y-SNPS from Exome results

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Posts: 26
Joined: Sat Mar 17, 2012 10:48 am
PostPosted: Wed Jun 06, 2012 10:37 pm
Got my 23andMe 80X+ coverage Exome results back yesterday and let Greg M. take a quick look at
the VCF y-chromosome results. I have over 100 y-variants listed in the prototype analysis.

Here are Greg's comments:

Most interesting are the remaining two SNPs without rsIDs; the one at 21868651
is your L188. The other one at 14078015 appears to be completely new, the first
recorded instance of this SNP as far as I can tell.

Yes :P the 23andMe Exome results showed my family SNP L188! :D We need to collect the other Exome results to see
if there is value in mining what 23andMe has provided. I will work on extracting out the sequence information from the BAM file so that Greg can better evaluate the what was presented in the draft VCF results file.

The complete MTdna sequence is also present in the raw data. We need to get more of these results extracted out to see if the result is of sufficient quality to submit to Genbank.

R-L48+, Z326+, L188+
R1b-Z319+, Z325+, CTS2509+ , L188+ Previously known as the R1b-Z326 null425 cluster
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Posts: 46
Joined: Wed Mar 14, 2012 3:28 pm
Location: Edmonton, AB
PostPosted: Thu Jun 07, 2012 2:53 am
I'm half-way through surveying the R1b (xL11) SNPs which Greg recently identified at https://www.box.com/s/d07b0fc683933615a9c1, and so far have found a primer pair candidate for one that will be of importance to R-L150* members: Z2103; actually it's the only one so far.

Interestingly, Z2103 also lies within PRKY (Protein kinase, Y-linked) http://ymap.ftdna.com/cgi-bin/gb2/gbrow ... 4..7309588, at chrY:7246135 (NCBI36), and might be covered by the Exome data. Are you able to find out if your data has coverage for this position?

Also of interest, Z2109 is situated within ADLICANP; but since it is so near the centromere, I have low hopes for sequencing this using conventional PCR. http://ymap.ftdna.com/cgi-bin/gb2/gbrow ... id=general

Posts: 26
Joined: Sat Mar 17, 2012 10:48 am
PostPosted: Sun Jul 22, 2012 1:39 pm
23andMe Exomes from individuals in haplogroups C3 through my R-Z326 are showing a number of unique y-SNPs. Right now no surveyed Exomes from U312/P312 or the L21 regions have yielded new SNPs. A small number of identified SNPs appear to correlate with existing Z-series SNPs. Others cannot be confirmed or identified within the 1000 genomes data set due to the low sequencing coverage in those samples. A number of the new SNPs also appear to apply to several recently defined haplogroups and thus don't have much value for providing additional structure to the current haplotree. Design of primers for several of the SNPs is being considered.
R1b-Z319+, Z325+, CTS2509+ , L188+ Previously known as the R1b-Z326 null425 cluster

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