SequenceSafe – making personalized medicine more personal

SequenceSafeOk, that’s not a real device – just a mock-up of something that I think might be useful. SequenceSafe is intended to solve three problems:

  • Giving everyone access to their sequenced genome in a way that brings positive benefits to their healthcare.
  • Solving one of the biggest challenges of mass whole genome sequencing – where to put the data.
  • Ensuring that a person’s sequenced genome stays confidential.

The idea is pretty simple. An individual sends a sample for sequencing and the result is a SequenceSafe that holds the sequence data. The owner keeps this in a safe place and takes it along to doctor or pharmacy visits. The SequenceSafe never releases the whole sequence. Instead, the device acts as an oracle – health care professionals can ask it questions about aspects of the sequence and get responses. Health care professionals can connect to the device via bluetooth or USB and SequenceSafe only operates once the owner has authorized its use with a fingerprint.

Additionally, the SequenceSafe accumulates the owner’s medical history. This could be by their doctor adding notes, family medical history and other observations or else collecting data directly from fitness trackers so that the SequenceSafe can build up a complete medical picture.

For example, right now if there’s a need to run a test for a particular inherited genetic anomaly, it is necessary to send a sample to a lab that runs it against a gene panel, returning the result days later. Using SequenceSafe, the healthcare professional can run a virtual gene panel by asking the SequenceSafe to run the tests against the genome sequence, getting the results right then and there.

As another example, SequenceSafe could help a pharmacist tune dosage for drugs based on a person’s genetic characteristics. Let’s say that the copy number of a gene has a significant effect on the required dosage of a drug. The pharmacist could ask the SequenceSafe that question and get a result that ensures that the right dosage is used.

Are there other ways of doing this? Certainly. Whole genome sequences could be stored in the cloud, co-located with servers that run the enquiry software. But how does anyone guarantee the security of the information? Even if it is stored encrypted, it needs to be decrypted for analysis and that exposes the data in the cloud. I am of course assuming that people will care about who is able to access their sequenced genome! Another question is who is paying for the storage and processing…

SequenceSafe scales perfectly with the number of users – billions of people could be in possession of their sequenced genomes without causing all kinds of storage nightmares. It is paid for with a one time purchase, when the genome is sequenced.

Of course there is one security hole – some lab has to sequence the customer’s sample and load the SequenceSafe. This cleartext sequence is encrypted with a public key supplied by the SequenceSafe allocated to the customer and the cleartext version destroyed. The customer would receive the SequenceSafe and the encrypted data in case the SequenceSafe was lost or failed so that it could be loaded into a replacement device. Customers would just have to trust that this is all being done correctly but it seems like a much smaller risk than storing the data permanently in a cloud, just waiting for someone to hack the system.

Will something like this ever be made? I hope so – I think it could be a great way of bringing personalized medicine to very large numbers of people. I’d love to be able to raise some funds and make this happen – I am pretty sure that the technology exists today to make this device a reality. And, just for once, it really would be a case of “making the world a better place” :-).

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4 thoughts on “SequenceSafe – making personalized medicine more personal

  1. Pingback: Game of Genomes | richards technotes

  2. Pingback: SequenceSafe – solving the “who owns my genomic data” conundrum | richards technotes

  3. rogerclarkmelbourne

    I don’t think the system would be workable because it requires standardisation of heath care computer systems which can interface with this device.

    My understanding is that there are dozens of proprietary healthcare data systems, each of which would need to write a module to interface with this device (assuming they even have the ability to add a module), and I can’t see how you would get leverage to get them all to write a module to communicate with the SequenceSafe

    Reply
    1. richard Post author

      The SequenceSafe hardware is only one part of the system. There is a desktop app or tablet app that goes along with it. This is how medical professionals access the data on the device. It provides the bioinformatics processing, utilizing cloud servers if it absolutely has to. I do not know exactly how difficult the processing would be to satisfy most queries. The assumption is that the data on the SequenceSafe already contains the results from heavy processing functions such as basic sequencing, variant calling etc. The hope is that the day to day queries are simple enough to process that a typical desktop (or tablet) can handle it.

      An obvious complaint with this is that it means that doctors etc have to have yet another piece of software on their computers. Since no system currently does this anyway, I don’t think it’s unreasonable to require a separate app for the SequenceSafe. Yes, the app would probably have to integrate with existing medical records systems but that’s what software engineers are for :-). Ideally, it would not be a case of persuading other companies to do the integration. However, if the SequenceSafe took off and became the de-facto standard, even that would be possible.

      Reply

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