The $1000 Genome? – Not Exactly

HiSeqXTen

You may have seen the headlines and the announcement this week by Illumina, manufacturer of gene sequencing equipment, that the $1000 genome is finally here.  Hallelujah –  jump for joy – right?  Sign me up – where can I order???

Well, not so fast.

It’s a great headline – and depending on how you figure the math – it’s not entirely untrue, but it’s a real struggle to get there.  Some marketing maven did some real spreadsheet magic!  What is that old saying, “lies, damned lies and statistics”?  Maybe that’s a little harsh, but it’s not too far off.

So, is the $1000 genome here or not?  Well, kindof.  It depends on how you count, and who you are.  You see, it’s a math thing.

It’s kind of like a mortgage.  How much did your house cost?  Let’s say $100,000 – that was the price on the “for sale” sign.  But by the time you get the mortgage paid off, 30 years later, the cost of that house is way more than $100,000, probably more than $250,000 and if you add in the cost of taxes, closing costs and maintenance, even more.  This will only depress you, so don’t think about, especially when you sell your house for $150,000 and declare that you “made” $50,000.  But I digress…

So, let’s translate this to the $1000 genome.

Dr. David Mittleman, Chief Scientific Officer for Gene by Gene, Ltd., parent company of Family Tree DNA, was at the conference this week where the Illumina announcement was made. I asked him several questions about this new technology and if it was ready for prime time yet.

His first comment shed some light on costs.

“The HiSeqX Ten system is actually a ten-pack of new HiSeq instruments, each costing 1 million dollars. So you have to spend $10 million on equipment before you can even get started.”

Ouch.  I guess I won’t be buying one anytime soon!

To begin with, without the cost of the kits or processing or staff or software or installation or financing or support contracts or profit, a company would have to sell 10,000 kits at $1000 to even bring the cost of the equipment to $1000 per kit.

So, how did Illumina figure the cost of the $1000 genome?  The $1000 is broken down as $800 on reagents, $135 on equipment depreciation over 4 years, and $65 on staff/overheads.

This means that to obtain that $1000 per genome price, you have to run the equipment at full capacity, 24X7, 18,000 kits per year, for 4 full years.  And that still doesn’t include everything.  You also need service contracts, installation, additional labor, etc.  You can read more about the math and cost of ownership here.

And sure enough, when I asked David about who has purchased one so far, there are two buyers and both are institutions.  This is an extremely high end product, not something for the DTC consumer marketspace.

Now this isn’t to say this announcement is a bad thing – it’s not – it’s just not exactly what the headlines suggest.  It’s the $1000 genome for those with deep pockets who can purchase a $10,000,000 piece of gear and then run 18,000 samples, for 4 years, plus expenses.  But yes, it does technically break down to $1000 per test as long as you hit all of those milestones and ignore the rest of the expenses.  If you can afford $10 million and have the staff to run it, you probably don’t care about the cost of installation, labor and support contracts.  They are just necessary incidentals – like gas for my lawn mower!

In spite of the fancy math, it’s truly amazing how far we’ve come when you consider that a single full genome sequence still cost about 3 million in 2007, and in November 2012 Gene by Gene was the first to offer full sequencing commercially and offered it to their customers for an introductory price of $5495.  Of course, with no analysis tools and few testers, I can’t imagine what one would do with those results.  This has changed somewhat today.  The full genome with some analysis is available today to consumers for $7595, but the question of what is available that is genealogically useful to do with these results still remains, and will, until many more people test and meaningful comparisons are available.

The Illumina announcement also raises the issue of software investment to do something useful with the massive amount of data this new equipment will generate…also nontrivial, and that software does not exist yet today.

There are other issues to be addressed as well, like open access libraries.  Will they exist?  If so, where?  Who cares for them?  How are they funded?  Who will have access?  Will this data be made available in open access libraries, assuming they exist?

Illumina has reported that entire countries have approached them asking for their population to be sequenced, which also begs questions of privacy, security and how exactly to anonymize the samples without them becoming useless to research.  This high tech watershed announcement may spur as many questions as answers, but these issues need to be resolved in the academic environment before they trickle down to the consumer marketspace.

This is not to minimize the science and technology that has propelled us to this breakthrough.  It is a wonderful scientific and technological advancement because it will allow governments or large institutes to do huge population-wide studies.  This is something we desperately need.  Think for a minute if our Population Finder ethnicity results were based on tens of thousands of samples instead of selected hundreds.

For genetic genealogists, we are poised to benefit in the future, probably the more distant than the near future.  The $1000 genome for consumers not only isn’t here, it’s not even within sniffing distance.  So put your checkbooks away or better yet, buy a Big Y or a Family Finder test for a cousin, something that will benefit you in the short term.

This next step in the world of genetic discovery is exciting for research institutes, but it’s not yet ready for consumer prime time.  We will be the beneficiaries, but not the direct consumers….yet…unless you want to move to one of those countries who wants their entire population sequenced.  Our turn will come.  Maybe the next time we see an announcement for the $1000 genome it will be calculated in normal home-owning-human terms.

If you’d like to see the product announcement and a cool video that Illumina created, take a look here.  The video is short and provides a neat way to look at genetic history.

7 thoughts on “The $1000 Genome? – Not Exactly

  1. Why recommend BIG Y over Full Genome? BIG Y costs 50% but delivers only 25% of Full Genome. And why recommend Family Finder over 23andMe? 23andMe is 10 times better than Family Finder. Are you on FTDNA payroll?

    • The comment was relative, meaning those tests being useful as compared to the full genome test which is not today. I don’t care for your tone, but I will answer the question. I am not on the payroll of Family Tree DNA. In the About Me section of this blog, from day 1, I have always made it clear that I have a contractual relationship with Family Tree DNA who sells the Personal DNA Reports that I write for people. So your snippy insinuations are not news. However, I do recommend Family Tree DNA over 23andMe for autosomal testing, especially if someone is going to choose just one, because, among other reasons like response rate, Family Tree DNA never sells my data out the back door to God knows who. My DNA is never used for anything I don’t approve of. I don’t feel that 23andMe is better than Family Tree DNA in any capacity, except for health which is not an option at the present time. I’ve written about and used both companies. As for the Big Y and the Full Genomes products, we’ll see when both are delivered and have tools for analysis and comparison. The Big Y certainly has a price advantage and Family Tree DNA has a proven track record in this industry. They are likely to be here next year and 5 years from now. Furthermore, your results at Family Tree DNA will be incorporated together, mtDNA, autosomal, STR, SNP and Big Y – something no one else can do.

      • IMHO, 23andMe doesn’t hold a candle to FTDNA when it comes to genetic genealogy. I’ve tested with both from the beginning, and still can’t figure out where 23andMe would place me on the R haplotree; they don’t provide terminal SNPs. The haplogroup they show doesn’t match anything on the ISOGG tree, whereas FTDNA has been testing SNPs since the first National Genographic Project came out in 2005 when I first got into this. Since then and with the addition of Geno 2.0 their database has grown tremendously so those looking for cousins stand a better chance of a match. My several closest matches are from FTDNA, not 23andMe. Still, for those simply searching for cousins and not that interested in SNP subclades, testing with every company, even Ancestry, has its benefits; some people are in one and not the other. But for those of us who are also keen on population genetics, it’s a no-brainer. And I have absolutely no connection whatsoever with FTDNA.

      • At 23andMe one can easily revoke the permission to use one’s data for research, by simply going to their account settings and changing it. So that is not a big problem.

        I have not found any of the companies to be particularly well designed to optimize the user’s experience, or to get the most possible out of the data.

        As for longevity, probably ancestry.com will be around long after Gene by Gene and 23andMe pass away.

  2. It’s so true that this Illumina announcement has been misunderstood by many.

    Yet it is probably not the end of the cost reductions possible. As you note, Illumina will sell these by onesies to big institutions, except maybe to BGI who could buy a dozen if their deep pockets want to expand the sequencing of the Chinese population.

    If Illumina could mass produce these machines, and the consumables, then the costs may go down (especially for the consumables.) Imagine if the US had a national genomic project, to sequence everybody over the next decade. Illumina could ramp up production and probably do better than $1000/person.

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