Welcome everyone to the new 1000 Genomes Project forum!

Moderators: Rootsy, GregRM

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Posts: 102
Joined: Thu Mar 15, 2012 4:26 pm
Location: USA
YDNA:
J2a1i (father)
MtDNA:
I1a1b
PostPosted: Tue May 01, 2012 1:35 am
Hi everybody,

I hope my fellow SNP-hunters will come and use this forum to carry on the great collaborative research that was so successful the first time around on DNA-Forums. I've passed the link on to a few key people, and I hope they'll decide to participate soon. Anyone else who would like to take part -- just jump on in!

Bonnie
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Posts: 387
Joined: Wed Mar 14, 2012 4:51 pm

YDNA:
R-L21>DF13**
MtDNA:
H11a2a
PostPosted: Tue May 01, 2012 1:50 pm
Thank you Bonnie and crew.
148326 DF13** Celtic, Goidelic 111 Marker: GD1/67 & GD3/111 Watterson USA, Cook(UK/Scot Heritage) with a GD5/111, Codere(Watterson(McWalter))IOM GD8/111 and Ross Scotland GD13/111. Cluster 13*-1130-A1: 20 off-modals from L21.
Sorted slow to fast: 531=>12, 497=15, 511=11, 19=>15, 385a=12, 441=14, 552=25, 447=24, 513=11, 557=<15, 446=14, 464d=18, 456=18, 534=16, 449=31, 576=17, 710=36 and 712=>21 68-111Panel
DF13>FGC5496.
https://drive.google.com/file/d/0By9Y3j ... sp=sharing

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Joined: Wed Mar 14, 2012 2:16 pm
PostPosted: Tue May 01, 2012 2:05 pm
I hope this thread discusses clear guidelines as to the reliability of 1000 Genomes data. The R1a1a haplogroup got burned by Z1917 and Z1918 (recommended by someone on the old forum), and I'm worried about the new Z2029, Z2031, and Z2032 as well. (These latter three were derived from a GregRM spreadsheet, but were not specifically recommended by him.) At the very least, we need to emphasize the uneven quality of 1000 Genomes reads, and the great caution their interpretation requires. Those who think that we are on the verge of inexpensive, reliable whole-Y sequencing appear to be seriously mistaken.

On the other hand, I have seen a report that James Wilson (formerly of Ethnoancestry) has independently verified the validity of Z87, Z88, Z289, Z660, Z661, Z645, and Z647. All these SNPs were originally extracted from 1000 Genomes data. I am waiting for confirmation and details. (Has he found a positive example for each one? Has he placed each one in a specific position in the haplotree? Etc.)

Of course, the R1a1a haplogroup has the severe handicap of a lack of sampling. The 1000 Genomes Project chose not to include anyone east of the Netherlands and west of China, so the handful of R1a1a samples in the project are Utahan, Orcadian, or Finnish. Nevertheless, the project has supplied us with several very useful SNPs: Z280, Z284, Z93, Z94, Z287, and Z283.
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Posts: 387
Joined: Wed Mar 14, 2012 4:51 pm

YDNA:
R-L21>DF13**
MtDNA:
H11a2a
PostPosted: Tue May 01, 2012 2:50 pm
lgmayka wrote:I hope this thread discusses clear guidelines as to the reliability of 1000 Genomes data. The R1a1a haplogroup got burned by Z1917 and Z1918 (recommended by someone on the old forum), and I'm worried about the new Z2029, Z2031, and Z2032 as well. (These latter three were derived from a GregRM spreadsheet, but were not specifically recommended by him.) At the very least, we need to emphasize the uneven quality of 1000 Genomes reads, and the great caution their interpretation requires. Those who think that we are on the verge of inexpensive, reliable whole-Y sequencing appear to be seriously mistaken.

...

I would agree, the "Researcher" is using a simple technic to test samples and subject to the new primers working correctly, this is a stair step process including Tree placement of new SNPs. The L21 group is being lead by testers who have helped confirm Isogg tree placement based on certain requirements. So far, giving this group of secret researcher actions, almost the entire L21 top tier of SNPs has been replaced. Not to forget the research results of WTY up to and presently which has helped find many private and public SNPs. The L21 group has also had a mis-projection as well. But it was taken in stride by the group.

For me (a L21*) and alot of others who have been in a 'hurry up and wait' mode of waiting for new SNPs. I was once only P312 positive and M222 negative but was drop dead excited when L21 was discovered. I have been in this mode since. I have tested WTY which was negative and negative for all old and new top tier snps. I am still waiting for my first terminal snp below L21. Testing now for the newest DF series SNP, DF63 which has been defined as a brother SNP to another new DF13 SNP. DF13 is expected to the the 'Big Kahuna' (Coined by MikeW) which is expected to include 90% of L21.

MJost
148326 DF13** Celtic, Goidelic 111 Marker: GD1/67 & GD3/111 Watterson USA, Cook(UK/Scot Heritage) with a GD5/111, Codere(Watterson(McWalter))IOM GD8/111 and Ross Scotland GD13/111. Cluster 13*-1130-A1: 20 off-modals from L21.
Sorted slow to fast: 531=>12, 497=15, 511=11, 19=>15, 385a=12, 441=14, 552=25, 447=24, 513=11, 557=<15, 446=14, 464d=18, 456=18, 534=16, 449=31, 576=17, 710=36 and 712=>21 68-111Panel
DF13>FGC5496.
https://drive.google.com/file/d/0By9Y3j ... sp=sharing

Posts: 326
Joined: Thu Mar 15, 2012 1:14 am

YDNA:
R1b-Z12*
MtDNA:
I3b (FMS)
PostPosted: Tue May 01, 2012 3:05 pm
lgmayka wrote:Those who think that we are on the verge of inexpensive, reliable whole-Y sequencing appear to be seriously mistaken.


Yes, as also evidenced by difficulties experienced to date by Thomas Krahn in his Roche 454 project.

And I gather that Thomas is talking about only 25% to 30% of the Y as being feasible for sequencing.
Use Profile/Edit Profile in User Control Panel to add your Y-DNA and mtDNA values.

Posts: 326
Joined: Thu Mar 15, 2012 1:14 am

YDNA:
R1b-Z12*
MtDNA:
I3b (FMS)
PostPosted: Tue May 01, 2012 3:08 pm
There was a link on DNA-Forums to the list of candidate SNPs in the Z series, but I didn't bookmark it. Would somebody kindly publish that link here, please.
Use Profile/Edit Profile in User Control Panel to add your Y-DNA and mtDNA values.
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Posts: 227
Joined: Wed Mar 14, 2012 4:10 pm
Location: Brazil
YDNA:
J1b M365+ J1a ISOGG
MtDNA:
H1ao1
PostPosted: Tue May 01, 2012 11:18 pm
I think FTDNA is still developing the new 454 sequence. In the Finch2 we can find 717 new SNPs (YSC0000307 to YSC0001024) found in a hg J-M267* 454 sequence. The new 1K SNPs Z series was the best development in genetic genealogy (Y DNA) in the last years. FTDNA should be more communicative about the new developments such as the cost of the new 454 sequence and when (and if) it will be available for us, the customers. If more than 700 SNPs were found in a single test we could expect another "Copernican" revolution in the entire Y phylogeny and a new level of resolution, accuracy and historical precision.
Y DNA - Barcelos - Minho - Portugal. Colonial Brazil
MtDNA - Ilha Terceira, Azores, Portugal
Brazilian Portuguese Founding People
http://www.familytreedna.com/public/m365/
http://www.familytreedna.com/public/Brasil/
http://j1bm365.blogspot.com.br/
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Posts: 102
Joined: Thu Mar 15, 2012 4:26 pm
Location: USA
YDNA:
J2a1i (father)
MtDNA:
I1a1b
PostPosted: Mon May 21, 2012 2:43 am
GTC wrote:There was a link on DNA-Forums to the list of candidate SNPs in the Z series, but I didn't bookmark it. Would somebody kindly publish that link here, please.


Sure -- sorry! I had wanted to make sure it was OK, and I've been given the go-ahead. It's
https://docs.google.com/spreadsheet/ccc?key=0Agq_ez43qXCjdFlxemtlUnZ1Qk01cVhMRVBFcm5WX3c&authkey=CIOag_UD

Posts: 326
Joined: Thu Mar 15, 2012 1:14 am

YDNA:
R1b-Z12*
MtDNA:
I3b (FMS)
PostPosted: Mon May 21, 2012 3:08 am
^ Many thanks.
Use Profile/Edit Profile in User Control Panel to add your Y-DNA and mtDNA values.
User avatar
Posts: 102
Joined: Thu Mar 15, 2012 4:26 pm
Location: USA
YDNA:
J2a1i (father)
MtDNA:
I1a1b
PostPosted: Mon May 21, 2012 3:23 am
lgmayka wrote:I hope this thread discusses clear guidelines as to the reliability of 1000 Genomes data.


Yes, the data is certainly not something simple and straightforward to work with. I've been chewing over and over a set of J results in which there were contradictory patterns -- one set of SNPs implied a certain topology of the phylotree, and another set would have implied a different arrangement. After a lot of time spent scrutinizing them, I've been able to discard most of one of these groups, and I feel pretty confident that the first set is right, but there are still about three SNPs that look about as good as most, which still contradict the main group. Nevertheless, the preponderance of the evidence points to a split at a very early point in J1, where HG01253's (and probably GRC10035555/Quxuq's) lineage branches off on the one hand, and the other branch includes both J1c-L136 and J1d-Z1834. We don't yet know which side Ricardo's subclade, J1b-M365, would belong to.

This isn't overturning any previously held dogmas, but it incidentally does end up confirming my guess that the Z1834+, DYS388=13 clade might not be the most basal in J1. Peter Hrechdakian and I had discussed and wondered about this years ago.

Anyway -- the point I wanted to make was that you can't look at each SNP individually, in isolation. I'm excited about the SNP we found that was derived in both GRC10035555's 454 results, and HF01253 in the 1K genomes data, but if it were contradicted by a lot of others, I wouldn't want to pursue it. Fortunately, there are dozens of others in the 1K genomes data that confirm it.

Bonnie
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