Viriato's Update |23andMe GSA chip for their new V5 raw DNA file results

[Brás Garcia de Mascarenhas]

Aug 10 2017 NOTICE to 23andMe Customers: 23andMe is now using the GSA chip for their new V5 raw DNA file results. This format is not compatible with the regular GEDmatch upload, but can be used with the GEDmatch Genesis upload. Use the link in the lower right column of this page.

GEDmatch Genesis Beta: https://genesis.gedmatch.com/Welcome.htm

Eurogenes K36 Admixture Proportions (old chip)


Population
Amerindian -
Arabian 0.25
Armenian 0.54
Basque 3.81
Central_African -
Central_Euro 2.52
East_African 1.19
East_Asian -
East_Balkan 3.39
East_Central_Asian -
East_Central_Euro 1.72
East_Med 5.88
Eastern_Euro 1.96
Fennoscandian 3.44
French 5.05
Iberian 19.19
Indo-Chinese -
Italian 15.85
Malayan -
Near_Eastern 0.67
North_African 5.12
North_Atlantic 6.88
North_Caucasian -
North_Sea 13.02
Northeast_African -
Oceanian 0.39
Omotic -
Pygmy -
Siberian -
South_Asian -
South_Central_Asian 0.65
South_Chinese -
Volga-Ural -
West_African -
West_Caucasian -
West_Med 8.49

Eurogenes K36 Admixture Proportions (V5 chip)


Population
Amerindian -
Arabian 0.17
Armenian 0.49
Basque 3.88
Central_African -
Central_Euro 2.48
East_African 1.17
East_Asian -
East_Balkan 3.42
East_Central_Asian -
East_Central_Euro 1.76
East_Med 6.09
Eastern_Euro 1.86
Fennoscandian 3.30
French 4.99
Iberian 19.31
Indo-Chinese -
Italian 16.00
Malayan -
Near_Eastern 0.60
North_African 5.11
North_Atlantic 6.77
North_Caucasian -
North_Sea 13.08
Northeast_African -
Oceanian 0.39
Omotic -
Pygmy -
Siberian -
South_Asian -
South_Central_Asian 0.63
South_Chinese -
Volga-Ural -
West_African -
West_Caucasian -
West_Med 8.50

[Brás Garcia de Mascarenhas]

The differences are not very significant but I wonder if it will deviate a little bit on PCA maps.

[Brás Garcia de Mascarenhas]

Main difference between the old chip and the new one (in red)

Population
Amerindian -
Arabian 0.25 (-0.08%)
Armenian 0.54 (-0.05%)
Basque 3.81 (+0.07%)
Central_African -
Central_Euro 2.52 (-0.04%)
East_African 1.19 (-0.02%)
East_Asian -
East_Balkan 3.39 (+0.03%)
East_Central_Asian -
East_Central_Euro 1.72 (+0.04€)
East_Med 5.88 (+0.21%)
Eastern_Euro 1.96 (-0.10%)
Fennoscandian 3.44 (-0.14%)
French 5.05 (-0.06%)
Iberian 19.19 (+0.12%)
Indo-Chinese -
Italian 15.85 (+0.15%)
Malayan -
Near_Eastern 0.67 (-0.07%)
North_African 5.12 (-0.01%)
North_Atlantic 6.88 (-0.11%)
North_Caucasian -
North_Sea 13.02 (+0.05%)
Northeast_African -
Oceanian 0.39 (0%)
Omotic -
Pygmy -
Siberian -
South_Asian -
South_Central_Asian 0.65 (-0.02%)
South_Chinese -
Volga-Ural -
West_African -
West_Caucasian -
West_Med 8.49 (+0.02%)

[Brás Garcia de Mascarenhas]

As I said the difference is not that much but calculations made there is a difference of 1.39% from the previous raw data to the new one.

[Longbowman]

So our raw data has changed?

[Brás Garcia de Mascarenhas]

So our raw data has changed?

I believe the chip reading our raw data has changed. At least it is was what I assume from what they wrote: "23andMe is now using the GSA chip for their new V5 raw DNA file results.". You also need to use Gedmatch Genesis to run the new uploaded kit.

The differences are subtle though, on mine there was a difference of 1.39%. On the other hand, if every time they upgrade their chip there is a variance of 1% in the next five chips upgrades we would have a deviance of 5% which is a lot and can totally change a lot of stuff :) Pretty interesting.

[Iloko]

I thought you have to pay an upgrade fee to get the new V5 data? Or no?

[Pahli]

How do you get the v5 raw data? Either I haven't got the update yet or I'm doing something wrong

[Brás Garcia de Mascarenhas]

I thought you have to pay an upgrade fee to get the new V5 data? Or no?

Do we? I am not aware of it to be honest.


How do you get the v5 raw data? Either I haven't got the update yet or I'm doing something wrong

I haven't done anything besides downloading my raw data again and uploading it to GEDmatch Genesis Beta.

[Pahli]

Do we? I am not aware of it to be honest.



I haven't done anything besides downloading my raw data again and uploading it to GEDmatch Genesis Beta.

I ran the calculators again and there seems to be a very little difference, not enough to change any distances tho.

[Petalpusher]

As I said the difference is not that much but calculations made there is a difference of 1.39% from the previous raw data to the new one.

The difference is much lower than that, keep in mind it's percentages of a K36, so of course your own offset is still on 100% but if you add all the differences regardless of their relationship (some negate themselves), then the baseline is 3600 points, of percentages. This is a very minute difference, maybe a pixel or two on a pca.

You sure you have V5 data? i tried to redownload mine, it still says csxcx_V4 on the file. I was assuming it was only for those who will test from now on with the new chip, i cannot imagine them re sequencing everybody for free.

Btw props for
East_Central_Euro 1.72 (+0.04€)

[Pahli]

The difference is much lower than that, keep in mind it's percentages of a K36, so of course your own offset is still on 100% but if you add all the differences regardless of their relationship (some negate themselves), then the baseline is 3600 points, of percentages. This is a very minute difference, maybe a pixel or two on a pca.

You sure you have V5 data? i tried to redownload mine, it still says csxcx_V4 on the file. I was assuming it was only for those who will test from now on with the new chip, i cannot imagine them re sequencing everybody for free.

Btw props for

I don't think its the v5 either, it labeled my raw data as v4, so I assume you have to upgrade to get the v5 raw data.

[Noman]

From 23andme


Our new v5 chip is based on Illumina's Global Screening Array (GSA) and has over 600,000 SNPs.

Customers will have access to the same reports that we currently offer. Upgrades are not free, but customers will be able to purchase upgrades at a discounted rate.

Results shouldn’t change significantly, however, there may be some slight differences in Ancestry Composition, DNA Relatives, and small changes in your haplogroup assignment.

Our phasing algorithms have been updated so family members can still be phased, even if they are on different chips.

[Pahli]

From 23andme

If its cheap enough, I'll do it.

[Petalpusher]

From 23andme

That makes sense. Likely they are going offer algorythm upgrade for those before V5, which im not sure will be worth. Phasing makes the most difference always.

600 000 snps is ridiculous overkill for ancestry but why not if they can, might be more useful for health and things.

[Brás Garcia de Mascarenhas]

The difference is much lower than that, keep in mind it's percentages of a K36, so of course your own offset is still on 100% but if you add all the differences regardless of their relationship (some negate themselves), then the baseline is 3600 points, of percentages. This is a very minute difference, maybe a pixel or two on a pca.

You sure you have V5 data? i tried to redownload mine, it still says csxcx_V4 on the file. I was assuming it was only for those who will test from now on with the new chip, i cannot imagine them re sequencing everybody for free.

Btw props for

Vous avez absolument raison. My bad :picard1: It is still V4. With that said, GEDmatch Genesis is reading my raw data differently.

[Brás Garcia de Mascarenhas]

0.04€ is a lot of money in Eastern Europe :laugh:


https://www.youtube.com/watch?v=B5NuuJQT8ZM

[Brás Garcia de Mascarenhas]

From 23andme

Might give it a shot depending on how much they ask for it.

[Petalpusher]

Vous avez absolument raison. My bad :picard1: It is still V4. With that said, GEDmatch Genesis is reading my raw data differently.

it's normal, even different uploads can get you 0,1% differences. As i said, if you really want to improve the accuracy of your datas further, test a parent or even siblings are an improvement. It's diminishing returns at some points but it basically filters all your ambiguous SNPs

[Brás Garcia de Mascarenhas]

it's normal, even different uploads can get you 0,1% differences. As i said, if you really want to improve the accuracy of your datas further, test a parent or even siblings are an improvement. It's diminishing returns at some points but it basically filters all your ambiguous SNPs

If I test my parents on 23andme it will update my ancestry results on it as well? That's what I am mostly interested in as I still have nearly 30% broadly south\north European.

[Petalpusher]

If I test my parents on 23andme it will update my ancestry results on it as well? That's what I am mostly interested in as I still have nearly 30% broadly south\north European.

Yea the AC is updated after phasing for each new person you test, but don't expect to sort out all your broadly stuff, i still have some after phasing although it's less, it generally made more sense for me (fe i got less British, more French&German, less Iberian more Italian, etc..)

There's a whitepaper on 23andme explaining the whole process of phasing and its benefits.

[Dick]

I gots some SSA now with the new chip.

[Brás Garcia de Mascarenhas]

I gots some SSA now with the new chip.

https://www.theapricity.com/forum/image.php?u=15977&dateline=1502315023https://www.theapricity.com/forum/image.php?u=15977&dateline=1502315023https://www.theapricity.com/forum/image.php?u=15977&dateline=1502315023https://www.theapricity.com/forum/image.php?u=15977&dateline=1502315023https://www.theapricity.com/forum/image.php?u=15977&dateline=1502315023https://www.theapricity.com/forum/image.php?u=15977&dateline=1502315023https://www.theapricity.com/forum/image.php?u=15977&dateline=1502315023https://www.theapricity.com/forum/image.php?u=15977&dateline=1502315023https://www.theapricity.com/forum/image.php?u=15977&dateline=1502315023https://www.theapricity.com/forum/image.php?u=15977&dateline=1502315023https://www.theapricity.com/forum/image.php?u=15977&dateline=1502315023https://www.theapricity.com/forum/image.php?u=15977&dateline=1502315023https://www.theapricity.com/forum/image.php?u=15977&dateline=1502315023https://www.theapricity.com/forum/image.php?u=15977&dateline=1502315023https://www.theapricity.com/forum/image.php?u=15977&dateline=1502315023https://www.theapricity.com/forum/image.php?u=15977&dateline=1502315023https://www.theapricity.com/forum/image.php?u=15977&dateline=1502315023https://www.theapricity.com/forum/image.php?u=15977&dateline=1502315023

[Ion Basescul]

Noice