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Wing Genealogist
11-06-2017, 09:55 PM
Is anyone here a member of the BeNeLux DNA Project (formerly the Brabant DNA Project)? It is my understanding only project members can access there database to see the frequency of various SNPs.

I am interested in trying to get the percentages for U106 as well as its subclades. Does anyone know how deep the subclade level goes? Are they using NGS testing, or some sort of chip-based testing, or what???

gotten
11-07-2017, 12:47 AM
First they test 38 STR markers and predict a haplogroup, afterwards they do a basic subhaplogroup confirmation with a select number of SNPs (presumably sanger-sequenced).

Here is a list of the original SNPs that are tested.
M11
M12
M123
M136
M137
M153
M157
M158
M161
M166
M17
M18
M180
M205
M21
M215
M222
M223
M224
M227
M241
M242
M253
M26
M267
M269
M27
M280
M281
M284
M285
M286
M289
M317
M318
M319
M320
M321
M327
M335
M339
M34
M340
M343
M35
M357
M359
M365
M367
M369
M37
M377
M378
M379
M390
M410
M419
M47
M56
M62
M65
M67
M68
M69
M70
M72
M73
M78
M81
M81
M87
M92
M99
MEH2
P109
P15
P16
P18
P2
P215
P25.1
P259
P279
P297
P310
P312
P36.2
P37.2
P56
P58
P66
P72
P77
P78
P81
P84
P95
P98
PK5
SRY10831.2
SRY2627
U8
U16
U1
U13
U106
U152
V12
V13
V22
V6
V65


I believe that they have expanded this list with a few SNPs below U152, U106 and P312 (listed below), and I think they also test some more below G2a (P15).

U106: Z18, Z381,L48,U198
P312: M529,Z195
U152: L2, L20

Even though I have access to that forum, I think it is a bit unscrupulous to copy paste the latest statistics as the most recent data has not been published yet.

A subset of the data (the Brabant duchy and Belgium) has been published as several books written in Dutch in 2010 and 2011 (DNA Brabant, ISBN: 9789080430501 and DNA Belgie, ISBN: 9789080430525). The former Brabant duchy study shows that 137 out of 507 kits were U106 with no further breakdown into subgroups.

Dewsloth
11-07-2017, 12:51 AM
Interesting project. I only have one 4th great grandparent from Liège, and I don't carry her mtDNA. My YDNA isn't atypical for the area but my records begin in Hesse (although one report says a lot of Walloons moved there after the 30 Years War, so who knows?).

Wing Genealogist
11-07-2017, 01:02 AM
Given the rather limited number of SNPs (below U106), it has limited usefulness. But it would be interesting (to me at least) to see the percentage of U106 which is Z381 & percentage of U106 which is Z18. These are the largest subclades of U106 (with Z381 being many times larger than Z18). There are also a bunch of very small subclades as well. Knowing the percentage of Z381 & Z18 would allow a calculation of the percentage of all of the smaller clades combined.

Do you know if they plan on publishing an updated study at some time? This is a hotspot for U106, so any tidbits of information we can uncover would be beneficial.

gotten
11-07-2017, 02:43 AM
They intend to release the information through some medium (by book or publication) but at the moment I'm not hopeful that this will happen soon. The bulk of the project is done on a volunteer basis by less than a handful of people.

Have you taken a look at the Genome of the Netherlands and the recent Flemish SNP variation study? Both are published and use full genome sequencing (although the sets are smaller at 250 fathers and 270 males tested, respectively). GoNL only has global statistics per variant, Flemish SNP variation study has variants for each individual sample.

Here are some numbers:

Flemish U106: 67 / 270
GoNL U106: 83 / 250
Flemish Z18: 5
GoNL Z18: 12
Flemish Z381: 54 (21 are S264, 0 are S4078, 28 are L48, 20 are Z9, 5 are L47)
GoNL Z381: not covered (17 are S264, 4 are S4078, L48 is not covered, 27 are Z9, 6 are L47)

GoNL data is available on their website: here (http://www.nlgenome.nl/?page_id=9)
Flemish data is in supplementary info on publisher's website: here (http://www.fsigenetics.com/article/S1872-4973(17)30220-X/addons)

You can delve into both these resources to get a idea of the occurrence rates of subclades of U106 in the Benelux. In any case there seems to be a gradient from south to north, where U106 becomes more abundant (with U152 dropping) towards the north (this is also known from STR studies).

Wing Genealogist
11-07-2017, 09:05 AM
Gotten,
I have accessed both the GoNL and the recent Flemish SNP Variation Study. I have also accessed the Open Search database by Human Longevity Inc. I am really not personally all that interested in numbers tested (except for the total number of males tested in the dataset) but rather the percentages. I am adding this information to a U106 spreadsheet I maintain (on a separate dataset tab)

Published read-only link (Google account not required): https://docs.google.com/spreadsheets/d/e/2PACX-1vQhEo8_IfiZjGP_WLl01aL1IV939Drm26HIMb20mQE16mFBbk FO72xCn2mEa3Argekny5MGrbIQZXLU/pubhtml
Shared read-only link (Google account not required, allows downloads): https://docs.google.com/spreadsheets/d/1rpJP0Bt4qUQb9wWBFA7i1tLPV75ie_qS0iplwvvlVmQ/edit?usp=sharing

Celt_??
11-10-2017, 02:58 PM
FTDNA has a Y-DNA Benelux Geographic Project and its Y-DNA results are public here: https://www.familytreedna.com/public/benelux/default.aspx?section=ycolorized

It has 719 members with fairly good SNP testing for the U106 Haplogroup. But you will have to do your own calculations.
However, I would point out that they have a large number of "Ungrouped" members beginning at the bottom of page 1 and extending onto page 2 which implies to me that the Administrators are no longer actively managing this Project. You would need to add in the R-U106 found in the Ungrouped to get a more accurate percentage of the total - but not difficult to do.

Wing Genealogist
11-10-2017, 03:14 PM
FTDNA has a Y-DNA Benelux Geographic Project and its Y-DNA results are public here: https://www.familytreedna.com/public/benelux/default.aspx?section=ycolorized

It has 719 members with fairly good SNP testing for the U106 Haplogroup. But you will have to do your own calculations.
However, I would point out that they have a large number of "Ungrouped" members beginning at the bottom of page 1 and extending onto page 2 which implies to me that the Administrators are no longer actively managing this Project. You would need to add in the R-U106 found in the Ungrouped to get a more accurate percentage of the total - but not difficult to do.

I have looked at the FTDNA Benelux Project. While U106 can be predicted with over 95% accuracy by a STR marker (DYS492=13) this STR is in the 67 STR panel. A significant number of folks in the project have only taken 37 STRs (or less) so I have no way of knowing which ones of these (predicted to be R-M269) are U106+ or U106-. As a result, I feel it would simply be too much work for me to count up all of the 67/111 STR marker kits in the project, then count up the 67/111 kits which have either tested U106+ or have DYS492=13. This would then only give me the percentage for U106 overall (and I am trying to keep track of the subclades as well). It would basically be too much of an effort for me to check the SNP results for all U106+ folks to figure out the estimates for the subclades, and even if I did this, the numbers would be so small, that the result would likely not represent an accurate prediction of how well represented the subclades actually are in these Low Countries.

The beauty of projects like the GoNL and even to a lesser degree the private Benelux project is the fact everyone is tested out to the same level, and with enough individuals, you can get a relatively accurate picture of the breakdown of U106 subclades in the particular country/countries the project is studying.

gotten
11-10-2017, 04:09 PM
FTDNA has a Y-DNA Benelux Geographic Project and its Y-DNA results are public here: https://www.familytreedna.com/public/benelux/default.aspx?section=ycolorized

However, I would point out that they have a large number of "Ungrouped" members beginning at the bottom of page 1 and extending onto page 2 which implies to me that the Administrators are no longer actively managing this Project.
I concur, the Netherlands (https://www.familytreedna.com/public/Netherlands/) and Benelux (https://www.familytreedna.com/public/benelux) projects on FTDNA are poorly to not maintained. The Netherlands Y (https://www.familytreedna.com/groups/netherlands-y) project which is the smallest of the three is still active but also a lot more strict about who can join.

I think a pro-active Dutch FTDNA group would really help with getting more Dutch people tested all the way (Big-Y).

Getting statistics from FTDNA groups can give you an indication of subhaplogroup occurrence but you have to be aware that the tested individuals are biased (for instance due to surname groups or affluence). Scientific studies such as GoNL try to be more homogeneous.

Celt_??
11-10-2017, 06:35 PM
I concur, the Netherlands (https://www.familytreedna.com/public/Netherlands/) and Benelux (https://www.familytreedna.com/public/benelux) projects on FTDNA are poorly to not maintained. The Netherlands Y (https://www.familytreedna.com/groups/netherlands-y) project which is the smallest of the three is still active but also a lot more strict about who can join.

I think a pro-active Dutch FTDNA group would really help with getting more Dutch people tested all the way (Big-Y).

Getting statistics from FTDNA groups can give you an indication of subhaplogroup occurrence but you have to be aware that the tested individuals are biased (for instance due to surname groups or affluence). Scientific studies such as GoNL try to be more homogeneous.

My Dutch brother-in-law (Den Hertog, Utecht: E-M35) is in both FTDNA Projects and I agree with you ;~)

rafc
01-22-2018, 12:00 PM
I've been a longtime member of the Benelux project at FTDNA, and I also thought it was a shame there was no active project for people from the Low Countries. It's taken a while, but now I and another co-admin of the E-M35 project haven taken over the Benelux project and reactivated it. Ungrouped people have now been classified and people who don't have a clear link to the Benelux have been moved to a group apart. You can visit us here: https://www.familytreedna.com/groups/benelux/