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Peter M
08-12-2014, 10:51 AM
Is there an overview somewhere on the web of the SNPs supported by (1) the Geno2 chip and (2) the Chromo2 chip ?

I'm aware the Chromo2 chip supports P312, DF27, and DF99, but are there any other key differences that might direct a suspect P312+ to one of those chips ?

E.g. is DF100/CTS4528 supported by Geno2 or Chromo2 ??

It could well be, most people in this world are focussing completely on Big-Y. My impression is, there's still a lot of people, e.g. those with 37 markers and a red "R-M269" estimate from FT-DNA, who might be more interested in ordering a chip test than investing 3x as much in a Big-Y test. Strange thought ??

rms2
08-12-2014, 01:08 PM
Hi, Peter.

I just emailed you an Excel file of Chromo2 SNPs that includes their alternate names. Hopefully, you didn't already have it.

DF100/CTS4528 is included in Chromo2. It is S1200.

Peter M
08-12-2014, 03:45 PM
With rms2's spreadsheet and a few other sources, I've made an overview of P312 SNPs on both chips:



Name


S-Name
Geno2
Chromo2


M269


--
-
-


L23


--
+
-


L51


--
+
-


L11


S127
+
-


P311


S128
-
+



U106

S21
+
-




Z18
S493
+
+




Z381
S263
+
+



DF100

S1203
-
+



CTS4528

S1200
+
+



P312

S116
-
+




L21
S145
+
+




U152
S28
+
-




DF27
S250
-
+




DF19
S232
+
+




L238
S182
-
-




DF99
S11987
-
+


Please note both (1) L11 and P311 and (2) DF100 and CTS4528 are considered phylogenetically equivalent.

There still are a few questions:

(1) Is it correct Chromo2 doesn't support L23 and L51 (there doesn't seem to be a published S-name for those SNPs) ?
(2) I cannot find U106/S21 and L238/S182 in the rms2 file; are these SNP not supported by Chromo2 ??
(3) Is it correct Chromo2 doesn't support U152 ?

(4) Are there any other errors or omissions in this overview ???

ArmandoR1b
08-12-2014, 03:48 PM
CTS4528 is included in Geno 2.0. I uploaded a spreadsheet that has the Geno 2.0 markers that are tested by Geno 2.0.

https://www.dropbox.com/s/a0zw9hcdzm0y1pb/Geno%202.0%20%20SNP%20markers.xlsx

You can also go to the SNP page of the DF100 project and see that CTS4528 is included in the Geno 2.0 results of testees.

https://www.familytreedna.com/public/DF100-CTS4528-L11-P310-L151-P311/default.aspx?section=ysnp

Joel
08-12-2014, 06:46 PM
R1b-S21 is on the Spreadsheet that has the Chromo2 Y genotypes for 2000 anonymised individuals. Also L238/S182

Joel

VinceT
08-12-2014, 09:59 PM
R1b-S21 is on the Spreadsheet that has the Chromo2 Y genotypes for 2000 anonymised individuals. Also L238/S182

Joel

Hmm.. not on the copy I have. Neither S21 nor S182 were in the C_2000_v2 spreadsheet I have (retrieved from http://www.yourgeneticgenealogist.com/2014/02/britainsdna-chromo2-y-snp-results.html), but apparently were being genotyped as an additional process.

rms2
08-13-2014, 01:43 PM
I am pretty sure that S21 (U106) and S28 (U152) are included in Chromo2. Both SNPs were originally discovered by Dr. Jim Wilson back in 2005(?) or thereabouts and are featured on BritainsDNA members' homepages as "Germanic" and "Alpine" respectively.

Joel
08-13-2014, 05:33 PM
I took the Chromo2 Y genotypes for 2000 anonymised individuals spreadsheet and changed the rows to columns and got this for R1b-S21. I also took out the repeat results. I didn't take out the repeats for S28, but the list should be a similar length as below.

R1b-S21 R1b-S170
R1b-S21 R1b-S172
R1b-S21 R1b-S186
R1b-S21 R1b-S21*
R1b-S21 R1b-S261
R1b-S21 R1b-S263
R1b-S21 R1b-S264
R1b-S21 R1b-S265
R1b-S21 R1b-S266
R1b-S21 R1b-S267
R1b-S21 R1b-S268
R1b-S21 R1b-S271
R1b-S21 R1b-S272
R1b-S21 R1b-S274
R1b-S21 R1b-S276
R1b-S21 R1b-S29
R1b-S21 R1b-S352
R1b-S21 R1b-S353
R1b-S21 R1b-S375
R1b-S21 R1b-S376
R1b-S21 R1b-S380
R1b-S21 R1b-S385
R1b-S21 R1b-S3933
R1b-S21 R1b-S500
R1b-S21 R1b-S512
R1b-S21 R1b-S514
R1b-S21 R1b-S515

GoldenHind
08-13-2014, 05:49 PM
I am pretty sure that S21 (U106) and S28 (U152) are included in Chromo2. Both SNPs were originally discovered by Dr. Jim Wilson back in 2005(?) or thereabouts and are featured on BritainsDNA members' homepages as "Germanic" and "Alpine" respectively.

I would be surprised if Chromo 2 doesn't test for L238/S182 as well, as their previous incarnation Ethnoancestry was the first commercial company to offer testing for it, and I know Jim Wilson was very interested it as an indicator of Norse origins in Britain. That being said, it may not have been included in the spreadsheet they released.

Joel
08-13-2014, 06:41 PM
Here are the results on the Wilson Spreadsheet. They are on columns BAZ-BBE

1007 1008 1520 1691 1767 1773
R1b-S182 R1b-S182 R1b-S182 R1b-S182 R1b-S182 R1b-S182

VinceT
08-14-2014, 02:44 AM
Your spreadsheet may be different than the one at https://www.britainsdna.com/download/C2_2000_v2.zip (C2_2000_v2.xlsx dated 2014-02-24)?
I retrieved it yet again, and confirmed that S21 is missing, as is S28 and S182 (in column A). However S21 was included in my raw data (but not S28 or S182), and I was sub-typed as R1b-S21*.

Note that the sample sub-typing in rows 2 and 3 were provided by supplementary PCR assay tests not directly provided by Chromo2. Perhaps that is where the confusion lies?

Joel
08-15-2014, 07:12 PM
Hi Vince,

I did have a different spreadsheet. I just downloaded an apparently newer one. My notes from the spreadsheet say that "Row 2 has the unique identifier for each sample. Row 3 indicates the inferred haplogroup, and row 4 the inferred subtype, as of February 2014. Rows 5 - 14503 are the genotyping results for all 14498 Y SNPs on the Chromo2 chip (NOT including SNPs that were tested by DNA sequencing or Taqman, such as S28 and S21, which were only tested when phylogenetically relevant), including the 271 SNPs that are currently known to be phylogenetically uninformative or have failed (rows 14232-14503). Column 1 gives the SNP name; column 2 indicates the ancestral (negative) genotype, column 3 indicates the derived (positive) genotype for this SNP, called to the Illumina TOP strand. Columns 4 - 2003 are the genotyping results for each of the 2000 samples." Emphasis added. Also he's a little off on the rows as I have them.

I believe that you are right. However, I can only assume that by the testing that was done, the above S28's and S21's in Rows 2 and 3 can be inferred. The note also syas that S21 was only tested when phylogenetically relevant. I assume that was your case(?) So if there was a positive below S21, it can be inferred that you are S21. If there is none downstream, I'm guessing that they had to test for S21 to make sure. But, hey, I'm new to this and just trying to figure this out myself.

Joel

VinceT
08-15-2014, 09:07 PM
Joel,

Yes, Dr. Wilson knew beforehand that I was U106* from testing with FTDNA and Full Genomes Corp., and so S21 was tested by other means (Taqman in this case, I guess). I also provided him with my FGC BAM file and FGC's reports in order to provide data for a future iteration of the Chromo chip. My Chromo2 specific results only went as far as S128+ S116- S1200-.

Incidentally, none of my some 45+ new SNPs found by Full Genomes Corp. matched with the GoNL (Dutch) data that was used in the Chromo2's design.

rms2
08-17-2014, 01:02 AM
I think the results reported in this thread (http://www.anthrogenica.com/showthread.php?3019-BritainsDNA-result&p=48689&viewfull=1#post48689) are from the Chromo2 test, and they include an S28+ result.

rms2
08-17-2014, 12:49 PM
I think the results reported in this thread (http://www.anthrogenica.com/showthread.php?3019-BritainsDNA-result&p=48689&viewfull=1#post48689) are from the Chromo2 test, and they include an S28+ result.

Subsequent posts in that thread offer further clarification and are relevant to the topic of this thread.