Upgrading to the New Chip? What to Expect.

When we announced the release of our newest genotyping platform and offered an extended holiday sale last year, people who had been waiting for an affordable opportunity to get a glimpse of their genomes jumped at the chance. Existing customers also acted on the news, signing up friends and family and even purchasing upgrades for themselves. As we mentioned in an earlier press release, the latest genotyping platform (“V3″) provides customers with data on nearly one million SNPs, compared to about 600,000 on the previous version (“V2″). The process of upgrading platforms also provided us with additional data about SNPs on V2 that enabled us to improve our genotype calling algorithms for many SNPs systematically across both platforms, in addition to the algorithmic improvements we make routinely throughout the year.

As an existing customer on V2, you may be wondering whether you should upgrade, and what to expect if you do. Keep in mind that unless you’re interested in sifting through the raw data, you might not gain that much from upgrading right away. The real value of V3 will come over time as 23andMe researchers pull together information from the scientific literature to provide meaningful connections between specific SNPs and health conditions, and improve algorithms for ancestry analyses. When and if you upgrade is a decision you should evaluate for yourself after seeing the information for V3 accumulate.

Some who have already upgraded, however, may notice specific differences between V2 and V3 on top of the sheer number of SNPs. Although a major consideration for V3 was backwards compatibility, about 30,000 SNPs that were available on V2 are not available on V3 simply because the SNPs did not successfully make it through the manufacturing process (this is expected for large genotyping platforms). There is also a small subset of SNPs that will require manual adjustment before the data can be reported reliably back to customers, including SNPs specific to the Y chromosome and mitochondrial DNA, as well as several SNPs used to calculate results for the ABO Blood Type Health Lab. The majority of these cases should be addressed in the next few weeks.

Other differences, all very slight, that customers upgraded to V3 may notice are addressed in this community post (you must be logged into your account to view). These include small changes to percentages in Ancestry Painting, Relative Finder, and Family Inheritance, as well as minor changes to specific haplogroup assignments.

Customers can expect to have the following approximate numbers of SNPs for their genotyping platform:

V2 only: 576,000 SNPs

V3 only: 967,000 SNPs

V2 + V3 (upgraded): 996,000 SNPs

The number and exact set of SNPs for which you have genotype data — as opposed to a “no call” result — will differ from these numbers and vary from person to person due to data quality control measures. V2 customers who upgrade to V3 will have “no calls” from their V2 results filled in by V3 data if the SNP is present on V3 and their V3 result for it passed quality control. The raw data files for the two genotyping platforms will also be merged to provide a single raw data file.

We are excited to welcome the thousands of new 23andMe members who have just received their data and are beginning to explore the features of the service. We look forward to keeping everyone up to date on the latest research connecting genetics to your health and ancestry!

Customers genotyped on previous versions of the platform can learn more about upgrading here. Note that upgrades require a subscription to the Personal Genome Service.

For specific questions about your account or about the service, please contact help@23andme.com.