That "$1000 genome" is going to cost you $72M

Written by Shawn Baker on .

Illumina made a huge splash at the JPM Healthcare conference, announcing two new instruments (while apparently quietly killing off a number of older platforms). We’ll follow up on the details later, but the thing that most people are talking about is the final arrival of the vaunted, near-mythical $1000 genome.

It’s here, it’s here! The $1000 genome is here! Well, almost. It will be here by the end of March.

But you can’t have one.

Well, maybe you can, but only if you match the following criteria:

1) You’ve got $10M in your capital budget. The HiSeq X, the machine that will deliver the $1000 genome, costs $1M. And each purchase order is a minimum of ten machines. They don’t appear to work together in any special way to deliver the $1000 genome. It’s just that Illumina wants you to buy at least ten of them at a time.

2) You’re willing and able to run the machines 24X7X365 for four straight years. To get the instrument amortization costs down to $135 per genome, they stretched out the lifecycle to four years. Four years is a long time in this industry. Four years ago is when the GAIIx finally hit 95Gb per run. Not too many people are running GA’s anymore.

3) You’ve got 72,000 samples. That’s how many samples you’ll need to run over those four years.

4) All of your samples are human whole genomes. The HiSeq X 10 only works with human whole genomes. No exomes. No other mammalian species. No RNA-Seq, ChIP-Seq, Methyl-Seq, etc.

5) You have $62M in your operating budget. That’s how much those 72,000 samples are going to cost you to run through the sequencer.

6) Your labor is extremely efficient and extremely cheap. The $62M budget only includes $65 per sample for library prep, which includes both the reagents AND the labor.

7) You don’t need to pay for the building you’re in and you can work in the dark. The budget doesn’t include overhead.

8) You don’t really want to analyze or store the data. The $1000 might get you a basic alignment, but nothing else.

But enough negativity – the $1000 genome is here!

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About the Author

Shawn Baker

Shawn Baker



Shawn Baker, co-founder and Chief Science Officer, has over 15 years of experience in the field of genomics. He joined Illumina when it was a small 15 person startup, first as a research scientist and later as the marketing lead for their gene expression and regulation sequencing products.


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