Comparing 23andMe chip versions

[Maciamo]

23andMe was founded in 2006. Its original test (v1) cost $998. It was replaced in September 2008 by a more affordable test (v2) that only cost $400 and really kickstarted the company's rise. Two years later, v3 was released, which increased the number of SNPs to close to one million. Oddly enough the newest version (v4), released in Nov. 2013 only has 60% of the v3's SNPs. From May 2015 the number of SNPs was further lowered. I have not find any explanation for the reduction of SNPs in v4 and v4 bis.



Chip version
Introduced
Illumina BeadChip platform used
SNPs genotyped
Y-DNA SNPs
mtDNA SNPs


v1
November 2007
Illumina 4-sample HumanHap550 Plus
576,000
1,880
?


v2
September 2008
Illumina 4-sample HumanHap550 Plus
597,000
1,821
2,040


v3
November 2010
Illumina 12-sample HumanOmniExpress Plus
992,000
1,766
2,459


v4
November 2013
Illumina 24-sample HTS iSelect HD
611,000
2,329
3,154


v4 bis
May 2015

598,897
?
?


v5
July 2017
Infinium Global Screening Array-24 v1.0 BeadChip
630,429
3,733
4,318

[Walhaz]

Is there any simple explanation for why the change was made if it's less precise than the previous one? Is it just a matter of cost for 23andme? I'm new to all this, so forgive my ignorance.

[Hayward]

It probably is due to cost. They did mention that they wanted to be able to process more samples at the same time.

[Expredel]

I just took a look at what appears to be a v5 data file. 630429 autosomal SNPs, 3733 Y SNPs, and 4318 MT SNPs.

I got the Y haplogroups it tests for listed here:

https://www.eupedia.com/forum/threads/34791-Writing-a-genome-analyzer?p=523163&viewfull=1#post523163

Edit: There are only 3557 Y SNPs as the data file has over a hundred duplicate positions. Add 323 nocalls and it's down to 3234.

The mtDNA has duplicate positions and nocalls as well.

[Maciamo]

Thanks Expredel. I have updated the table. The new v5 chip has considerably more Y-DNA and mtDNA SNPs. It also uses a Global Screening Array (GSA) like Living DNA.

[Expredel]

The AncestryDNA info is slightly outdated as well, v1 tests 885 SNPs, v2 tests 1692 Y SNPs. I guess it would need to be pointed out clearly that you have to extract the results yourself.

The nocalls for 23andme appear to be random between files. I wonder if most of the additional SNPs are there to serve as reference points and fix alignment issues caused by deletions.

[woman_of_the_world]

A lot of people these days are interested in the raw DNA data file that can be downloaded for free from these ancestry genetic testing websites. This enables them to upload it on third party tools like Promethease and Xcode Life to get additional information about their health for as low as $10. 23andMe's latest chip includes the most number of health related markers. So you can get information about predisposition to 100s of diseases and lifestyle related traits.