Genome Expression Sequencing

Do You Really Need Whole Genome Sequencing

These days whole genome sequencing has almost become a buzzword in the scientific community. A common myth is that in order to get true value out of sequencing, you need to gather data on the whole genome. This has largely been pushed by different institutes as the “gold standard” with the chief argument being that more data equals better insights.

Anyone who has worked with large data sets and analysis can tell you that this is simply not the case. The phrase “garbage data in; garbage data out” rings true across all industries – biology included. For most researchers, the reality is that they have a specific field of study. For example, a human oncologist researcher may have a specific interest in the genes BRCA1, BRCA2, and TP53 as their core with a handful of extra genes commonly found in contributing towards cancer mutations. Should this human oncologist perform a whole genome sequencing? Probably not and here’s why.

How Much Does It Cost for Whole Genome Sequencing

The whole human genome sequencing kit costs approximately $735 from Illumina. With all of the additional kits needed for various quality control checks, this price increases to around $775. Assuming that our example of a human oncologist having 6 samples, we come out to an approximate total raw sequencing cost of around $1,375 (of course, this doesn’t include any profit margins or the overhead of the facility but we’ll leave that out for now). That means the per sample raw cost is around $229 per sample.

However, the real number this human oncologist should be concerned about is the cost of storing this data. 6 human whole genome sequencing samples nets a file size of around 1.2TB of information. The mutation files are generated separately and net around 750MB of information. So in total, this human oncologist needs to figure out how to store 1.95TB of data for an indefinite time frame. You could store it on your computer but you won’t really be able to search it. CD-ROMs are too small and USB drives means that the data is really locked (a.k.a. Not able to be searched). The only real option that makes sense is a database that allows researchers to perform queries against it.

This is where the costs explode if our human oncologist isn’t careful. To store ~2TB of data for one year on a partially managed data storage platform can cost around $7,400 per year ($617/mo), which rockets the per sample cost per year up to $1,462.50. Not so cost friendly just to have your data accessible!

Saving Time and Money with Targeted Sequencing

If we look at the flip side, the cost of targeting sequencing is much more attractive. A targeted cancer panel has an approximate cost of around $3,000 (no profit or facility overhead included). This means that the per sample raw cost is around $500 per sample – or around 2x the cost of the whole genome. However, the data produced is a fraction that of the whole genome sequencing, generating around just 10GB of data. This would cost approximately $37 per year to store the data; a difference for 200x. Adding it all up, the per sample cost per year is significantly cheaper coming in at $537 per year – nearly 3x cheaper than performing whole genome sequencing.

The Other Hidden Costs of Whole Genome Sequencing

There are other major cost factors that are not included in here. One of the big factors is that targeted sequencing can be performed on a much smaller and cheaper device whereas human whole genome sequencing must be performed on a device approximately 10x the cost. For a facility to cover that cost, they must add a premium onto the per sample cost of sequencing which will increase the whole genome sequencing rate significantly.

The entry price point for a Next Generation Sequencer from Illumina capable of sequencing the whole genome is around $250,000 as opposed to a targeted genome sequencer costing around $50,000. If you spread out the whole genome sequencing device over a 3 year payback period, a facility could be adding on as much as $250 to each sequencing run. The targeted genome sequencer would come in at around an additional $46 per sequencing run.

There are additional cost savings on the bioinformatics and data analysis side. Instead of performing queries against a significantly larger data set, researchers have the data most relevant to them immediately accessible. You are effectively cutting out 99% of the noise and providing focus on the signals pertaining to your research.

Each project is unique and may in fact require a whole genome sequence run, but it’s beneficial for you to consider the long term storage costs and noise data. At The Sequencing Center, we provide targeted human genome sequencing specifically for that reason. Our customers benefit from a complete end-to-end solution that allows them to have access to their data without having significant overhead costs.


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