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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 4:16 pm
Let me add that, although we must make every effort to carefully vet the SNPs we recommend, there's no way that we'll be able to ensure that every one of them will work well in the lab, or be able to define the new branches that everyone wants. This is an experimental process. The SNPs we list in Greg's spreadsheet are listed as "candidate variants." Then Thomas develops those that look most promising and technically feasible. However, having them get to the point of being available for ordering is not equivalent to a guarantee that they'll be useful. People who order new 1K Genomes SNPs are choosing to participate as fellow researchers in trying out these SNPs. As in WTY participation, there's always a risk that the results will be less than satisfying. This is the nature of science, isn't it?

Bonnie

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

YDNA:
R1b-Z12*
MtDNA:
I3b (FMS)
PostPosted: Tue May 22, 2012 12:41 am
Your point is well taken, but I'm happy to say that in R1b-L48 land Greg's candidates have done spectacularly well and advanced many of us past the L48 stalemate. New clusters of families and suggested families now abound.
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Posts: 623
Joined: Wed Mar 14, 2012 2:16 pm
PostPosted: Tue May 22, 2012 11:54 pm
GTC wrote:Your point is well taken, but I'm happy to say that in R1b-L48 land Greg's candidates have done spectacularly well and advanced many of us past the L48 stalemate.

The number and usefulness of SNPs gleaned from 1000 Genomes data is somewhat proportional to the number of 1000 Genomes samples in that haplogroup. Unfortunately, the 1000 Genomes project does not recognize any land mass between the Netherlands and China, so Central-Eastern European haplogroups have gotten very limited results (R1a1a1-Z280) or none whatsoever (R1a1a1-M458, I2a2-Dinaric, I1-Polish). My own attempt to "stretch" the data beyond its natural limitations was disastrous.

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

YDNA:
R1b-Z12*
MtDNA:
I3b (FMS)
PostPosted: Wed May 23, 2012 3:46 am
lgmayka wrote:
GTC wrote:Your point is well taken, but I'm happy to say that in R1b-L48 land Greg's candidates have done spectacularly well and advanced many of us past the L48 stalemate.

The number and usefulness of SNPs gleaned from 1000 Genomes data is somewhat proportional to the number of 1000 Genomes samples in that haplogroup. Unfortunately, the 1000 Genomes project does not recognize any land mass between the Netherlands and China, so Central-Eastern European haplogroups have gotten very limited results (R1a1a1-Z280) or none whatsoever (R1a1a1-M458, I2a2-Dinaric, I1-Polish). My own attempt to "stretch" the data beyond its natural limitations was disastrous.


I don't know how the project's designers arrived at the regional spread in terms of the project's objectives (which I gather were more medical than genealogical), but I sympathize with R1a and I haplogroups not having adequate representation in the data. You guys sure could do with a lot more new SNPs. Let's hope that future such projects do it better for you.
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Posts: 26
Joined: Sat Mar 17, 2012 10:48 am
PostPosted: Sun Jul 22, 2012 1:54 pm
It appears that data associated with the recent Complete Genomics publication on their LFR technology is available. The y-chromosome coverage present in the Complete Genomic's runs seems to be much higher than the typical 1000Genomes data. I am currently extracting out some of the y-variant results associated with the LFR publication for Greg M. and the data miners to evaluate. The y-variant files are showing between 2400 and 4800 y-SNPs/dels/insertions being identified per sample.

See ftp://ftp2.completegenomics.com/LFRPubl ... etal.2012/ June 6th publication. Also see http://www.completegenomics.com/LFR/
R1b-Z319+, Z325+, CTS2509+ , L188+ Previously known as the R1b-Z326 null425 cluster

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

YDNA:
R1b-Z12*
MtDNA:
I3b (FMS)
PostPosted: Sun Jul 22, 2012 2:13 pm
Thanks for that news. Anything that promises more new SNPs is great but I'm not sure that I understand what is being referred to. How many individuals were tested and over what geographical spread?
Use Profile/Edit Profile in User Control Panel to add your Y-DNA and mtDNA values.
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