Polish DNA from studies on GEDmatch

[Peterski]

I will post here kit numbers of academic Polish samples from studies that I'm uploading to GEDmatch Genesis.

Poles from Tambets et al. 2018:

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1522-1

Tambets 2018 sample Poland135 - kit number LK5810440
Tambets 2018 sample Poland148 - kit number KC6230115
Tambets 2018 sample Poland149 - kit number HE4756510
Tambets 2018 sample Poland150 - kit number HN5578439
Tambets 2018 sample Poland151 - kit number XD1211284

^^^
Here is what these Polish samples get in Fig. 3 from this study:

https://media.springernature.com/full/springer-static/image/art%3A10.1186%2Fs13059-018-1522-1/MediaObjects/13059_2018_1522_Fig3_HTML.png

[Peterski]

Poles from Behar et al. 2013:

https://www.ncbi.nlm.nih.gov/pubmed/25079123

Behar 2013 sample Pole_Poland1 - kit number UR9122953
Behar 2013 sample Pole_Poland2 - kit number GT5237590
Behar 2013 sample Pole_Poland3 - kit number XV5220138
Behar 2013 sample Pole_Poland5 - kit number QT5909459
Behar 2013 sample Pole_Poland6 - kit number YA5670771
Behar 2013 sample Pole_Poland9 - kit number PK5923501
Behar 2013 sample Pole_Poland11 - kit number TF3777282
Behar 2013 sample Pole12p_1m - kit number LZ6789348
Behar 2013 sample Poland132 - kit number KZ8706898
Behar 2013 sample Poland133 - kit number AZ8283838
Behar 2013 sample Poland136 - kit number EK6054770
Behar 2013 sample Poland137 - kit number TK3628144
Behar 2013 sample Poland138 - kit number EZ6423511
Behar 2013 sample Poland140 - kit number XF3966585
Behar 2013 sample Poland141 - kit number DR5396941
Behar 2013 sample Poland142 - kit number LK5514818
Behar 2013 sample Poland143 - kit number GL2046169

[Cumansky]

What region? Do you have PCA for Tambets 2018?

[Peterski]

What region?

Apparently some of them are Estonian Poles (those which are not called Pole_Poland, are from Estonia).

Now I've uploaded Poles from Pagani 2016, one is from Wrocław, one from Kohtla-Järve, two unspecified:

Poles from Pagani et al. 2016:

https://www.ncbi.nlm.nih.gov/pubmed/27654910

Pagani 2016 sample Pole1 Kohtla-Järve - kit BD1045630
Pagani 2016 sample Pole2 - kit number JR7565919
Pagani 2016 sample Pole3 - kit number PB4657964
Pagani 2016 sample Pole4 Wroclaw - kit LG8363351

From the spreadsheet with details about each sample:

https://i.imgur.com/XK0s3zH.png

^^^
This is where the place is located: https://en.wikipedia.org/wiki/Kohtla-J%C3%A4rve

Edit:

This thread is mainly to show people how crappy are Polish samples available in studies published to date. :)

I was saying this on TA for a long time but some people didn't believe that scientific samples can be crappy.


What region? Do you have PCA for Tambets 2018?

They have matches from Estonia, so probably they are Estonian Poles (only samples labeled as "Pole_Poland" are from present-day Poland):

https://i.imgur.com/s2q8o7S.png

Estonia used to belong to Poland, but I think it is misleading that samples which are ethnic Poles from Estonia are labeled as "Poland133" etc.

=====

These famous Estonian Poles were first published by Behar in 2013/2014, not by Kushniarevich in 2015:

http://polishgenes.blogspot.com/2015/09/finno-ugric-poles-in-kushniarevich-et.html

https://lh3.googleusercontent.com/mLz9jbs5RxTTisauuK0t4ZaPpFJbCswGVaX2jbNLBLc=w250-h272-no

Kushniarevich used samples genotyped by Behar, but Behar didn't say that they were Poles from Estonia.

Kushniarevich 2015 was the first study which labeled them properly as ethnic Polish minority in Estonia.

=====

Historically Latvia has had a much larger Polish minority than Estonia, they should test also Latvian Poles:

https://www.theapricity.com/forum/showthread.php?267735-The-Forgotten-Minority-Latvia-s-Poles

[Cumansky]

Make PCA, I send my Polish kit #..

[Peterski]

BTW how to get a truly representative sample of Poles:

https://www.theapricity.com/forum/showthread.php?272797-Types-of-ethnic-Polish-surnames&p=5699037&viewfull=1#post5699037

You need to sample regional groups from all these areas:

https://www.theapricity.com/forum/showthread.php?285873-Map-of-ethnic-Poles-in-1918-compared-to-pre-1772-borders-of-Poland


Make PCA, I send my Polish kit #..

Okay please send me in a private message.

Edit:

This study has Poles from Warsaw but so far I couldn't find where to download these genomes:

https://www.cell.com/current-biology/fulltext/S0960-9822(08)00956-1

[Cumansky]

Okay send me in a private message.

Make PCA, I post here GEDmatch Polish kit #.

What is the good calculator?

[Peterski]

Make PCA, I post here GEDmatch Polish kit #.

What is the good calculator?

Okay post just kit numbers and I will choose calculator later.

[Cumansky]

Nah, make first, use kits from study as foundation.

Then I send.

[Cumansky]

Okay post just kit numbers and I will choose calculator later.

Ok, I will post here Polish kits, Puntdnal K13 calc..

[Lucas]

To be honest some Estonian Poles were without above than average Fennoscandian admix. But yes, some have even Siberian on K36. Which is impossible for Poles from Poland.

[Cumansky]

South Polish - Kit# MrVlachZyraxes

# Population Percent
1 NE_Europe 55.07
2 SW_Europe 25.17
3 West_Asia 9.84
4 SW_Asia 3.71
5 Siberia 1.81
6 Oceania 1.27
7 NE_Asia 1.09
8 West_Africa 0.79
9 Americas 0.48
10 South_Africa 0.3
11 East_Africa 0.29
12 SE_Asia 0.17

66.7% Russian + 33.3% Bosnian @ 2.6

[Cumansky]

South Polish - Kit# ER4993477

# Population Percent
1 NE_Europe 60.86
2 SW_Europe 23.45
3 West_Asia 8.58
4 SE_Asia 2.12
5 West_Africa 1.92
6 SW_Asia 1.88
7 Americas 0.93
8 Oceania 0.22
9 South_Africa 0.05

94.7% Polish + 5.3% Dominican @ 2.94

[Cumansky]

South Polish - Kit# A470811

# Population Percent
1 NE_Europe 49.4
2 SW_Europe 26.35
3 West_Asia 14.08
4 SW_Asia 4.45
5 Americas 1.14
6 Siberia 0.94
7 South_Asia 0.76
8 NE_Asia 0.75
9 East_Africa 0.74
10 Oceania 0.61
11 West_Africa 0.52
12 South_Africa 0.27

80.9% Belarusian + 19.1% Ossetian @ 2.57

[Cumansky]

South Polish - Kit# H532283

# Population Percent
1 NE_Europe 52.48
2 SW_Europe 30.78
3 West_Asia 7.51
4 SW_Asia 3.1
5 Siberia 2
6 South_Asia 1.54
7 South_Africa 1.22
8 Americas 0.71
9 NE_Asia 0.61
10 Oceania 0.04

68.5% Russian + 31.5% French_Basque @ 2.73

[Cumansky]

South Polish - Kit# A176124

# Population Percent
1 NE_Europe 49.47
2 SW_Europe 27.61
3 West_Asia 13.87
4 SW_Asia 4.34
5 Siberia 1.66
6 East_Africa 1.16
7 NE_Asia 0.94
8 Americas 0.57
9 Oceania 0.19
10 SE_Asia 0.1
11 South_Asia 0.09

52.5% Serbian + 47.5% Russian @ 2.37

[Cumansky]

South Polish - Kit# A228632

# Population Percent
1 NE_Europe 59.93
2 SW_Europe 26.34
3 West_Asia 7.76
4 West_Africa 1.54
5 SW_Asia 1.42
6 Siberia 1.34
7 NE_Asia 0.81
8 East_Africa 0.32
9 Oceania 0.29
10 South_Africa 0.21
11 SE_Asia 0.03

87.7% Belarusian + 12.3% Lithuanian @ 2.75

[Cumansky]

South Polish - Kit T349352

# Population Percent
1 NE_Europe 53.85
2 SW_Europe 28.37
3 West_Asia 8.77
4 SW_Asia 3.48
5 East_Africa 1.52
6 Oceania 1.04
7 South_Asia 1.02
8 Siberia 0.96
9 SE_Asia 0.74
10 South_Africa 0.15
11 Americas 0.1
12 NE_Asia 0.01

62% Belarusian + 38% Slovene @ 2.63

[Cumansky]

South Polish - Kit# M248190

# Population Percent
1 NE_Europe 58.18
2 SW_Europe 24.58
3 West_Asia 7.62
4 SW_Asia 4.53
5 South_Asia 1.94
6 SE_Asia 0.89
7 Siberia 0.67
8 Americas 0.65
9 NE_Asia 0.52
10 East_Africa 0.41

75.7% Estonian + 24.3% Romanian @ 2.24

[Cumansky]

South Polish - Kit# A941477

# Population Percent
1 NE_Europe 52.21
2 SW_Europe 26.41
3 West_Asia 11.53
4 SW_Asia 3.84
5 South_Asia 1.77
6 Americas 1.47
7 Oceania 1.29
8 East_Africa 0.89
9 South_Africa 0.21
10 NE_Asia 0.2
11 Siberia 0.17

60.4% Moldavian + 39.6% Estonian @ 2.94

[Cumansky]

South Polish - Kit M499914

# Population Percent
1 NE_Europe 54.62
2 SW_Europe 25.76
3 West_Asia 9.89
4 SW_Asia 3.97
5 SE_Asia 1.61
6 South_Asia 1.3
7 East_Africa 1.09
8 Americas 0.94
9 South_Africa 0.64
10 Oceania 0.12
11 West_Africa 0.06

52.5% Moldavian + 47.5% Lithuanian @ 2.88

[Cumansky]

South Polish - Kit# KA9035494

# Population Percent
1 NE_Europe 47.34
2 SW_Europe 32
3 West_Asia 10.59
4 SW_Asia 4.7
5 Siberia 1.18
6 Oceania 1.07
7 SE_Asia 0.95
8 South_Asia 0.79
9 South_Africa 0.72
10 Americas 0.68

91.2% Slovak + 8.8% Spaniard @ 2.74

[Cumansky]

Okay post just kit numbers and I will choose calculator later.

11 South Polish kits added..

[Peterski]

To be honest some Estonian Poles were without above than average Fennoscandian admix (...)

Maybe they are not from Estonia? It seems you named at least one sample wrongly.

What you uploaded as Estonian_Pole1 is the same sample as Pole12p_1m from Behar and Pole4 Wroclaw from Pagani:

https://i.imgur.com/8Ug3d9A.png

So this is not an Estonian Pole, that's why does not have above average Fennoscandian but scores South Polish in K15.


11 South Polish kits added..

Do you have some more or are these all for now?

[Nazarene]

I've never met a Pole in my life, but Peterski is a real brother. Much love for Poland.

[Lucas]

Maybe they are not from Estonia? It seems you named at least one sample wrongly.

What you uploaded as Estonian_Pole1 is the same sample as Pole12p_1m from Behar and Pole4 Wroclaw from Pagani:

https://i.imgur.com/8Ug3d9A.png
Mayeb this one yes, but there were additional too.

So this is not an Estonian Pole, that's why does not have above average Fennoscandian but scores South Polish in K15.



Do you have some more or are these all for now?

[Cumansky]

Maybe they are not from Estonia? It seems you named at least one sample wrongly.

What you uploaded as Estonian_Pole1 is the same sample as Pole12p_1m from Behar and Pole4 Wroclaw from Pagani:

https://i.imgur.com/8Ug3d9A.png

I post some more later..

For PCA if you can do it, there is good variety Poles already..

[Roy]

South Polish - Kit# KA9035494

# Population Percent
1 NE_Europe 47.34
2 SW_Europe 32
3 West_Asia 10.59
4 SW_Asia 4.7
5 Siberia 1.18
6 Oceania 1.07
7 SE_Asia 0.95
8 South_Asia 0.79
9 South_Africa 0.72
10 Americas 0.68

91.2% Slovak + 8.8% Spaniard @ 2.74

Why are those kits so over the place?

[vbnetkhio]

Poles from Behar et al. 2013:

https://www.ncbi.nlm.nih.gov/pubmed/25079123

Behar 2013 sample Pole_Poland1 - kit number UR9122953
Behar 2013 sample Pole_Poland2 - kit number GT5237590
Behar 2013 sample Pole_Poland3 - kit number XV5220138
Behar 2013 sample Pole_Poland5 - kit number QT5909459
Behar 2013 sample Pole_Poland6 - kit number YA5670771
Behar 2013 sample Pole_Poland9 - kit number PK5923501
Behar 2013 sample Pole_Poland11 - kit number TF3777282


These are the coordinates given for these samples in the study: 52.9743978146,19.6763955101
They land in some uninhabited spot in Kujawy-Pomerania, on the border with Mazovia.

You labeled them as Mazovia, do you have some additional info on them?

[vbnetkhio]

Poles from Pagani et al. 2016:

https://www.ncbi.nlm.nih.gov/pubmed/27654910

Pagani 2016 sample Pole1 Kohtla-Järve - kit BD1045630
Pagani 2016 sample Pole2 - kit number JR7565919
Pagani 2016 sample Pole3 - kit number PB4657964
Pagani 2016 sample Pole4 Wroclaw - kit LG8363351

From the spreadsheet with details about each sample:

https://i.imgur.com/XK0s3zH.png

^^^
This is where the place is located: https://en.wikipedia.org/wiki/Kohtla-J%C3%A4rve




pole2 and 3 have coordinates landing near Warsaw

[Peterski]

These are the coordinates given for these samples in the study: 52.9743978146,19.6763955101
They land in some uninhabited spot in Kujawy-Pomerania, on the border with Mazovia.

You labeled them as Mazovia, do you have some additional info on them?

Davidski claims that these Behar samples are from Warsaw. But coordinates indeed land in that spot.

That spot is a location in what has historically been known as Ziemia Dobrzynska (Land of Dobrzyn):

https://en.wikipedia.org/wiki/Dobrzy%C5%84_Land

It is part of Mazovia historically, but possibly with some genetic influences from Baltic Old Prussians.

You should not use them for making Kujawy-Pomerania average, they are not typical for this region.

[vbnetkhio]

Davidski claims that these Behar samples are from Warsaw. But coordinates indeed land in that spot.

That spot is a location in what has historically been known as Ziemia Dobrzynska (Land of Dobrzyn):

https://en.wikipedia.org/wiki/Dobrzy%C5%84_Land

It is part of Mazovia historically, but possibly with some genetic influences from Baltic Old Prussians.

You should not use them for making Kujawy-Pomerania average, they are not typical for this region.

OK. They are currently in the Mazovian average, I'll leave them there.

[ScandinavianCelt]

I match this kit quite a lot: Kit LG8363351 (Pagani 2016 Pole4 Wroclaw)

Chr B37 Start Pos'n B37 End Pos'n Centimorgans (cM) SNPs Segment threshold Bunch limit SNP Density Ratio
1 15,732,793 18,179,691 4.5 424 193 116 0.32
1 39,087,604 41,299,109 3.3 304 217 130 0.26
1 234,398,880 235,766,162 3 279 183 109 0.29

Chr B37 Start Pos'n B37 End Pos'n Centimorgans (cM) SNPs Segment threshold Bunch limit SNP Density Ratio
2 7,810,042 9,804,994 6.4 362 199 119 0.28 (largest piece, apparently)
2 121,077,184 124,363,708 4.2 519 196 117 0.27
2 144,376,033 149,668,181 3.3 566 204 122 0.26

Chr B37 Start Pos'n B37 End Pos'n Centimorgans (cM) SNPs Segment threshold Bunch limit SNP Density Ratio
3 62,272,627 64,477,681 4.4 462 191 114 0.26
3 69,667,120 71,999,251 3.5 418 188 113 0.29
3 114,104,227 116,509,468 3.7 364 219 131 0.27
3 186,656,113 187,860,667 3.7 322 193 115 0.3

Chr B37 Start Pos'n B37 End Pos'n Centimorgans (cM) SNPs Segment threshold Bunch limit SNP Density Ratio
4 25,465,790 26,841,503 3.4 294 187 112 0.32
4 37,513,594 39,397,291 3.3 450 200 120 0.3
4 142,117,424 146,720,570 3.3 597 167 100 0.3

Chr B37 Start Pos'n B37 End Pos'n Centimorgans (cM) SNPs Segment threshold Bunch limit SNP Density Ratio
5 14,782 1,282,414 3.2 231 208 125 0.32
5 32,472,109 34,826,730 4 389 176 105 0.26
5 35,028,272 38,381,406 4 505 183 110 0.25
5 143,225,966 148,624,898 5 824 208 125 0.26
5 157,616,208 161,722,397 4 680 230 138 0.28

Chr B37 Start Pos'n B37 End Pos'n Centimorgans (cM) SNPs Segment threshold Bunch limit SNP Density Ratio
6 125,333,797 130,183,688 3.8 633 206 123 0.28

Chr B37 Start Pos'n B37 End Pos'n Centimorgans (cM) SNPs Segment threshold Bunch limit SNP Density Ratio
7 29,535,998 31,072,469 3.1 314 230 138 0.32
7 152,853,444 154,182,625 4.3 273 215 129 0.28

Chr B37 Start Pos'n B37 End Pos'n Centimorgans (cM) SNPs Segment threshold Bunch limit SNP Density Ratio
8 10,459,589 12,685,033 4.2 405 180 108 0.3
8 41,984,864 52,969,933 3.5 754 239 143 0.3

Chr B37 Start Pos'n B37 End Pos'n Centimorgans (cM) SNPs Segment threshold Bunch limit SNP Density Ratio
10 2,408,852 3,264,432 3.2 254 231 139 0.31
10 73,445,707 78,324,698 3.7 725 221 132 0.36

Chr B37 Start Pos'n B37 End Pos'n Centimorgans (cM) SNPs Segment threshold Bunch limit SNP Density Ratio
11 19,906,795 20,838,106 3.1 263 226 136 0.32
11 69,596,523 71,923,542 3.8 385 218 131 0.33
11 122,643,880 123,911,634 3.3 319 222 133 0.35

Chr B37 Start Pos'n B37 End Pos'n Centimorgans (cM) SNPs Segment threshold Bunch limit SNP Density Ratio
14 36,649,246 40,284,332 3.1 509 209 125 0.3

Chr B37 Start Pos'n B37 End Pos'n Centimorgans (cM) SNPs Segment threshold Bunch limit SNP Density Ratio
15 58,166,867 60,128,571 4 419 225 135 0.31
15 70,351,649 74,113,332 3.9 670 228 137 0.36

Chr B37 Start Pos'n B37 End Pos'n Centimorgans (cM) SNPs Segment threshold Bunch limit SNP Density Ratio
16 84,302,585 84,888,295 3.2 232 207 124 0.31

Chr B37 Start Pos'n B37 End Pos'n Centimorgans (cM) SNPs Segment threshold Bunch limit SNP Density Ratio
17 8,552,660 9,715,714 4.9 286 214 128 0.33
17 16,779,412 21,110,226 3.2 432 191 114 0.3

Chr B37 Start Pos'n B37 End Pos'n Centimorgans (cM) SNPs Segment threshold Bunch limit SNP Density Ratio
19 3,491,368 4,811,671 4.3 245 208 125 0.33
19 18,707,048 28,556,284 3.1 653 222 133 0.31

Chr B37 Start Pos'n B37 End Pos'n Centimorgans (cM) SNPs Segment threshold Bunch limit SNP Density Ratio
20 2,502,740 4,391,844 3.5 379 220 132 0.31
20 7,677,668 9,292,176 3.6 297 211 127 0.28
20 40,538,333 42,528,772 3.3 413 231 139 0.3

Chr B37 Start Pos'n B37 End Pos'n Centimorgans (cM) SNPs Segment threshold Bunch limit SNP Density Ratio
21 46,654,418 48,041,492 3.2 275 213 128 0.26

Chr B37 Start Pos'n B37 End Pos'n Centimorgans (cM) SNPs Segment threshold Bunch limit SNP Density Ratio
22 49,708,767 51,177,257 3.6 342 235 141 0.29


Largest segment = 6.4 cM

Total Half-Match segments (HIR) 153cM (4.265 Pct)
41 shared segments found for this comparison.
453323 SNPs used for this comparison.
70.335 Percent of SNPs are full identical.

[ScandinavianCelt]

I ended up matching 10 of the samples of the 30 I think you posted above. What's strange is I get lots of segments with some samples, but the largest segments are on three of them that have just ONE matched segment of 9.4 cM each. Weird.

https://i.postimg.cc/15XtzyyH/polish-matches.jpg (https://postimg.cc/crqZ9ygg)

If you have any more Silesian KIT #, please tag me on them.

Thanks.

[ScandinavianCelt]

I ended up matching 10 of the samples of the 30 I think you posted above. What's strange is I get lots of segments with some samples, but the largest segments are on three of them that have just ONE matched segment of 9.4 cM each. Weird.

https://i.postimg.cc/15XtzyyH/polish-matches.jpg (https://postimg.cc/crqZ9ygg)

If you have any more Silesian KIT #, please tag me on them.

Thanks.


Just in case anyone cares:


The first 10 chromosomes (all I have time for right now) shared with the Wroclaw sample give me an nMonte result at no ADC of:

No ADC:

54.4% Lithuanian
44.0% Tabassaran
1.40% Estonian

.5x ADC:

61.6% Ukrainian_Belgorod
33.4% Tabassaran
3.4% Erzya
1.4% Lithuanian
.2% Estonian

2x ADC:

87.8% Ukrainian_Belgorod
10% Tatar
2% Erzya
.2% SW Russian

That's using the DNAGenics Studio App with Eurogenes K13 Original calc.

The direct K13 Global Admix results are:

42.5% Baltic
29.86% West Asian
25.22% N.Atlantic
1.03% South Asian
.71% Oceanian
.67% Siberian

I'll try to finish the entire segment matching with that Wroclaw sample later and update it. It might change a bit.