Living DNA is the 1st DNA Tester to Drop the Illumina Chipset

Question

UK-based Living DNA announced 22 October, that they are moving away from the Illumina GSA (Global Screening Array) genotyping array microchip they have used since the company opened, opting instead for an offering from Thermo Fisher Scientific under its Affymetrix brand. Living DNA is the first major direct-to-consumer (DTC) autosomal DNA testing company to cease using Illumina, and we can only make educated guesses at the reasons.

The industry has been watching closely for many months to see what the introduction of Illumina's GSA chip would mean to the genealogy marketplace. Living DNA launched 22 September 2016 selling its first test kits in the UK. It exclusively employed the GSA chip. As of September 2017, with its "v5" product, 23andMe had moved from the Illumina OmniExpress chip to the GSA chip, as well. The 800-pound gorilla in DTC genetic testing, AncestryDNA, continues to use the OmniExpress chip, as do large industry players Family Tree DNA and MyHeritage.

For genealogical matching, the wrench in the works has been that the OmniExpress and GSA chips--while both are testing over 665,000 of the approximately 10 million identified SNPs among the 3.2 billion base pairs of the human genome--look at only about 23% of the same SNPs. Almost 80% of the SNPs tested by each microarray product are unique and can't be directly compared.

Living DNA, in their Facebook Group, has promised more details next week. But given the uncertain history the past year has brought regarding chipsets and genetic genealogy, I believe Living DNA's move has the potential to prove a bold one. And it certainly can't be one undertaken lightly. The Axiom Array product from Thermo Fisher Scientific looks to be highly configurable and, using the UK Biobank version of it as a reference, would likely be testing at least some 821,000 markers, ergo the higher overlap described by Living DNA's announcement. The Axiom myDesign GW Array would have the capability of testing up to 1.3 million SNPs depending upon how it is configured.

This will be a very interesting development to watch. I have no insider information, but you can find more background and speculation in this post.

Comments

Wow!  And thanks!

It immediately brings to mind a number of questions, such as:

• The number one question for existing customers is, will there be a retest of existing GSA-based tests?  Will there be an upgrade of our results to include the additional SNP's?
• Perhaps already answered somewhere, but does Living DNA store our DNA, so that a retest with the new chip is even possible?
• How will the quality compare?  Does it do more reads?
• Will there be greater coverage of the Y chromosome?  In other words, better competition with FTDNA?
• How about better coverage of STR's?
• And lastly, any update of its mtDNA coverage?

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LivingDNA has a thread on Facebook where they are fielding some of your questions.

https://www.facebook.com/livingdna/posts/2149559351960395

They say you will not need to retest, as the SNP overlap is sufficient for their reports. They do store your DNA.

Steve Evans posted this note in Genetic Genealogy Tips & Techniques

"Ann Turner The new Affymetrix chip is now being used by Living DNA and comprises 759,727 at- SNPs, 15,227 X-, 34,216 Y- and 3,982 mt- SNPs. So that’s a significant increase in the at- tested and an increase on the Y-."

Microarrays can't be used for STRs.

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Thank you!

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Yeah, ya know? I don't miss 17-hour days.    Trying to get a blog post online before 5:00 a.m. ain't fun, and then not being able to get back to a thread I started until, technically, the next day...

I really don't have any insider knowledge about this change at Living DNA (sorry Rob, and thanks Ann!), but developments continued today. I've added a "Recent Updates" section to that blog post that you can access directly via this link.

There was so much activity on Living DNA's Facebook page that they posted a new blog post today that includes a brief FAQ section gleaned from customer questions during the first 36 or so hours post-launch. Also included is the interesting news that Living DNA has been working for a year to find a processing laboratory in the U.S. with which to partner. Following 29 October 2018, all U.S. residents purchasing a test from Living DNA will send samples to this U.S. laboratory, not to the UK. The name of the laboratory was not disclosed.

Living DNA also affirmed that their version of the Thermo Fisher Scientific Axiom chip will include tested loci for:

• 759,757 autosomal SNPs
• 34,216 Y-chromosome SNPs
• 15,227 X-chromosome SNPs
• 3,982 mtDNA SNPs
• 813,182 total loci investigated

All microarray coverage is, of course, variable because certain degrees of customization are possible, but by comparison the published specification of the Illumina OmniExpress chip shows 713,599 total SNPs, and the GSA chip 665,608 total SNPs. Let me also hasten to add that total SNP count doesn't really mean a great deal; more isn't always better.

Last, I'll add that Living DNA's David Nicholson affirmed my memory may not be as porous as I sometimes think.    In the blog post I noted that, with Illumina's announcement of the GSA chip, I remembered--but couldn't locate corroboration--there was also mention that they would be phasing out the OmniExpress chip as end-of-life (still used by, as a reminder, AncestryDNA, Family Tree DNA, and MyHeritage). David indicated that, during business planning for Living DNA, they were advised by Illumina that the OmniExpress chip was being discontinued and that Living DNA needed to use the GSA chip instead. This may or may not have affected 23andMe's decision to move to the GSA chip because, from available information, its targeted SNPs seem more aligned with some of 23andMe's mission for medical relevance in DTC DNA testing. And there certainly is nothing wrong with the GSA chip per se; it's just that comparing results for genealogy have proven to be...difficult.

Regardless, now well over a year since the introduction of the GSA chip--and with AncestryDNA's sales skyrocketing during that period--there may be some second-guessing, at least on some fronts, about the GSA chip which shares so few tested SNPs in common with the OmniExpress.

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I *think* that AncestryDNA v2 is an entirely custom chip, and they constitute enough of a mass market all by themselves to make it worthwhile for Illumina to continue production.

23andMe was part of a consortium involved in designing the GSA chip, but LivingDNA was the first to employ it.

https://www.illumina.com/science/consortia/human-consortia/global-screening-consortium.html

I appreciate the time you spent composing your posts!

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Many thanks, Ann. I've added the GSA consortia info--which I'd forgotten about--to the updates.

About 10:30 a.m. London time yesterday, Living DNA's offices lost all telephone and WiFi services for a few hours. It can't be because the lines were burning up, but I believe the volume of reactions from existing customers caught them off guard. Judging from their Facebook page and online chatter, things seemed to have calmed down the past 24 hours.

On Ancestry v2, they certainly never reveal too many details to us, but I wonder if anyone has ever done a by-SNP comparison with presumably "standard" OmniExpress output to see just how customized the chip is. In GEDmatch ('course that's partially driven by GEDmatch's "dictionary" of SNPs) I've seen very high SNP correlation numbers between Av2 and FTDNA in one-to-one matching, so had assumed that Ancestry's customization was simply post-production programmatic, not in physical manufacturing.

I have a feeling if we could have been flies on the wall at Illumina in 2016 when they were strategizing product development for the upcoming 12- and 24-month periods, that DTC genealogy would still have been way down the impact list. At the beginning of 2016 the total number of DTC kits sold was around 3.5 million. Nothing to sneeze at, but I don't think they could even have guessed at the 24-month growth. By the end of 2017, there had been about 12 million sold. Leah Larkin's most recent numbers, from August, when extrapolated could put us easily into the 20-million range by year end. As it currently stands, it looks like around 70% of those, give or take, would be on some version of the OmniExpress chip. Gotta be into numbers that made Illumina executives think, "Ya know, maybe we shouldn't turn down and repurpose that assembly line just yet..."

And you're very welcome, Ann. But all I do is type a lot.  

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At the recent ASHG meeting in San Diego, an Illumina Microarray Manager said that on average in 2019 there would be "1 microarray processed every second".

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Thanks, Greg. I can believe it...especially if the reference was to one-per-second during, say, a 50-hour business week. If it's every single second, that'd be, what, about 31 million microarrays. Still believable, but let's all gear up to buy new tests!  

BTW, ASHG did a great job this year with social media coverage for the San Diego meeting. Kudos to them.

Answer 1

FWIW, I jokingly asked:

"I assume [LivingDNA has] been keeping my spit on ice and will re-test it with  the new chip free-of-charge and will have the new results before the end of the week!"

To which the response was:

"In response to all of your comments below, we are excited that it has moved to its next-generation DNA chip. The new DNA chip, Sirius, is designed to be universally compatible with all chips on the market, including the original Orion Living DNA chip. At this stage, there is no need for an existing customer to upgrade to the new chip and all existing customers will continue to get regional breakdown upgrades, Haplogroup enhancements and Family Networks as they are released. More details will follow next week."

It seems that that was a lengthy was of saying "No!"