Wednesday, 23 November 2016

Exome testing combined with a Geno 2.0 Next Generation test from Helix

Helix, a new genetics start up company in the US, has just announced the launch of the first product on its new pay-as-you-go sequencing platform –  a National Geographic Geno 2.0 Next Generation test. When you order the test the company will sequence your exome. That's the part of your genome which includes all the genes. Your DNA is then stored by the company and you can order additional DNA products as and when they become available. These will include reports on nutrition, health and fitness produced by other partner companies. Presumably Helix hopes that customers will be encouraged to pay for enough add-on products to recoup the costs of the exome sequencing. At present the Helix test is only available to US residents.
Helix is using a technology called Exome+ which they describe as follows:
The “exome” is comprised of all the DNA that encodes for protein—and because proteins are the machinery of your cells, the exome represents some of the most important and well-studied pieces of your DNA. But the exome is only part of your DNA story. The genetic experts at Helix have identified other important information-rich areas to sequence (hence, Exome+).
However, rather than using all the data from the exome, the Helix Geno Next Generation test is done using just a subset of these SNPs. Helix explain that they "provide National Geographic with more than 200,000 markers from your autosomal chromosomes, the Y-chromosome, and mitochondrial DNA". The breakdown of the markers tested is provided on the product page:
  • Maternal line: over 3,000 markers on mitochondrial DNA
  • Paternal line (for males): over 10,000 markers on the Y chromosome
  • Hominin and regional: over 200,000 markers across the entire genome
It is not clear how many of the SNPs used by Helix overlap with the SNPs used on the current Geno 2.0 NextGen test from the Genographic Project. The chip used for the standard Geno 2.0 NextGen test has around 700,000 autosomal SNPs, 20,000 Y-SNPs and 4000 mtDNA SNPs. The new Helix test therefore provides less coverage than the existing test. This is presumably because there are fewer ancestry informative markers in the exome.

Customers in the US who wish to order a Genographic test now have no other option but to buy the Geno Next Generation Helix Kit. The higher-resolution Geno 2.0 Next Gen test is still available for customers outside the US. Presumably the company will wait and see how the test fares in the US before deciding whether or not to roll it out to the rest of the world.

Unfortunately because the new Helix test covers so few markers it will no longer be possible for US customers to transfer their results to the Family Tree DNA Family Finder database to search for genealogical matches. They will also not be able to upload their results to the free third-party websites such as GedMatch and DNA.Land.

At the moment Helix customers cannot access their raw data. The website says that they are actively working on a feature to allow customers to "purchase access to the raw data set containing your complete DNA sequence data in 2017". It remains to be seen how much this will cost, but if someone is interested in having their exome sequenced then the Helix test might turn out to be a cost-effective way of doing so.

The concept of pay as you go sequencing is interesting but I would have thought it would make sense to wait until the full information is available from whole genome sequencing rather than ordering an exome sequencing test. In the current Full Genomes Corporation sale it is already possible to buy 30x whole genome sequencing for $1250, and 15x whole genome sequencing for $795. The Full Genomes test includes a full interpretation of the Y-chromosome data. The raw autosomal data can be uploaded to Promethease for a small fee of $5 for health reports. Veritas Genetics offers a 30x whole genome sequencing test for $999 which includes health and trait reports. No Y-chromosome interpretation is provided though this can be purchased though YFull for $49.  However, the Veritas test needs to be authorised by a doctor. No doubt the cost of whole genome sequencing will come down in price in the next few years to a more affordable level.

Update 1st February 2017
Further information about the new Helix test is provided in an article on GenomeWeb Helix readying for summer launch of genomics apps addressing broad consumer interests (31 January 2017). Here are two relevant quotes from the article:

"In November Helix began offering National Geographics' ancestry product Geno 2.0. Customers can order the spit kit through Helix and view their results online, although not yet through Helix's platform. This is allowing Helix to test out its ability to handle a large product launch, so by summer it can smoothly introduce multiple apps across all six categories."

"The company [Helix] has projected that the initial sequencing and app-based interpretation will cost around $200, a price point that Helix believes more healthy people — those who otherwise don't have a medical reason to seek more expensive testing — will choose to pay out of pocket. Helix is also betting that its app-based model will uncover novel uses for genomic data and enable a responsible path to delivering this information to consumers, by placing them in charge of what they want to learn: something "fun" (and some might argue light on scientific validity), like their wine tasting profile, or something that can impact their future wellbeing and that of their families, such as their hereditary risk for breast cancer."

Update 2nd December 2017
For further details about the Helix platform see the Helix Personal Genomics Platform White Paper.

According to this blog post from Razib Khan it is expected that the raw data download will be available early in 2018 and will cost in the region of $600.

A further update from Razib Khan explains that the test will sequence around 30,000,000 markers.

Further reading
With thanks to Gerard Corcoran, James Kane, David Mittelman and Ann Turner. 


James Larry Vick said...

For those who order the Veritas Genetics WGS test, YFull will analyze the Y chromosome data for $49.

Debbie Kennett said...

Thanks for that information Larry. I'll update the post.