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k.o.gran
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« on: July 23, 2012, 07:16:18 AM »

Does anyone have any news on when FTDNA is going to update their deep clade test? I believe it was announced that it's going to happen this year? The current version is borderline useless for L21.

Current test below L21: 9 SNP's where one is likely private.
Current ISOGG tree below L21: 31 SNPs where one is unpublished

Hopefully DF49 will be added to the ISOGG tree above DF23 before FTDNA updates their tree. I don't believe we need to prove its position in regards to DF23 as the anonymous researcher has already done so.

However, I wish S190 wasn't on the tree as the only way to cross test for it is through a ridiculously expensive test.

-Kai
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df.reynolds
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« Reply #1 on: July 23, 2012, 10:18:40 AM »

Does anyone have any news on when FTDNA is going to update their deep clade test? I believe it was announced that it's going to happen this year? The current version is borderline useless for L21.

Current test below L21: 9 SNP's where one is likely private.
Current ISOGG tree below L21: 31 SNPs where one is unpublished

Hopefully DF49 will be added to the ISOGG tree above DF23 before FTDNA updates their tree. I don't believe we need to prove its position in regards to DF23 as the anonymous researcher has already done so.

However, I wish S190 wasn't on the tree as the only way to cross test for it is through a ridiculously expensive test.

-Kai
I suspect the first gating factor is publication of Dr. Karafet's update of the Y-Haplotree, which rumors have suggested will be out late summer or early fall.

I'm hoping FTDNA will use Dr. Karafet's paper as a basis for their update, but will also add newer SNPs as well. Given the way that publishing a paper works, I would suspect that Dr. Karafet's paper is unlikely to include anything found after the beginning of this year.

Other rumors suggest that FTDNA may (finally) improve their IT process such that updating their haplotrees can occur on an ongoing basis. Not holding my breath on that one; I'm still waiting for micro-allele values to be included in the Y-STR reports, and I believe that has been promised for at least three years.

There has been a fair bit of controversy over including "S" SNPs on the ISOGG tree when the location has not been published. No one is particularly happy about it, but bottom-line is the ISOGG tree is intended as a comprehensive reference, so it would be hard to justify excluding them. Particularly in this case where S190 defines a well established group (Little Scots), and we know what the haplotypes for the SNP look like. Which is more than we have for some SNPs from published research papers.

--david
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k.o.gran
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« Reply #2 on: July 23, 2012, 11:22:01 AM »

Does anyone have any news on when FTDNA is going to update their deep clade test? I believe it was announced that it's going to happen this year?
I suspect the first gating factor is publication of Dr. Karafet's update of the Y-Haplotree, which rumors have suggested will be out late summer or early fall.

I'm hoping FTDNA will use Dr. Karafet's paper as a basis for their update, but will also add newer SNPs as well. Given the way that publishing a paper works, I would suspect that Dr. Karafet's paper is unlikely to include anything found after the beginning of this year.

I'm unfamiliar with Dr. Karafet. Is it so that FTDNA's haplotree isn't based on the ISOGG tree, but rather a different publication/revision of the tree?

-Kai
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df.reynolds
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« Reply #3 on: July 23, 2012, 12:05:57 PM »

Does anyone have any news on when FTDNA is going to update their deep clade test? I believe it was announced that it's going to happen this year?
I suspect the first gating factor is publication of Dr. Karafet's update of the Y-Haplotree, which rumors have suggested will be out late summer or early fall.

I'm hoping FTDNA will use Dr. Karafet's paper as a basis for their update, but will also add newer SNPs as well. Given the way that publishing a paper works, I would suspect that Dr. Karafet's paper is unlikely to include anything found after the beginning of this year.

I'm unfamiliar with Dr. Karafet. Is it so that FTDNA's haplotree isn't based on the ISOGG tree, but rather a different publication/revision of the tree?

-Kai

FTDNA bases their tree on the "YCC" tree, which was most recently officially revised in 2008 in a paper that Dr. Karafet was the lead author on. Dr. Karafet is at U of Arizona, same as Dr. Hammer (who also has the title of FTDNA's Chief Scientist).

Quote from: FTDNA
In 2002, the YCC, a collaborative group of population geneticists from major academic research labs, was formed. They tested samples for all known SNPs, then published an inclusive tree of the major haplogroups and their subclades. (YCC 2002) In 2008, the tree was updated. (Karafet 2008) The revised tree included newly discovered SNPs and corrected the placement of those already on the tree.

Dr. Karafet's work is significant in that in addition to gathering data from a large number of sources, she will independently verify the placement of the SNPs using the large collection of samples that U of A has.

FTDNA's update in early 2011, which they stated was based on a YCC update, was largely based on as yet unpublished work of Dr. Karafet's.

--david
« Last Edit: July 23, 2012, 12:10:28 PM by df.reynolds » Logged
k.o.gran
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« Reply #4 on: July 23, 2012, 01:18:14 PM »

Thank you so much for explaining it for me. I (wrongly) believed the FTDNA tree was based on the ISOGG tree. I believe it would have been much better for us if it was so instead of basing it on a paper that comes out every 4-6 years.

-Kai
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razyn
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« Reply #5 on: July 23, 2012, 05:55:38 PM »

I believe it would have been much better for us if it was so instead of basing it on a paper that comes out every 4-6 years.

Sometimes the distinction between academic rigor and rigor mortis is a tough call.

Also, the Brits probably spell that rigour.
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rms2
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« Reply #6 on: July 23, 2012, 06:00:29 PM »

I believe it would have been much better for us if it was so instead of basing it on a paper that comes out every 4-6 years.

Sometimes the distinction between academic rigor and rigor mortis is a tough call.

Also, the Brits probably spell that rigour.

I think the main difference is that rigor mortis only lasts about two or three days, then things loosen up. ;-)
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Arch Y.
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« Reply #7 on: July 25, 2012, 01:27:34 AM »

I believe it would have been much better for us if it was so instead of basing it on a paper that comes out every 4-6 years.

Sometimes the distinction between academic rigor and rigor mortis is a tough call.

Also, the Brits probably spell that rigour.

Good parallelism! However, this week my academic rigor with three research papers and mid-term exams have caused mental rigor mortis... :-(

Arch

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Mark Jost
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« Reply #8 on: July 25, 2012, 09:19:38 AM »

I am glad you educators love to beat the drum, over and over and over..... I wouldnt have the patience.
« Last Edit: July 25, 2012, 09:19:50 AM by Mark Jost » Logged

148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
gtc
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« Reply #9 on: July 25, 2012, 11:56:50 AM »

I think the main difference is that rigor mortis only lasts about two or three days, then things loosen up. ;-)

And then the real stink begins ...
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gtc
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« Reply #10 on: July 25, 2012, 12:02:49 PM »

Other rumors suggest that FTDNA may (finally) improve their IT process such that updating their haplotrees can occur on an ongoing basis. Not holding my breath on that one; I'm still waiting for micro-allele values to be included in the Y-STR reports, and I believe that has been promised for at least three years.

I have it through the grapevine, from a very reliable source, that FTDNA will be "recasting" [their terminology] its database sometime this year which will allow for displaying micro-alleles.

As for their haplotree, I have often wondered if it was engineered for tricky looks rather than updatability.
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df.reynolds
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« Reply #11 on: July 25, 2012, 03:05:24 PM »

FTDNA Deep Clade testing being discontinued in favor of Geno 2.0.
http://www.yourgeneticgenealogist.com/2012/07/national-geographic-and-family-tree-dna.html
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k.o.gran
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« Reply #12 on: July 25, 2012, 03:30:03 PM »

FTDNA Deep Clade testing being discontinued in favor of Geno 2.0.
http://www.yourgeneticgenealogist.com/2012/07/national-geographic-and-family-tree-dna.html

Wow... That seems very interesting, but I must admit I have a lot of questions! What is the goal of this test? From the blog post it seems like a Population Finder test on steroids using autosomal-, Y-, mtDNA- and X-SNPs, but will it be useful for matching purposes? I'm thinking, will it include Y-STRs? Will the results be added to the Family Finder database? I can't wait to get more information!

-Kai
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Stephen Parrish
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« Reply #13 on: July 27, 2012, 10:09:44 AM »

k.o. -

Geno 2.0 will not include Y-STRs.

Stephen
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Mike Walsh
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« Reply #14 on: July 27, 2012, 10:53:48 AM »

k.o. -

Geno 2.0 will not include Y-STRs.

Stephen

I saw a note that Thomas Krahn set that SNPs discovered after Nov 2011 would not be in this new testing package.

Does anyone know what the list of "just missed" are?   DF27 is one I particularly was curious about?
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Richard Rocca
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« Reply #15 on: July 27, 2012, 12:12:30 PM »

k.o. -

Geno 2.0 will not include Y-STRs.

Stephen

I saw a note that Thomas Krahn set that SNPs discovered after Nov 2011 would not be in this new testing package.

Does anyone know what the list of "just missed" are?   DF27 is one I particularly was curious about?

Unfortunately, the primers for DF27 were not prepared until earlier this year.
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Dubhthach
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« Reply #16 on: July 27, 2012, 03:11:42 PM »

Hopefully we will get a full list of SNP's in the Gen 2.0 product. Obviously DF41 won't be include but I wouldn't be surprise if the include L744/L746 and L745. I'd also be curious given they mention other labs if they will have data on S190, given that no information has been released by Ethnoancestry/Scotland's DNA regarding primers etc.
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df.reynolds
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« Reply #17 on: July 27, 2012, 07:40:23 PM »

... I'd also be curious given they mention other labs if they will have data on S190, given that no information has been released by Ethnoancestry/Scotland's DNA regarding primers etc.

Sorry, I know for a fact that S190 and the other proprietary markers from ScotlandsDNA.com will *not* be included in Geno 2.0.

--david
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Stephen Parrish
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« Reply #18 on: July 27, 2012, 07:56:07 PM »

In reply to Mike's most recent post in this thread, will Geno 2.5 include SNPs discovered after November 2011?

Stephen
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gtc
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« Reply #19 on: July 28, 2012, 09:28:16 AM »

In reply to Mike's most recent post in this thread, will Geno 2.5 include SNPs discovered after November 2011?

Stephen

In reply to Mike's most recent post in this thread, will Geno 2.5 include SNPs discovered after November 2011?

Stephen

I take it 2.5 is a typo?

As for 2.0, it seems to be the replacement for deep clade with extra benefits, however it doesn't seem to offer any immediate attraction to those who already tested to their known bounds in R1b.

For the time being I'm taking a back seat to see what emerges.
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Mark Jost
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« Reply #20 on: July 28, 2012, 11:01:15 AM »

I ordered the Geno test for three main reasons. 1) the X AIMs are interesting 2) You can not order a WTY without it. Most WYT applicants have to have a DeepClade anyway (not knowing if should be a difference with those who have already WTY. And 3) I am at a brick wall with no new snps to test so I am hoping this one will have a few unknown SNP under DF13.

MJost
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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
k.o.gran
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« Reply #21 on: July 28, 2012, 12:03:31 PM »

Mark,

Does the order form allow you to enter your kit number to have the test linked to your existing login? Just curious how this works.

-Kai
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Mark Jost
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« Reply #22 on: July 28, 2012, 01:29:53 PM »

Since Genome 2 project wont be competing with FtDNA, FtDNA will be, in some format be accessing results and, assumingly importing this data to an existing kit number. But who knows.

The order process didnt ask for FtDNA info.

MJost
« Last Edit: July 28, 2012, 01:31:07 PM by Mark Jost » Logged

148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
df.reynolds
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« Reply #23 on: July 28, 2012, 01:33:58 PM »

Mark,

Does the order form allow you to enter your kit number to have the test linked to your existing login? Just curious how this works.

-Kai

Quote from: Bennett Greenspan
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.

From Roberta Estes' blog:
http://dna-explained.com/2012/07/26/geno-2-0-qa-with-bennett-greenspan/

--david
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