a few months, we'll have some empirical data to examine this question, but I would hazard a guess that Geno 2.0 could have some predictive value for 2nd cousin relationships. At that level, there are multiple segments of substantial length.

Ann Turner

It does not match you with relatives and is not a competing product with FF. Its focus is ancestral origins.
CeCe

Dear Doug,
I agree with your comments. I thought I would mention that Emily Aulicino's blog at http://genealem-geneticgenealogy.blogspot.com/ says that the reference populations being used will be downloadable.
Sincerely,
Tim

Hi Doug,

Here's what Spencer said "We are working on a manuscript on the reference population data, which includes both Genographic and 1K Genomes populations, and the data will be released when we publish it." I asked if he knew about when that might be and he said that of course, it depends on the publication, etc., but he's hopeful for this fall.

Roberta

This test will have value both for individuals who have identified their haplogroup via advanced SNP testing and for those who are interested in deeper ancestry information. We need to consider that 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.

Wayne

However, one aspect of Geno 2.0 is very intriguing:
---
After this new chip was created by Illumina specifically for NationalGeographic, about 1200 samples were run as proof of concept, including 400WTY (Walk the Y), 350 mitochondrial full sequence and 500 Y samples. All ofthe samples run are checked and tested for all of the SNPs on the chip. Ofcourse, females' samples will fail on all of the Y haplogroup locations,
etc.

Just based on this test run alone of 900 Y chromosome kits, the haplotreeexpanded from 862 SNPs to a total of 6153.
---

Since the only SNPs on the chip are ones already found by some other method,this apparently means that Geno 2.0 is finding thousands of additionalinstances of known SNPs. For example, P189 is already well known as adefiner for E1b1a. But if someone runs Geno 2.0 on a member of the EuropeanN1* clade, he will find that clade to be P189+ also. This P189.2 can thenbe added to the haplotree.

I am still afraid that some will opt for this test instead of the FMS or full-sequence mtDNA test. Both will get them a deep subclade designation. Right now FTDNA requires the FMS for that. 23andMe currently assigns deep subclade designations based on about 15% of the mtDNA sequence. Geno 2.0 will test about 19%. This test will no doubt do a good job in determining their subclade up to the level of PhyloTree Build 14, probably better than 23andMe. However, some of use are looking for subclades which will be in Build 15 - or Build 20. That takes the FMS. As of now, FTDNA still needs to redesignate most of their those with FMS results to the level of Build 14, which was released over three months ago.

I join those in seeing many good things in the new Geno 2.0 test, but I am somewhat concerned in reading a phrase from CeCe’s blog in which she was seemingly citing Spencer Wells as her source:

“..... this team started from scratch choosing SNPs for the Illumina iSelect HD chip platform one and a half years ago.”

That would have been when the current quite outdated version of the deep clade test was established. Only a few of the 2338 Z-series of candiate SNPs in the 1000 Genomes Project were identified or the thousands of singleton SNPs. Some of the Z SNPs have filled in major gaps in the haplogroup trees for a number of haplogroups. Additional important SNPs were found in Walk through the Y testing from the L-series in the last year and a half.

If I am reading this correctly as to the time when these SNPs were chosen for the chip, all the important discoveries since early 2011 will be ignored in Geno 2.0 and we are back to buying $29 tests for each of these new Z and L SNPs since the last deep clade test.

Perhaps Thomas Krahn can clarify. Please tell us this isn’t so.

Ray Banks

I said "started" a year and a half ago. They worked up until much more recently. I don't have the exact date and don't quote me, but didn't I just read someone said up until November 2011 on one of the threads? Regardless, Spencer said that they are already working on an updated version of the chip, so many SNPs discovered after the "cut-off" will be included in the next chip.
CeCe
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Old 07-27-2012, 09:17 AM   #4
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This is an interview with Bennett Greenspan who heads Familytreedna. He talks about the relationship with National Geographic and how their products and Familytreedna products can be used in genetic genealogy.

Geno 2.0 – Q&A with Bennett Greenspan

Geno 2.0 – Q&A with Bennett Greenspan
Posted on July 26, 2012
Bennett Greenspan was gracious enough to call me with the answers to several questions and responses to comments and speculation on blogs and lists today. He wants to thank everyone for their interest and personal support for the ongoing research and the new product. I am putting these in a question and answer format.

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.

Q: When will the new Y tree be available?

A: FTDNA is vetting the Y tree in conjunction with the Genographic Project and prior to the release of these data. This won’t occur until they will have had enough samples to fully vet the 12,000 tree SNPs, confirming the positions on the tree and that all SNP’s are working correctly.

Q: What is the difference between the full mitochondrial sequence (FMS) test and the Geno 2.0 test for mitochondria?

A: Chips can only tell you what is programmed on them. The Geno 2.0 test is not as complete as the FMS. Geno 2.0 includes all mtdna SNPs approved for research purposes at Family Tree DNA plus all known mutations found in Genbank. The Geno 2.0 chip includes a total of about 3,100 locations, more than any other product using this same technology.

This test is very complete for European-centric haplogroups, such as H. However the test is anthropological in nature, not genealogical. This means that while you will receive your haplogroup assignment to the same level as a full sequence test, you will not receive other genealogical information that could be critically important to your research. (Private SNP’s that are unknown will not be ‘discovered’ via chip testing).

If you want your anthropological information, meaning haplogroup information only, then the Geno 2.0 kit is the way to go.

Geno 2.0 has 50% more mtDNA SNP’s than the next best chip technology for mtDNA. The only thing better is the full sequence test. The full sequence test is the only test that can be universally used for scientific research as well.

Q: There seems to be some confusion surrounding what products to order for what purposes.

Geno 2.0

Product Purchase?
Y DNA – 12,000 SNPS – Deep Ancestry – Haplogroup identification Yes
Mitochondrial DNA – Anthropology – Deep Ancestry – Haplogroup Identification Yes
Ethnicity – Worldwide Populations – Ancestral Informative Markers – Deep Ancestry – 137,000 total SNP locations – covers many SNPS not in Family Finder Yes
FTDNA Products

Product Purchase?
Y- DNA Regular STR tests, 12, 25, 37, 67 and 111 markers Yes
Mitochondrial DNA tests for genealogical comparisons Yes
Family Finder –for genealogical matching – cousin matching provided from Family Tree DNA data base Yes
Y DNA deep clade test Order Geno 2.0 unless time is of the essence
Y DNA WTY – after running Geno 2.0 on kit, discuss with Family Tree DNA
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Old 07-31-2012, 12:12 PM   #5
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From:
DNAeXplained – Genetic Genealogy
July 30, 2012

Geno 2.0 Answers from Spencer Wells
Posted on July 30, 2012
Lots of folks have had questions about the Geno 2.0 kits and different aspects of the testing. Dr. Spencer Wells, National Geographic’s Scientist in Residence for the Genographic Project has been kind enough to answer some of the questions he’s been receiving. I know the genetic genealogy community appreciates the continued communication and involvement from Dr. Wells. Thanks Spencer!!

1. How many SNPs do we have in the test?

A total of around 146,000 ancestry-informative markers (AIMs): ~130,000 autosomal and X-chromosomal, ~13,000 Y-chromosomal, and ~3200 mtDNA

2. What is the different between the Genographic Project and the 23andme test? And ancestry.com?

Genographic is a non-profit National Geographic research project focused on mapping the human journey, and encompasses three core components: scientific research, public participation and the Legacy Fund. Our public participation component is available through the purchase of a Geno 2.0 DNA testing kit. Our custom-designed genotyping chip looks at the markers outlined above, and is simply the best available platform for the study of genetic ancestry. For-profit companies, including Ancestry and 23andMe, use slightly modified off-the-shelf chips which were optimized for medical research, not population history.

3. Do we offer ancestry painting?

I assume you are referring to the chromosomal “painting” on the 23andMe website, and no – at this time we don’t offer this feature. It is relatively straightforward to implement, however, and if there is sufficient interest among our participants, we may offer it in the future.

4. Do we give African Americans their Asian percentage?

Everyone receives a breakdown of their regional affiliations, expressed as percentages. This might include northeast Asian or southeast Asian in African Americans, if such components are present.

5. Do we plan on adding a West African or East African to the affiliation?

We are continuing to refine our analysis of the chip data, and may be expanding our list of regional affiliations.

5. How are we different from population finder?

It’s all about the markers: again, because we have created our chip specifically for the study of ancestry, we feel that it is the most accurate tool for determining population affiliation. Our AIMs were drawn from more than 450 world populations, and were chosen on the basis of their ancestry informativeness. We are continuing to refine our analytical methods to provide the best ancestry testing experience available anywhere.

Dr. Wells has been busy answering questions today. Cece Moore has some additional comments on her blog as well. http://www.yourgeneticgenealogist.co...-wells-on.html

MONDAY, JULY 30, 2012

A Short Update from Spencer Wells on Geno 2.0
This morning I received an email from Dr. Spencer Wells who leads the Genographic Project. He asked me to share some information with the community regarding the sources of the Y-SNPs included on the chip that will be used for Geno 2.0. He also commented on the role that he envisions for our citizen scientists within the genetic genealogy community in partnership with Geno 2.0.

To be absolutely clear, I will quote his email, as follows:

"...the Y-markers on the Geno 2.0 chip come from a variety of sources. The majority are entirely new, and are drawn from the work of our team and collaborators:

~3500 from Chris Tyler-Smith, drawn primarily from 1K Genomes data
~3500 from Li Jin, discovered by deep sequencing in East Asian populations from a variety of haplogroups
~5000 from Paolo Francalacci and Sergio Tofanelli, discovered by deep sequencing in Sardinian populations from a variety of haplogroups

The rest are drawn from the ISOGG tree, FTDNA, Hammer and other available sources. The final number of working assays for the rare markers (and thus those most likely to be of interest to the genealogical community) is yet to be determined, as we simply don't have access to all of the the positive controls necessary. This is where the genetic genealogy community can really help, by vetting the rare markers in samples with known phylogenetic positions... I see this as an opportunity for the community to take an active role in helping us to build the definitive Y-chromosome tree. It will also likely yield many markers with extraordinary specificity for family-defining lineages that will be important for genetic genealogy."

I am confident that I can speak for the community when I thank Dr. Wells for his willingness to engage our community and to share further details on this exciting subject with us.
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Old 10-14-2012, 08:02 AM   #6
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The GenoChip 2.0. is now shipping from National Geographic. Received my kit on 10-13-12. Looking forward to investigating the raw data and looking at National Geographics take on the data from the chip.
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Old 11-04-2012, 12:06 PM   #7
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Here is the abstract of a paper to be presented at a 6 Nov meeting of the American Society of Human Genetics. This looks like the long awaited Geno 2.0 description that Dr. Wells allegedly was to publish.

The GenoChip: a new tool for genetic anthropology
Title: The GenoChip: a new tool for genetic anthropology.(3377W) (2:15PM-3:15PM on Wed) (Poster)
Author(s): S. Wells, E. Greenspan, S. Staats, T. Krahn, C. Tyler-Smith, Y. Xue, S. Tofanelli, P. Francalacci, F. Cucca, L. Pagani, L. Jin, H. Li, T. G. Schurr, J. B. Gaieski, C. Melendez, M. G. Vilar, A. C. Owings, R. Gomez, R. Fujita, F. Santos, D. Comas, O. Balanovsky, E. Balanovska, P. Zalloua, H. Soodyall, R. Pitchappan, G. Arun Kumar, M. F. Hammer, B. Greenspan, E. Elhaik

"Background: The Genographic Project is an international effort aimed at charting human history using genetic data. The project is non-profit and non-medical, and through the sale of its public participation kits it supports cultural preservation efforts in indigenous and traditional communities. To extend our knowledge of the human journey, interbreeding with ancient hominins, and modern human demographic history, we designed a genotyping chip optimized for genetic anthropology research.

Methods: Our goal was to design, produce, and validate a SNP array dedicated to genetic anthropology. The GenoChip is an Illumina HD iSelect genotyping bead array with over 130,000 highly informative autosomal and X-chromosomal SNPs ascertained from over 450 worldwide populations, ~13,000 Y-chromosomal SNPs, and ~3,000 mtDNA SNPs. To determine the extent of gene flow from archaic hominins to modern humans, we included over 25,000 SNPs from candidate regions of interbreeding between extinct hominins (Neanderthal and Denisovan) and modern humans. To avoid any inadvertent medical testing we filtered out all SNPs that have known or suspected health or functional associations. We validated the chip by genotyping over 1,000 samples from 1000 Genomes, Family Tree DNA, and Genographic Project populations.

Results: The concordance between the GenoChip and the 1000 Genomes data was over 99.5%. The GenoChip has a SNP density of approximately (1/100,000) bases over 92% of the human genome and is highly compatible with Illumina and Affymetrix commercial platforms. The ~10,000 novel Y SNPs included on the chip have greatly refined our understanding of the Y-chromosome phylogenetic tree. By including Y and mtDNA SNPs on an unprecedented scale, the GenoChip is able to delineate extremely detailed human migratory paths. The autosomal and X-chromosomal markers included on the GenoChip have revealed novel patterns of ancestry that shed a detailed new light on human history. Interbreeding analysis with extinct hominids confirmed some previous reports and allowed us to describe the modern geographical distribution of these markers in detail.

Conclusions: The GenoChip is the first genotyping chip completely dedicated to genetic anthropology with no known medically relevant markers. We anticipate that the large-scale application of the GenoChip using the Genographic Project’s diverse sample collection will provide new insights into genetic anthropology and human history."
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Old 11-08-2012, 11:06 AM   #8
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This is a post from rootsweb.


There was a strictly enforced no photographs rule at the posters, so I
wasn't able to photograph posters as hoped. That said the Geno 2.0
poster was copied and available as a handout by the presenters. A scan
of the flyer is at:

http://www.millerfamilyhistory.com/geno2.jpg

Spoke with Spencer Wells for about 15 minutes. He said that raw results
would be available for download. He said that they will a social media
type set up for those who match to be able to compare common regions and
surnames. I personally was interested in his claim that the new test
will be able to distinguish both on the Y and the autosomal results,
English from German ancestry.

I spoke with those at the 23andMe booth and was told that 23andMe has
already phased all the results in preparation for a new feature coming.
She seemed to think that the phased data would be made available to
customers. She explained that it the data was phased using 1,000 Genomes
along with 23andMe's own data.

--Gary Miller

Further comments from the thread including Thomas from FTDNA

http://archiver.rootsweb.ancestry.co...-11/1352348501


PS at 60% DNA analysis on my sample today (Results soon? )
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Old 11-22-2012, 09:12 AM   #9
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Here is some information on Geo 2.0 one person at least has received results.


Screenshots on my blog:

http://www.yourgeneticgenealogist.co...irst-look.html
CeCe

David Reynold's listed the Y-SNPs from the empty file I provided here: https://www.dropbox.com/s/j8yel8ddsq...eno-Y-SNPs.txt

SNPs listed a CTS refer to Chris Taylor Smith who primarily works with 1000 Genomes data which is primarily European SNPs. These will be the primary source for new R-L21 Y-SNPs since R-L21 has European ancestry. SNPs listed as PF are from Paulo Francalacci which are the Sardinian SNPs. Some of these Y-SNPs could be useful for broader European research - specially around the Mediterranean Sea. SNPs listed as F are probably eastern Asian SNPs researched by Li Jin. Unless you are researching Asian ancestors, these Y-SNPs will probably have limited applicability for researchers of R-L21 ancestors. Also included are 570 L SNPs (primarily from FTDNA Walk the Y testing), 562 Z SNPs (from 1000 Genomes research), 273 M SNPs (Stanford University), 205 P SNPs (University of Arizona), 187 YSC SNPs (FTDNA beta testing using the Roche 454 scanner - stands for Y-SNP Candidate), 131 V SNPs (La Sapienza of Rome, Italy), 60 PAGES SNPs (Massachusetts Institute of Technology), 18 U SNPs (University of Central Florida) and 23 SNPs from numerous sources.

CeCe

CeCe posted an "empty" file, stripping the results of her correspondent so
we could at least see the list of markers. 17 is the chromosome number.
Presumably when you download your file, you'll see the bases listed in the
adjacent columns.


You can look up any SNP at dbSNP by substituting a different rs in this URL:

http://www.ncbi.nlm.nih.gov/projects...cgi?rs=2670854

Thread with more information at:
http://archiver.rootsweb.ancestry.co...-11/1353541599
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Old 12-11-2012, 10:16 AM   #10
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Just received my results from the Geo 2.0. If you want a flavor of the screens and the data supplied based on the test follow the link below. It has many screen shots to look at. I also have the raw data file from the test as well.

http://community.haplozone.net/index.php?topic=3225.0

My particular test correctly identified both my paternal and maternal terminal end snp correctly. Thats better than 23andme did with Version 2.0 of their chip. It will now be the task of the user community to compare files and look for possible new snp's in the tree. Still waiting on the release of the new tree from National Geographic and Familytreedna based on this new test with its paper on the subject as well.

My Geno 2.0 Results: Step-by-Step

http://www.yourgeneticgenealogist.co...p-by-step.html
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Last edited by KerryOdair; 12-12-2012 at 09:50 AM. Reason: Additional Geo 2.0 step-by-step information
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Old 12-14-2012, 03:23 PM   #11
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Thomas Krahn release of CTS and PF SNP's on ymap from rootsweb.
Geno Chip SNP positions on the Y chromosome


"We have now released the position of the new CTS and PF SNPs on ymap.
One of the Genographic colaborators didn't reply on our request for
permission yet, so the F series SNPs cannot be disclosed right now. We
decided not to wait for the others though.

Please bear in mind that this is all preliminary information and there
may be a lot of fuzziness on the actual positions on the tree.
We have to sort this out in a group effort working together with the
distinct haplogroup experts.

You can simply type your SNP name of interest into the "Landmark or
Region" field at
http://ymap.ftdna.com/cgi-bin/gb2/gbrowse/hs_chrY/
or you can download the complete list (daily updated) at
http://ymap.ftdna.com/GRC/refSeq/snps.gff

Also I received hundreds of requests due to inconsistencies that have
been observed. Please understand that I have no way to review SNP
calling data. The chips are called automatically with a batch script
software and we need to take the results as is. We'll certainly find out
that some of the SNPs will not be scored consistently and we can only
disregard them at this point. There is however no way to check an
individual SNP for a person or make corrections in such a dataset. If in
doubt, we need to sequence the specific marker with classical technology
but we can't offer this for free. We'll try to resolve every discrepancy
that way, but give us enough time to do so.

I hope this helps,"

Thomas

Thomas Krahn
FTDNA's Genomics Research Center
Thomas Krahn is a Member of FTDNA's Scientific Advisory Board.
Thomas is the Technical Laboratory Manager of FTDNA's Genomics Research Center in Houston. Graduated from the Technical University of Berlin with an MSC (Dipl. Ing.) in biotechnology and genetics. Thomas specializes in complex kinship testing and family reconstructions. He is an expert in developing new molecular biological methods and assays to resolve questions of biological heritage.
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Old 12-15-2012, 06:46 PM   #12
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This is a very nice distilled file created by Dr. Tim Janzen of the Thomas Krahn file for the y snps.



Dear All,
I downloaded Thomas' file from
http://ymap.ftdna.com/GRC/refSeq/snps.gff and decided to parse the data into
a more readily usable format. I deleted some unnecessary columns and
manipulated the data in various ways to make the file more user friendly.
The revised file may be downloaded as an Excel file from my Dropbox account
at

http://dl.dropbox.com/u/21841126/FTD...20browser.xlsx.

I hope that this file will be helpful to Y SNP researchers.
Sincerely,
Tim Janzen
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Old 12-18-2012, 08:59 AM   #13
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Having great fun with all this new data from the Geo 2.0 test. We already have 11 people in our E-M35 project with returned results. It is going to be an order of magnitude of new discoveries on the Ytree. This test is a baseline of accumulated knowledge in the last six years of Y information that can be tested by this new chip based on deep ancestry only. I had 346 positive Y snps in my test. About 40% were from the 1000 genome project, 40% from Sardinia snps, and 20% from various other sources.

It appears that I have sub V12 SNP in my Geno 2.0 test

V12------------------------------------------------------------------------------------------------NA19309, NA19359

--------- CTS693----------------------------------------------------------------------------------NA19818

--------------------CTS3553/CTS3346/CTS4005---------------------------------------------HG02330

--------------------------------------------------CTS6667/CTS8415---------------------------HG01497, ODair
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Old 12-24-2012, 09:28 AM   #14
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This is an early assessment of new snps to be tested that we were unable to before in the E-M35 Haplogroup. This is just a portion of the E haplogroup not to mention the other groups doing there own work in the Ytree. This was done by one of our researchers in the E-M35 group known as Steve or by his posting name Alf in our project. I think by seeing the numbers of snps how significant this new test is for deep subclad testing.

Geno 2.0 Analysis for E-M35

If you are reading this then the Haplozone Server, most likely in the spirit of the holiday season, has allowed me to post this so let me also extend my best wishes for the holidays to the members of the E-M35 forum.

I have completed my initial analysis of the Geno 2.0 Y Chromosome SNPs of interest to E-M35 based on a comparison with the 1KGP and CG data sets. As this is an initial analysis I expect as more of the raw data is analyzed that there will be some changes and refinements.

First the now released Geno 2.0 list of SNPs contains 13611 entries. In contrast the first raw file posted for an individual(and the one I used in my initial assessment) contained 12316 entries. I would be interested in hearing from those of you who have been able to download your raw data to see what your totals are.

In comparing what is on the chip with what people are seeing in their positive SNP downloads there are some questions which the raw data needs to clarify. The analysis would indicate that all the positive SNPs are not being reported and that some which are questionable are. For example there are around 111 SNPs on the chip that are at the M35 level and 62 at the M78 level and many more at the E and above levels. Only some of these are being reported in those initial downloads that people have been looking at and as will be discussed further this also applies to the levels below this. Therefore the raw data files will be needed to understand this.

I won’t speculate any further on what I described in a previous post as “pattern noise” because I have not spent any time on these other than to say that I would wait for the raw data or FTDNA to clarify these. The one I did look at, CTS6891, came from the 1KGP. There it was not found positive in any of the E-M35 samples and appears to have been positive in only two individuals. One was not in a haplogroup I had typed and the other was an E-P154.

The results of my initial assessment of the individual groups are as follows:

L618-V13 Branch:

I see around 37 SNPs from the V13 “equivalent” group. This includes a few well known and evaluated SNPs (V13, V36, etc.) but it also includes many that were identified in the 1KGP but were either not assigned Z#s or no primers were ever developed. In addition to E-V13 people these should be most useful to the L618* and L1920* people. This sounds like a lot but in the 1KG data there were something like 86 identified. The V13 data indicates that roughly 12ky ago that branch separated from the V22 branch and that the “equivalent” period lasted to around 5ky ago. There are also around 18 sub V13 SNPs on the chip. A few are well known to this project but also included are some singleton SNPs from the 1KGP so it will be interesting to see the raw data on these. What remains to be seen is if there are any sub V13s on the chip that cannot be currently recognized or whether any that are on the chip can be found in any member of the E-M35 project.

V22 Branch:

There appear to be around 24 V22 SNPs on the chip. Because there was only one V22 in the 1KGP project it is difficult to predict their placement on the tree however I can identify four (CTS2548, CTS2817, CTS5479, CTS8892) at this point that were also found in both the V22s sequenced by Complete Genomics. Some of the 24 appear to have not been seen in the V22s that have results. Others like CTS11457 and CTS6080 of interest to this forum were found in the 1KGP individual and I have updated the Tracker with those results. I count 5 sub V22s mostly from previously identified SNPs. I recommend looking at the raw data to understand the details.

V12 Branch:

There appear to be 11 SNPs at the V12 equivalent level and 43 sub V12s. Geno 2.0 has made available many of the sub V12 SNPs from the five V12s in the 1KGP. From Kerry’s test and the discussion associated with his results in this forum the V12 tree will become more refined. This branch as was mentioned above will clearly expand as the details from the raw data and a better understanding of the F series SNP is considered.

V65 Branch:

I see 28 V65 at an approximately equivalent level and 12 clearly sub V65. No one has tested yet from this group.

Z830 Level:

I count 16 SNPs at the Z830 level with one sub Z830 SNP not M34 or M293 related. Some of these were previously identified and assigned Z#s but primers have not been developed.

M34 Branch:

There are about 25 M34s at the equivalent level, 17 sub M34, 15 L795s and 1 sub L795 that can clearly be identified. There appears to be a reasonable representation of SNPs on the chip for this group but this group benefited from the 1KG Z SNPs so whether this adds much to that is not clear. If nothing else it will give some of that group a very cost effective way to test many SNPs of potential interest.

M293 Branch:

I see 30 M293 equivalents at present using the 1KGP data and 6 sub M293s. No M293s have yet reported their results at this time.

L19*-M183 Branch:

This group may have come out on top. I think there is a strong possibility that the L19* people will have their own SNP and maybe more. The M183 people finally get one of the sub M183 SNPs that we could not get for them in the 1KG Z process. It will be interesting to see how this works out for them. The Sardinian samples were very important to this group. I found 57 M183 equivalents and 10 sub M183 SNPs on the chip. I count 51 L19 equivalents, and 76 L19* SNPs.

I hope you find this assessment useful.

Steve
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Old 02-11-2013, 10:20 AM   #15
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This list of erratic SNPS in the Geno 2.0 test is being worked on by both FamilytreeDNA and National Genographic group. It is my understanding that they will be eliminating these false positives in the near future from test results.

"This is one of about a hundred SNPs, which have been erratically positive in GENO 2.0 across all the haplogroups. We talked about them on the list before. It seems they haven't been removed yet.

Here's the list:
CTS1034, CTS10436, CTS10713, CTS10738, CTS11085, CTS11454, CTS11844, CTS12173, CTS2080, CTS2223, CTS230, CTS2447, CTS295, CTS3234, CTS335, CTS3647, CTS3763, CTS3914, CTS4276, CTS4623, CTS4714, CTS477, CTS5458, CTS5580, CTS6010, CTS6353, CTS6384, CTS6891, CTS7453, CTS7492, CTS7859, CTS7951, CTS8133, CTS8178, CTS8244, CTS9096, CTS947, CTS9512, CTS9548, F1173, F1221, F1300, F1327, F1369, F1707, F1754, F1831, F1833, F1842, F1870, F1882, F2000, F2137, F2150, F2177, F2223, F2494, F2503, F2546, F2631, F2845, F2887, F2932, F3035, F3039, F317, F3187, F3225, F3394, F3397, F3455, F375, F3948, F3965, F4131, F4277, F830, F842, F869, F889, F910, F942, F943, F969, L366, L477, L493, L515, L516, L517, L552, L594, M263, PF4208, PF4330, PF5061, PF6868, PF7392, Z148, Z191, Z365.

Sincerely,

Itaï Perez."
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Old 07-17-2013, 10:18 AM   #16
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New software Tool From Chris Morley:

"Dear list,

I have put together a process for automating the generation of a Geno
2.0-based Y-SNP phylogeny.

See my report "An experimental computer-generated Y-chromosomal
phylogeny, leveraging public Geno 2.0 results and the current ISOGG
tree" at [ http://ytree.morleydna.com/Experimen...oPhylogeny.pdf ].
The current ISOGG tree (v. 8.61) was used as the starting point for this
version of the experimental tree.

Additionally, [ http://ytree.morleydna.com ] features a Y-SNP subclade
predictor. Given a set of Y-SNP calls, it will (i) predict the subclade,
(ii) show the phylogenetic placement (when available) of reported SNPs,
and (iii) identify unplaced positive SNPs. It can use either the ISOGG
tree or my experimental tree as the basis for classification. It
accommodates FTDNA-transferred Geno 2.0 data, and also the Full Genomes
demo data.

It's not perfect, but it's a start. It should save some time when
analysing kits with more than a handful of tested SNPs.

I invite your feedback.

Chris Morley"
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Old 08-07-2013, 09:17 AM   #17
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More information on developments on his new phylogenetic tool

"Keep in mind that only a finite number of Y-SNPs could be selected for inclusion on the chip, and there are tradeoffs between even coverage and phylogenetic resolution. After a certain point, trying to fit an additional terminal Y-SNP on the chip comes at the expense of leaving out another one -- either a basal Y-SNP, or a phylogenetically redundant Y-SNP from another branch.

(My next update will feature a separate proof-of-concept phylogeny built using Y-SNP calls from the two Full Genomes demo datasets.) But for those interested in experimenting, future releases of my phylogeny will be accompanied by a CSV summary file with the columns "name, parent, SNPcount, cumuSNPcount, kitCount, cumuKitCount". Expect the next version of my tree later in the week."

Chris Morley
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Old 08-12-2013, 09:18 AM   #18
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This is the link to the latest tree from Chris Morely dated 8-Aug-2013

http://ytree.morleydna.com/Experimen...ny20130808.pdf

It appears that he has 75 E1b1b1 tests in this new tree and a total of 1850 Geno 2.0 tests. That is a considerable number which includes tests from other groups than just E-M35.

He also at the end of the file has two FullGenomes sequenced demo samples using this program.

This is a link for Geno 2.0 raw data in zip file download format with over 100 samples.

https://www.dropbox.com/s/zv0khjlk6g...mpare_view.zip
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