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Author Topic: National Geographic and Family Tree DNA Announce Geno 2.0  (Read 29345 times)
Mike Walsh
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« Reply #150 on: November 11, 2012, 01:49:01 AM »

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Terry

I think a criticism of Dr Wells is my undoing. It wasn't obscene. I just think he is a little vague and unresponsive.

I guess that is bad. So be it. Bye.
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gtc
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« Reply #151 on: November 11, 2012, 01:56:30 AM »

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Terry

I think a criticism of Dr Wells is my undoing. It wasn't obscene. I just think he is a little vague and unresponsive.

I didn't see what you posted but I would not have expected obscenity from you in any case.

I agree with you that not a lot of what was (reportedly) presented was new to those of us who have been following Geno 2 news and commentary since it was first announced, but I guess SW is holding his fire for his forthcoming paper, which he reportedly said was in draft status (whether that's internal draft or peer-review draft is unclear).

Quote
I guess that is bad. So be it. Bye.

Bye? I hope you are not leaving us.
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Y-DNA: R1b-Z12* (R1b1a2a1a1a3b2b1a1a1) GGG-GF Ireland (roots reportedly Anglo-Norman)
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Heber
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« Reply #152 on: November 11, 2012, 08:13:35 AM »

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Terry

I think a criticism of Dr Wells is my undoing. It wasn't obscene. I just think he is a little vague and unresponsive.

I guess that is bad. So be it. Bye.

Mike,
I did not see anything offensive in your post. Nat Gen have spent three intensive days communicating their message at Florence, ASHG and FTDNA and the social media, blogs and Twitter are full of their announcements. It is perfectly legitimate to comment on their style of communication.
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Heber


 
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Terry Barton
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« Reply #153 on: November 11, 2012, 10:41:39 AM »

Mike, I hope you stay.  Terry
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seferhabahir
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« Reply #154 on: November 11, 2012, 01:44:48 PM »

These are all the mystery questions we waiting for. I suspect the raw data will be the most valuable part of the test, but I am most curious to see how the Geno 2.0 results will be mapped/reflected in FTDNA.
I hope that at least it will be easy one-button stuff for the consumer to get the data over to FTDNA where it could be seen in a project screen, regardless of the data format.  If we can see it and it is consistently formatted, we can deal with it.
For those who got a complimentary Geno 2.0 to test the chip, does anybody know when FTDNA will upload those results to the Nat Geo database as implied in their email below (or else make the results available within FTDNA to the testee)?

"Because your sample was used to help test the Geno 2.0 chip, your data - autosomal, mtDNA and Y (in the case of men) will be uploaded to the new National Geographic website at www.genographic.com later this fall."

Here is a post today from rootsweb on my question above...

---------------------------
From: "grandcross"
Subject: Re: [DNA] Geno 2 FYI..
Date: Sun, 11 Nov 2012 00:03:21 -0600

My very early WTY results (2007) also were chosen by Genographic and I was
advised of this in September. Bennett told me yesterday at the conference my
Geno 2 analysis would be made available before the first week of December.
He acknowledged some internal FTDNA administrative work would have to be
done before that happened, the point being he is aware we who participated
in this way are outside the normal access procedures for those who paid for
their kits.
---------------------------
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Y-DNA: R-L21 (Z251+ L583+)

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seferhabahir
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« Reply #155 on: November 11, 2012, 01:51:11 PM »

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Terry

I think a criticism of Dr Wells is my undoing. It wasn't obscene. I just think he is a little vague and unresponsive.

I guess that is bad. So be it. Bye.

Mike critique of Wells' communication was very mild compared to many other criticisms of experts in the field that have been posted here in the past. I hope Mike is just taking Veteran's Day weekend off.
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eochaidh
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« Reply #156 on: November 11, 2012, 11:25:58 PM »

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Terry

I think a criticism of Dr Wells is my undoing. It wasn't obscene. I just think he is a little vague and unresponsive.

I guess that is bad. So be it. Bye.

Mike critique of Wells' communication was very mild compared to many other criticisms of experts in the field that have been posted here in the past. I hope Mike is just taking Veteran's Day weekend off.

He's not coming back. He's had enough. What a shame. What a loss.
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Heber
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« Reply #157 on: November 12, 2012, 11:52:12 AM »

News from the FTDNA conference, Spencer Wells presentation. (Via Twitter).
1) Between 10,000 and 100,000 Geno 2.0 kits sold since "soft" launch
2) 43 Reference Populations. Will be updated every couple of months.
3) Geno 2.0 focused on anthropology not genealogy.
4) 50K - 100K overlap with FF and 23andme tests.
5) 6000 new SNPs to be added over next few months??
6) 2010 YCC Tree has 862 branches, Geno 2.0 chip has 6162 branches
7) 130000 validated auto and X SNPs. Paper coming soon.
8) AIMS taken from 450 world populations. More dense in old world.
9) Harness the power of the community to figure out what this genetic info means
10) New grants for community projects.


Thanks for the update.

If true, I wonder how/if the additional SNPs will be added/offered to the already tested kits, especially since they have stated in the past that they will not store DNA after the test is run.

Richard,
I was also surprised by the numbers and will try to clarify.
I understand the official launch will be around the 19th with the new web site and first results the week after Thanksgiving. We should get a good idea of which new SNPs are available at that stage.
Assuming they went from 862 - 6162 SNPs using the existing base of under 1000 samples and we assume they ramp up to 50,000 customers by end of year we could expect a lot of new SNPs discovered in that timeframe. I would assume the newly discovered SNPs would be included in subsequent versions of the chip.
I would expect them to have a release roadmap on an annual basis.
I do not know what the policy is for storing DNA. I remember mine was stored for Geno 1.0 and subsequently transferred to FTDNA. Is there a separate policy for kits used during the testing phase.

Edit
Thanks to CeCe, Katherine, Emily, Roberta for their Tweets.

Richard,

That 6000 number for new SNPs coming appears to be correct. New meaning not yet published or placed on the tree but identified by other researchers. Someone estimated there were already 24K subscribers based on a snapshot from the counter on the Nat Geo site. Here is a comment from Yahoo Groups.

"Spencer says 4,500 SNPs from 1000 gemomes project on the chip, 745 are z SNPs, but 3,850 are other SNPs from 1kG. His paper is not ready. In 2010 there were 862 SNPs on the y tree. now 6,000, plus 6,000 more coming.
>
autosomal results will show what native populations you are closest to, and percentage Mediterranean, North European, etc
>
Y and mtDNA result will show you in a circle with closest relatives around you, and you will be able so share stories."
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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-
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gtc
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« Reply #158 on: November 13, 2012, 10:19:59 AM »

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Terry

I think a criticism of Dr Wells is my undoing. It wasn't obscene. I just think he is a little vague and unresponsive.

I guess that is bad. So be it. Bye.

Mike critique of Wells' communication was very mild compared to many other criticisms of experts in the field that have been posted here in the past. I hope Mike is just taking Veteran's Day weekend off.

He's not coming back. He's had enough. What a shame. What a loss.

So, it's confirmed? Bummer!
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Y-DNA: R1b-Z12* (R1b1a2a1a1a3b2b1a1a1) GGG-GF Ireland (roots reportedly Anglo-Norman)
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wing_genealogist
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« Reply #159 on: November 13, 2012, 03:49:52 PM »

The release of the results of the Nat Geno 2.0 project will be warmly welcomed (with the promise of thousands of new Y-SNPs). However, there will be a fair bit of distress by the folks at ISOGG who then have the Herculean task of placing all of these new SNPs on their tree.

I hope folks will have patience with ISOGG through this process, and understand the expected delay will not be due to their ineffectiveness. The National Geographic Society (and FTDNA) have had at least a year to take these SNPs and add them to their tree. AFAIK ISOGG has not received an advanced copy of this tree, but must wait until NGS publicly releases it.
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Y-DNA - R1b M157.2 (a private/family subclade of Z6/Z352) 111 markers tested

mt-DNA - J1c2g with the following private mutations: 315.1C 522.1A 522.2C C9974T C16256T (FMS tested and submitted to GenBank)

Autosomal - shows as a typical English ancestry. Tested with 23andMe, FTDNA
Heber
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« Reply #160 on: November 13, 2012, 04:13:22 PM »

I would highly recommend that everyone read Roberta Esres blog on the FTDNA conference.
It is well written, compelling and funny.
Highlights include Spencer Wells update on Geno 2.0, Thomas Krahn, Michael Hammer and Bonnie Schrack made an amazing discovery on the base A Haplogroup with huge implications for the age and origin of mankind and an interesting presentation from Dr. Tyrone Bowes on finding an Irish or Scottish ancestors location based on recurring family names. The quality of all the presentations was very high. Roberta, CeCe Moore, Emily Aulicino, and Katherine Bourges provided a constant Twitter feed from the conference on #ftdna2012 which allowed me to follow it live from Munich.

http://dna-explained.com/


« Last Edit: November 13, 2012, 04:15:51 PM by Heber » Logged

Heber


 
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eochaidh
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« Reply #161 on: November 13, 2012, 05:23:14 PM »

My Geno 2.0 sample has been under analysis since Wednesday, 11/7/12. Perhaps that's a good sign. I'm R1b-DF23 and maybe they've found a new SNP between DF23 and M222.
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Mark Jost
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« Reply #162 on: November 13, 2012, 05:39:10 PM »

Has anyone read what kind of download file format the Geno2.0 will be?

MJost
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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)
Jdean
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« Reply #163 on: November 13, 2012, 07:07:15 PM »

My Geno 2.0 sample has been under analysis since Wednesday, 11/7/12. Perhaps that's a good sign. I'm R1b-DF23 and maybe they've found a new SNP between DF23 and M222.

Looking forward to hearing about your results Miles

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Heber
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« Reply #164 on: November 13, 2012, 07:08:49 PM »

Has anyone read what kind of download file format the Geno2.0 will be?

MJost

I would suspect that since there are 130K+ SNPs they would use NCBI Build 37.x and not reinvent the wheel. This would give a flat file rs........  "x" format in the download file and make it compatible with FTDNA and 23andme. A separate excel or cvs file could translate the known terminal SNP to shorthand format. I believe the longhand would nor be used. Just speculation on my part.
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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-
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« Reply #165 on: November 13, 2012, 07:26:29 PM »

Has anyone read what kind of download file format the Geno2.0 will be?

MJost

I would suspect that since there are 130K+ SNPs they would use NCBI Build 37.x and not reinvent the wheel. This would give a flat file rs........  "x" format in the download file and make it compatible with FTDNA and 23andme. A separate excel or cvs file could translate the known terminal SNP to shorthand format. I believe the longhand would nor be used. Just speculation on my part.

recent announcement in florence indicated that they will use the rs format
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gtc
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« Reply #166 on: November 13, 2012, 08:11:36 PM »

Has anyone read what kind of download file format the Geno2.0 will be?

MJost

I would suspect that since there are 130K+ SNPs they would use NCBI Build 37.x and not reinvent the wheel. This would give a flat file rs........  "x" format in the download file and make it compatible with FTDNA and 23andme. A separate excel or cvs file could translate the known terminal SNP to shorthand format. I believe the longhand would nor be used. Just speculation on my part.

recent announcement in florence indicated that they will use the rs format


I am expecting SNPs to be called by their rs number, as is the case with 23andMe's file. In any case, not all SNPs have "shorthand" labels like L21 (and for that matter not all SNPs have rs numbers).
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Mark Jost
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« Reply #167 on: November 13, 2012, 08:32:37 PM »

Thx, with all these new SNPs, I hope they provide a SNP association list as I am sure most are deeper into the trunk SNPs. We can script a search output for rs id, chr, position and genotype for M269 and newer easy enough.

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)
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« Reply #168 on: November 13, 2012, 08:43:46 PM »

Thx, with all these new SNPs, I hope they provide a SNP association list as I am sure most are deeper into the trunk SNPs. We can script a search output for rs id, chr, position and genotype for M269 and newer easy enough.

MJost

From some mutterings in the U106 group I get the feeling that it will be raw data only and association tables, etc, will be the responsibility of the user.

Perhaps somebody will create a look-up table that everybody can download and use (sounds like a nice job for our wonderful volunteer friends at ISOGG).
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Y-DNA: R1b-Z12* (R1b1a2a1a1a3b2b1a1a1) GGG-GF Ireland (roots reportedly Anglo-Norman)
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Heber
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« Reply #169 on: November 13, 2012, 08:44:34 PM »

Has anyone read what kind of download file format the Geno2.0 will be?

MJost

I would suspect that since there are 130K+ SNPs they would use NCBI Build 37.x and not reinvent the wheel. This would give a flat file rs........  "x" format in the download file and make it compatible with FTDNA and 23andme. A separate excel or cvs file could translate the known terminal SNP to shorthand format. I believe the longhand would nor be used. Just speculation on my part.

recent announcement in florence indicated that they will use the rs format


I am expecting SNPs to be called by their rs number, as is the case with 23andMe's file. In any case, not all SNPs have "shorthand" labels like L21 (and for that matter not all SNPs have rs numbers).

I would guess that the vast majority of SNPs would be identified by their rs number. I don't need 130K SNPs to identify my ancestors. So I will be happy with the ~20 defining mutations from my terminal SNP to M269 or M343 which I can memorise. It is up to the industry stakeholders including FTDNA, 23andme, Genographic, Academia, ISOGG, YCC etc. to come up with a naming convention which is open and practical. There should, IMO, be zero tolerance for proprietary naming conventions. I suspect it will be a combination of rs and shorthand labels. However time is running out as we are about to submerged by a tsunami of new SNPs.
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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-
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« Reply #170 on: November 13, 2012, 09:02:14 PM »

Thx, with all these new SNPs, I hope they provide a SNP association list as I am sure most are deeper into the trunk SNPs. We can script a search output for rs id, chr, position and genotype for M269 and newer easy enough.

MJost

From some mutterings in the U106 group I get the feeling that it will be raw data only and association tables, etc, will be the responsibility of the user.

Perhaps somebody will create a look-up table that everybody can download and use (sounds like a nice job for our wonderful volunteer friends at ISOGG).

ISOGG already provides a hyperlink from the Phylogenetic tree (long and shorthand) to the rs number, so it should not be a big issue to do the reverse. I believe they would appreciate more volunteers to look after specific branches of the tree.
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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-
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OConnor
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« Reply #171 on: November 15, 2012, 09:22:48 AM »

Message Deleted

Terry

I think a criticism of Dr Wells is my undoing. It wasn't obscene. I just think he is a little vague and unresponsive.

I guess that is bad. So be it. Bye.

Mike critique of Wells' communication was very mild compared to many other criticisms of experts in the field that have been posted here in the past. I hope Mike is just taking Veteran's Day weekend off.

He's not coming back. He's had enough. What a shame. What a loss.

So, it's confirmed? Bummer!

Does anyone know where else Mike posts besides here?
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R1b1a2a1a1b4


R-DF13**(L21>DF13)
M42+, M45+, M526+, M74+, M89+, M9+, M94+, P108+, P128+, P131+, P132+, P133+, P134+, P135+, P136+, P138+, P139+, P14+, P140+, P141+, P143+, P145+, P146+, P148+, P149+, P151+, P157+, P158+, P159+, P160+, P161+, P163+, P166+, P187+, P207+, P224+, P226+, P228+, P229+, P230+, P231+, P232+, P233+, P234+, P235+, P236+, P237+, P238+, P239+, P242+, P243+, P244+, P245+, P280+, P281+, P282+, P283+, P284+, P285+, P286+, P294+, P295+, P297+, P305+, P310+, P311+, P312+, P316+, M173+, M269+, M343+, P312+, L21+, DF13+, M207+, P25+, L11+, L138+, L141+, L15+, L150+, L16+, L23+, L51+, L52+, M168+, M173+, M207+, M213+, M269+, M294+, M299+, M306+, M343+, P69+, P9.1+, P97+, PK1+, SRY10831.1+, L21+, L226-, M37-, M222-, L96-, L193-, L144-, P66-, SRY2627-, M222-, DF49-, L371-, DF41-, L513-, L555-, L1335-, L1406-, Z251-, L526-, L130-, L144-, L159.2-, L192.1-, L193-, L195-, L96-, DF21-, Z255-, DF23-, DF1-, Z253-, M37-, M65-, M73-, M18-, M126-, M153-, M160-, P66-

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razyn
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« Reply #172 on: November 15, 2012, 10:51:54 AM »

Does anyone know where else Mike posts besides here?

There are several Yahoo groups on which you can find him, when he's in the mood to move a discussion.  I don't think he's in that mood right now, and maybe less so about the GenoChip than some other topics.  I'm interested in his proposed (or maybe in-progress) reorganization of the R1b haplogroup project at FTDNA, but that thread started here only two days before his departure.  Depending on your interests, check out the several links to haplogroup-specific discussions, below the descendancy chart at this one:

http://tech.groups.yahoo.com/group/R1b-YDNA/

I think Mike has sons still active in athletics at the University of Texas at Austin, and it's football season -- so genetic genealogy may not be the only craziness in his life at the moment.

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« Reply #173 on: November 15, 2012, 12:55:53 PM »

I think Mike has sons still active in athletics at the University of Texas at Austin, and it's football season -- so genetic genealogy may not be the only craziness in his life at the moment.

But he is lurking at the forum (Jean M, df.reynolds, Mikewww, Mike Forsyth). I think he will write again, of course.
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« Reply #174 on: November 15, 2012, 08:35:47 PM »

I think Mike has sons still active in athletics at the University of Texas at Austin, and it's football season -- so genetic genealogy may not be the only craziness in his life at the moment.

But he is lurking at the forum (Jean M, df.reynolds, Mikewww, Mike Forsyth). I think he will write again, of course.

I hope you're right. He's a big reason I come here.

I can't do the Yahoo thing, though. I just don't like the format.
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