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DMXX
03-07-2014, 09:18 AM
Following on from this thread, where users have shared their specific locations on Interpretome's PCA. Comparing everyone's positions relative to each other would be an interesting exercise.

To participate, please follow the instructions below. As details on Interpretome's maps can only be visualised by focusing on one region, this currently caters for those largely of West Eurasian ancestry genetically (North African, European, Middle-Eastern, South-Central Asian).

I'll be periodically updating the map as more samples come through. [P.S. please include your ancestral information as you'd prefer it shown on the map with your samples, thank you.]



1. Visit http://www.interpretome.com/ and upload your data
2. Select "PCA"
3. Pick the following settings:
-- HGDP:World
-- Resolution 100,000
-- Principal Components to Plot PC1, PC2
4. Click "Visualize!"
5. Once the map loads, highlight the area around your location to zoom in (thanks to Zeph for pointing this out)
6. Print screen, save to an image editor, and share on this thread (provide coordinates if desired as MfA's done)


1648

vettor
03-07-2014, 10:17 AM
Following on from this thread, where users have shared their specific locations on Interpretome's PCA. Comparing everyone's positions relative to each other would be an interesting exercise.

To participate, please follow the instructions below. As details on Interpretome's maps can only be visualised by focusing on one region, this currently caters for those largely of West Eurasian ancestry genetically (North African, European, Middle-Eastern, South-Central Asian).

I'll be periodically updating the map as more samples come through.



1. Visit http://www.interpretome.com/ and upload your data
2. Select "PCA"
3. Pick the following settings:
-- HGDP:World
-- Resolution 100,000
-- Principal Components to Plot PC1, PC2
4. Click "Visualize!"
5. Once the map loads, highlight the area around your location to zoom in (thanks to Zeph for pointing this out)
6. Print screen, save to an image editor, and share on this thread


done

I did not click the box on left with my name on it...............should I have?

http://imageshack.com/scaled/medium/833/z54p.jpg (http://imageshack.com/photo/my-images/833/z54p.jpg/) Uploaded with ImageShack.us (http://imageshack.com)

DMXX
03-07-2014, 10:44 AM
done

I did not click the box on left with my name on it...............should I have?


I can't use this for two reasons:
- As explained, you haven't zoomed in on your area. I need a definitive view within West Eurasia ("Once the map loads, highlight the area around your location to zoom in")
- Your location is in-between Europe and Africa. I can't plot you on the community map because of this.

You're welcome to include a zoom-in anyway, in case I manage to create a detailed worldwide map somehow in the future.

MfA
03-07-2014, 11:43 AM
My coordinates
X: 58,0791
Y: -52,479465

http://abload.de/img/desktop_2014_03_07_138udim.png

ZephyrousMandaru
03-07-2014, 01:20 PM
My coordinates
X: 58,0791
Y: -52,479465

http://abload.de/img/desktop_2014_03_07_138udim.png

Can these coordinates be superimposed on a map?

Mandoos
03-07-2014, 01:45 PM
not really fitting into the map indicated...but here is where I plot anyways

1558

soulblighter
03-07-2014, 02:50 PM
And here is my zoomed in plot
1559

Cood: -67.39,43.2885

MfA
03-07-2014, 03:19 PM
Can these coordinates be superimposed on a map?

I guess it can be similarly done by Palisto's calculators, but would that be accurate using only 7 reference samples?

DMXX
03-07-2014, 03:20 PM
Map updated to include MfA, soulblighter.


not really fitting into the map indicated...but here is where I plot anyways

1558

Thank you nonetheless; as mentioned to vettor, if I do manage to have the means of expanding this level of detail, I'll happily include the samples eventually.

vettor
03-07-2014, 06:47 PM
I can't use this for two reasons:
- As explained, you haven't zoomed in on your area. I need a definitive view within West Eurasia ("Once the map loads, highlight the area around your location to zoom in")
- Your location is in-between Europe and Africa. I can't plot you on the community map because of this.

You're welcome to include a zoom-in anyway, in case I manage to create a detailed worldwide map somehow in the future.

Thanks

I think it was an error anyway as I get a warning from interpretome that only 30 SNPs where loaded...............I re-downloaded a new file from 23andme and get the same issue

regards

AJL
03-07-2014, 07:05 PM
1561

(61.02, -52.65)

vettor
03-07-2014, 07:11 PM
Following on from this thread, where users have shared their specific locations on Interpretome's PCA. Comparing everyone's positions relative to each other would be an interesting exercise.

To participate, please follow the instructions below. As details on Interpretome's maps can only be visualised by focusing on one region, this currently caters for those largely of West Eurasian ancestry genetically (North African, European, Middle-Eastern, South-Central Asian).

I'll be periodically updating the map as more samples come through.



1. Visit http://www.interpretome.com/ and upload your data
2. Select "PCA"
3. Pick the following settings:
-- HGDP:World
-- Resolution 100,000
-- Principal Components to Plot PC1, PC2
4. Click "Visualize!"
5. Once the map loads, highlight the area around your location to zoom in (thanks to Zeph for pointing this out)
6. Print screen, save to an image editor, and share on this thread (provide coordinates if desired as MfA's done)


1560

just for your info

I did the same test with only Ydna genome and another with mtdna genome and got 2 different results
the y - in the nearEastern, close to european ............I guess anatolia
the mtdna - central south asian ......................my x-chromosome is 6% south-asian and the rest european

might be also interesting to later on do this type of tests

regards

Dr_McNinja
03-07-2014, 08:21 PM
My mother and I:

http://imgur.com/a/5rACs

She's on the top right

Sangarius
03-07-2014, 08:39 PM
Coordinates:
X: 54,15
Y: 58,38

Ethnicity: Turkish

Quite similar to MfA's position on the plot, just a tiny bit more left- and upwards shifted.

http://abload.de/image.php?img=screenshot2014-03-072iuf3r.png

Wulf Talented
03-07-2014, 08:50 PM
I hope this is okay...

1562

NK19191
03-07-2014, 09:02 PM
here is mine:

http://i1309.photobucket.com/albums/s632/nk191919/TestResults_zps32bcf68f.png

evon
03-07-2014, 09:15 PM
My family, we are all in the same spot, but i got more detailed lines then the rest, weird, i double checked and they are there every time..


Evon:
http://i1010.photobucket.com/albums/af228/njal2010/moi.png

Evon Aunt:
http://i1010.photobucket.com/albums/af228/njal2010/aunt.png

Evon Uncle:
http://i1010.photobucket.com/albums/af228/njal2010/uncle.png

Evon Granny:
http://i1010.photobucket.com/albums/af228/njal2010/gran.png

DMXX
03-07-2014, 09:36 PM
Updated, included AJL, Dr_McNinja and his mother, Sangarius, Wulf Talented, NK19191 and evon & family.

Evon's uncle and auntie are in practically the same spot with him and his grandma on either side, reflecting some intra-family diversity quite nicely. AJL looks pretty much in-between various Euro and Mid-Eastern ethnic groups, but looks quite close to what I'm guessing are South Europeans on his left. I remember you tend to cluster around Central Europe, so this isn't too far off?

MfA and Sangarius look in-between the Iranian and Assyrian mini-clusters we've created from the community results so far, but more Kurds and Turks would help fill the genetic void. NK19191 and myself, as usual, are like twin genetic brothers. Not surprising given the same sort of background (Azeri-Persian + minor Caucasus).

At this point, I'm deducing the European reference population furthest north is from the northeast somewhere, such as Finland or the Baltic states.


My mother and I:

She's on the top right

I'm presuming it's a proximity issue of some kind, but the South Asian cluster appears squashed on the West Eurasian map. The coordinates have proved very useful here in visually placing people from this part of Asia (e.g. you being -65, 45). Whatever's going on here might also explain evon's observation as well.

MfA
03-07-2014, 10:01 PM
At this point, I'm deducing the European reference population furthest north is from the northeast somewhere, such as Finland or the Baltic states.


I think furthest north of the graph would be the least East Eurasian and African shifted hence topmost. I believe they're Basque/Sardinians. The southern most Europeans on the graphs are Russians/Finns..
I added Swedish and Italian samples I have, as you can see the Swedish is more Asian shifted than Evon et al. and Finns would be even more shifted..

http://abload.de/img/desktop_2014_03_07_23r3o1l.png

AJL
03-07-2014, 10:07 PM
Updated, included AJL, Dr_McNinja and his mother, Sangarius, Wulf Talented, NK19191 and evon & family.

Evon's uncle and auntie are in practically the same spot with him and his grandma on either side, reflecting some intra-family diversity quite nicely. AJL looks pretty much in-between various Euro and Mid-Eastern ethnic groups, but looks quite close to what I'm guessing are South Europeans on his left. I remember you tend to cluster around Central Europe, so this isn't too far off?

Yes I generally cluster in south-central Europe somewhere between southeast France and Moldova, depending on the test.

DMXX
03-07-2014, 10:09 PM
I think furthest north of the graph would be the least East Eurasian and African shifted hence topmost. I believe they're Basque/Sardinians. The southern most Europeans on the graphs are Russians/Finns..
I added Swedish and Italian samples I have, as you can see the Swedish is more Asian shifted than Evon et al. and Finns would be even more shifted..


My initial thought was the increased placement northwards corresponding with the North European-specific components, given AJL, evon and Wulf are above everyone else. Then again, the northward shift of Assyrians relative to Iranians doesn't agree with this thought. Very useful, thanks for posting this. I agree with your assessment.

Humanist
03-07-2014, 10:13 PM
Yes I generally cluster in south-central Europe somewhere between southeast France and Moldova, depending on the test.

We are neighbors on the plot. :)

Dr_McNinja
03-07-2014, 10:50 PM
HRP0370, Afghan Pashtun: http://i.imgur.com/dVskGLc.png

RCO
03-07-2014, 11:25 PM
I am here, more or less 57,35 - 54 1565 Brazilian (Portuguese Colonial + Minor German + Distant Amerindian and African)

Dr_McNinja
03-07-2014, 11:26 PM
Is it just me or do different versions of data cluster in different places? The 23andMe V4 raw files I had are clustering further to the right and a little lower than where they should be

DMXX
03-07-2014, 11:27 PM
Final update for today: HRP0370 and lifeisdandy. These two deviate a bit more from the usual Mid-East and Euro contributions we've seen so far, which is great.

Thanks to all who've shared their locations so far; the chart's already looking like a masterpiece. Not touting my own pinpointing talents either; it's nice to see so many regulars featured.


Is it just me or do different versions of data cluster in different places? The 23andMe V4 raw files I had are clustering further to the right and a little lower than where they should be

Yes, there is some variation. I've also noticed the orientation changes somewhat if you keep Visualizing, even with the same raw file. I don't think it affects the overall placements if the coordinates are taken into account. The images I received from lifeisdandy differed quite a bit, but the coordinates didn't.

vettor
03-07-2014, 11:34 PM
got mine fixed by konrad of interpretome, see below ..................I had to smack around 23andme customer service first

http://imageshack.com/scaled/medium/829/5rz4.jpg (http://imageshack.com/photo/my-images/829/5rz4.jpg/) Uploaded with ImageShack.us (http://imageshack.com)


from 23andme
Our records indicate that you were genotyped on our V3 platform. Your 23andMe Personal Genome Service is a comprehensive genetic scan of about 1,000,000 SNPs.

8 MB is the expected file size for a zipped V3 Raw Data file. The file size should be closer to 30 MB once it is unzipped.


I have nearly 25 MB unzipped

vettor
03-08-2014, 12:02 AM
just to complete this topic..........what do the 3 letters mean below...I presume TSI = tuscan

http://imageshack.com/scaled/medium/849/jjb0.jpg (http://imageshack.com/photo/my-images/849/jjb0.jpg/) Uploaded with ImageShack.us (http://imageshack.com)

Sein
03-08-2014, 01:53 AM
Sorry for being so late, here are my results (I hope this is helpful):

1566

escalation
03-08-2014, 05:57 AM
Here's mine(I'm roughly 80% Assyrian and 20% Armenian):
http://i1275.photobucket.com/albums/y442/velum/eerer_zpsb4b9199b.png (http://s1275.photobucket.com/user/velum/media/eerer_zpsb4b9199b.png.html)

Palisto
03-08-2014, 10:42 AM
MfA and Sangarius look in-between the Iranian and Assyrian mini-clusters we've created from the community results so far, but more Kurds and Turks would help fill the genetic void.

1568

1569
From top to bottom: KD002, KD006, KD004, KD008, KD011, KD010, KD012, KD003, KD007, KD009, KD005

Tolan
03-08-2014, 10:49 AM
1570
PC2: 61.73
PC1: -51.81

DMXX
03-08-2014, 02:09 PM
Update n.4: includes RCO, vettor, Sein, escalation and Tolan. I've also added the update number and time on the chart to help keep track. I've described member results as accurately as possible based on profile info or my familiarity. If members take serious issue with the descriptions, please inform me and I'll correct it as advised. I have vettor and soulblighter in mind here.

Thank you for the Kurdish samples Palisto. The cluster they've formed is quite a dense one between Europe, South-Central Asia and the Near-East. If we don't get any more forum Kurds participating down the line, I'll use them instead.

vettor
03-08-2014, 06:03 PM
Update n.4: includes RCO, vettor, Sein, escalation and Tolan. I've also added the update number and time on the chart to help keep track. I've described member results as accurately as possible based on profile info or my familiarity. If members take serious issue with the descriptions, please inform me and I'll correct it as advised. I have vettor and soulblighter in mind here.

Thank you for the Kurdish samples Palisto. The cluster they've formed is quite a dense one between Europe, South-Central Asia and the Near-East. If we don't get any more forum Kurds participating down the line, I'll use them instead.

As for myself, I accept what you have for me .....................My Paternal and Maternal lineage (from ~1600) is North-Italian with a slant towards the Tyrol .............so your "national" marker for me is accurate.

regards

MitchellSince1893
03-08-2014, 07:22 PM
For those of European descent, you may be interested in this thread I started. http://www.anthrogenica.com/showthread.php?2289-Interpretome-POPRES-European

It uses the POPRES-European tool on the Interpretome website to identify which European nationality clusters your genome falls within.

Palisto
03-09-2014, 04:08 AM
1568

1569
From top to bottom: KD002, KD006, KD004, KD008, KD011, KD010, KD012, KD003, KD007, KD009, KD005



Thank you for the Kurdish samples Palisto. The cluster they've formed is quite a dense one between Europe, South-Central Asia and the Near-East. If we don't get any more forum Kurds participating down the line, I'll use them instead.

Some more Kurds:
1585

1586
From top to bottom: KD026, KD024, KD023, KD033, KD043, KD032, KD034

Hanna
03-09-2014, 01:29 PM
Can me and my aunt be included?

My placement ( Turkish):

https://fbcdn-sphotos-a-a.akamaihd.net/hphotos-ak-frc3/t1/1150849_271621136346899_903658174_n.jpg

My aunt ( Turkish):

https://fbcdn-sphotos-e-a.akamaihd.net/hphotos-ak-prn2/t1/1497570_271628659679480_305824211_n.jpg

icebreaker
03-09-2014, 02:01 PM
HRP0343, Turkish

DMXX
03-22-2014, 04:56 PM
Update n.5 - Now includes Hanna and her aunt, icebreaker.

Kurd
01-30-2015, 04:29 AM
Does anyone know whether Interpretome's website is still functional? I tried accessing it to upload my data, but the search engines kept timing out.

kenji.aryan
01-30-2015, 02:16 PM
Does anyone know whether Interpretome's website is still functional? I tried accessing it to upload my data, but the search engines kept timing out.

Its still functional brotha, few days ago only i tried it.

Kurd
01-30-2015, 04:45 PM
Its still functional brotha, few days ago only i tried it.

I was not able to get into Interpretome.com yesterday or today with any search engine. Could you please check to see whether you can get in today?

DMXX
01-30-2015, 04:51 PM
I was able to access it just now, Kurd. I had the same issue you had in the past, which was resolved when I switched browsers (Chrome->FF).

Kurd
01-30-2015, 05:43 PM
I was able to access it just now, Kurd. I had the same issue you had in the past, which was resolved when I switched browsers (Chrome->FF).

Still no luck.

I am using the latest version of FF. I updated my Java, unchecked pop-up blocker, and permitted add-ons from the site. It is still timing out.:(

kenji.aryan
01-31-2015, 01:43 AM
I was not able to get into Interpretome.com yesterday or today with any search engine. Could you please check to see whether you can get in today?

I think its not working but here is the link

http://esquilax.stanford.edu/

Kurd
01-31-2015, 01:55 AM
I think its not working but here is the link

http://esquilax.stanford.edu/

Thanks Kenji, I pinged the website, and ran their IP address through ARIN. I was able to get a couple of POCs at Stanford. I contacted them. They said that they would research it and get back with me.

Kurd
02-02-2015, 11:36 PM
Technical issues with the Interpretome website have been resolved. The following are my plots. They are a little eastern shifted than I had anticipated, but still within the Iranian ranges in general. I selected 100,000 SNPs for all PCA plots.

This is the HGDP World:

http://i1377.photobucket.com/albums/ah42/dil88888/HGDP%20World1_zpsw6cqknua.jpeg (http://s1377.photobucket.com/user/dil88888/media/HGDP%20World1_zpsw6cqknua.jpeg.html)

This one is the HGDP Asia (detailed):



http://i1377.photobucket.com/albums/ah42/dil88888/HGDP%20Asia%20detail_zpsbukcwzth.jpeg (http://s1377.photobucket.com/user/dil88888/media/HGDP%20Asia%20detail_zpsbukcwzth.jpeg.html)

This one is the HGDP Near East:

http://i1377.photobucket.com/albums/ah42/dil88888/HGDP%20Mid%20East1_zpspvtdudlw.jpeg (http://s1377.photobucket.com/user/dil88888/media/HGDP%20Mid%20East1_zpspvtdudlw.jpeg.html)

This one is for the Chromosome Painting. Not sure what some of the population codes are:

http://i1377.photobucket.com/albums/ah42/dil88888/Chromosome%20painting1_zpsuofkouso.png (http://s1377.photobucket.com/user/dil88888/media/Chromosome%20painting1_zpsuofkouso.png.html)

Kurd
02-03-2015, 03:14 AM
DMXX,

I guess I am guilty of "fail to follow instructions". I overlooked your instructions to zoom in, and I gave you some irrelevant plots.

Hopefully, this one is better:

http://i1377.photobucket.com/albums/ah42/dil88888/PCA%20HGDP%20World%20zoom_zpstg9bbdnd.jpeg (http://s1377.photobucket.com/user/dil88888/media/PCA%20HGDP%20World%20zoom_zpstg9bbdnd.jpeg.html)

Varun R
02-03-2015, 04:54 AM
(-66.97298, 44.9620684)

3707

Kurd
02-03-2015, 01:21 PM
This one shows the coordinates a little better. I have also added my daughter (below & to the left of me, 3/4 Kurd, 1/4 Punjabi), to gauge how much a punjabi contribution to the genome (wife is 1/2 Kurd, 1/2 Punjabi) shifts the coordinates. Ideally, I would also add my wife to the plot, but she is not genotyped as of now.

http://i1377.photobucket.com/albums/ah42/dil88888/Kurd%20amp%20Daughter%20PCA%20HGDP%20World%20small _zpsrhcclwob.jpeg (http://s1377.photobucket.com/user/dil88888/media/Kurd%20amp%20Daughter%20PCA%20HGDP%20World%20small _zpsrhcclwob.jpeg.html)

EDIT: Correction made to wife's and daughter's known ancestry.

Kurd
02-03-2015, 05:02 PM
In reviewing DMXX's community plot, I noticed that my coordinates are considerably south of the other Iranian/Kurd members. I am wondering if the Interpretome PCA program has been recalibrated since everyone posted a few months ago.

Can someone who had posted in early 2014 re-run their data through Interpretome, and check to see if they are now plotting south of where they had previously plotted.

Thanks.

DMXX
02-03-2015, 05:59 PM
^ I just checked my coordinates and they look about the same. I'm still midway between the European and South-Central clusters with a very slight shift towards Near-Eastern.

vettor
02-03-2015, 06:16 PM
In reviewing DMXX's community plot, I noticed that my coordinates are considerably south of the other Iranian/Kurd members. I am wondering if the Interpretome PCA program has been recalibrated since everyone posted a few months ago.

Can someone who had posted in early 2014 re-run their data through Interpretome, and check to see if they are now plotting south of where they had previously plotted.

Thanks.

If mine move , they moved very slightly in a NE direction, ............basically the same as before....did you follow the instructions as per first link


they only changed the legend of the naming, so there is no more european, but replaced by TSI or CEU or MEX etc

AJL
02-03-2015, 07:37 PM
In reviewing DMXX's community plot, I noticed that my coordinates are considerably south of the other Iranian/Kurd members.

Does Interpretome work on Markov-chain Monte Carlo algorithms? If so it may be possible for the same person to plot a little differently every time they try.

Kurd
02-03-2015, 09:06 PM
Does Interpretome work on Markov-chain Monte Carlo algorithms? If so it may be possible for the same person to plot a little differently every time they try.

I don't have the issue of being plotted differently every time I use it. It consistently plots me using the same coordinates. I was just wandering if the programming was updated since early 2014, however, based on the responses that I received, that does not appear to be the case.

vettor
02-04-2015, 05:11 AM
Does Interpretome work on Markov-chain Monte Carlo algorithms? If so it may be possible for the same person to plot a little differently every time they try.

it will change location if the person changes the PCA numbers

surbakhunWeesste
04-19-2015, 07:21 AM
I tried the Middle East/Jewish.

4382

world

4384

Salkin
04-19-2015, 07:41 AM
Curious, usually I plot pretty firmly European in these things.

4385

Salkin
04-19-2015, 08:10 AM
That's really odd. Did you use 100,000 snps?

Yep, all settings the same as DMXX specified in the OP. Tried it again now to double-check and got the same result. Apparently something is pulling me south.

jesus
04-19-2015, 08:54 AM
Yep, all settings the same as DMXX specified in the OP. Tried it again now to double-check and got the same result. Apparently something is pulling me south.

Did you run your 23andme or FTDNA raw data ?

Salkin
04-19-2015, 09:06 AM
Did you run your 23andme or FTDNA raw data ?

23andMe. I didn't think it took FTDNA. Might try that later.

Salkin
04-19-2015, 04:09 PM
23andMe. I didn't think it took FTDNA. Might try that later.

It's not accepting my FTDNA data, and the upload dialog says it only supports 23andMe and Lumigenix data.

Agamemnon
04-19-2015, 11:44 PM
Curious, usually I plot pretty firmly European in these things.

4385

My mother gets the same (plotting next to the Near East), and she's more "northern" than most Brits...

http://pichoster.net/images/2015/04/20/chart%20interpretome%20messed%20up.jpg

I'm getting equally messed-up results BTW.

Afshar
04-20-2015, 06:38 AM
Too bad, it doesnt process FTDNA files.

Agamemnon
04-20-2015, 01:50 PM
Are you on 23andme "V4" chip? That could be it. I think it only works with V2 and V3 chip files.

My mother's kit has the "V4" chip... My kit, on the other hand, has the "V3" chip.

tchekitchek
04-20-2015, 03:44 PM
I too plot in the Middle east, I'm as west european as one can be.

vettor
04-20-2015, 06:37 PM
Using my son's V4 data ............and using pca1 and pca2 ........he plots next to humanist as per post #1.

if I select pca1 and pca4 ( as stated for european use ) he plots , on the swiss and french border

so I guess the pca numbers used, are very important today , more so than months ago ..............and where updated recently by interpretome.

I can also tell by this sentence which was not there 6 months ago.

Additional individuals to plot
The selected individual (upper-right corner) is plotted by default. Load additional genotypes and select other individuals here. Select all, Select none

Agamemnon
04-20-2015, 08:18 PM
^^ Tried that, changed X & Y Axis many times and my mother still plots with Near Easterners, I don't think it's a stretch to suppose that something might be going on here.