[dddiaz1]

I have absolutely loved working in genomics. I am a huge believer that genomics will be a huge part of healthcare in the future, and i have two examples to motivate that point that I think may be interesting to the reader.

1) The Moderna vaccine was made with the help of illumina genome sequencing. They were able to sequence the virus and send that sequence of nucleotides over to moderna for them to develop the vaccine - turning a classically biology problem, into a software problem, reducing the need for them to bring the virus in house.

2) Illumina has a cancer screening test called Galleri, that can identify a bunch of cancers from a blood test. It identifies mutated dna released by cancer cells. This is huge, if we can identify cancer before someone even starts to show symptoms, the chances of having a useful treatment dramatically go up.

Disclaimer: I work for illumina, views my own.

I wrote some more about why genomics is cool from a technical point of view here (truly big data, hardware accelerated bioinformatics) : https://dddiaz.com/post/genomics-is-cool/

[mtlmtlmtlmtl]

The thing I'm most excited about long term is biocomputing.

Having Turing complete programmatic control over biological systems has an absolutely endless list of transformative applications.

Imagine being able to program bacteria that can "infect" the patient and attack tumor cells, or act as fodder to keep autoimmune disease in check.

Or let's say we could program stem cells into "liver repair mode" to go and differentiate into new liver cells.

Then the implications for things like drug synthesis with the ability to programmatically control enzyme levels to compile more or less arbitrary biosynthetic pathways into fast growing photosynthetic algea, turning CO2, water and sunlight into medicine.

It's still a long way off being at that level of applicability, but man oh man it's gonna change everything.

[tombakt]

Sounds great until natural selection kicks in, and because DNA replication is largely a lossy process, suddenly the thing you programmed the organism to do mutates to do something else a whole lot more problematic.

Imagine a software heisenbug, but instead it's a life form that you can't kill -9.

The idea of tailor-made medicines in a vat is awesome, but as far as creating a bacteria to "specially target" certain cells seems like a disaster waiting to happen.

[mtlmtlmtlmtl]

Those are certainly real problems, and I'm not a cell biologist, but I'm not convinced these problems are insurmountable.

For instance, it might be possible to use ECC to get around transcription errors. It could also perhaps be ensured that any rogue "clinical biocomputer" could be easily treated with antibiotics or specifically engineered bacteriophage virus.

Like I said, the technology is very far off from having real world applications like this. At the moment it feels like we're in the analogue of the 40s and 50s for conventional computing. The field is still just inventing the very basic building blocks. It's going to be very limited in use, wildly dangerous(look up mercury delay lines) and unreliable for decades to come.

[dekhn]

Polymerase without error correct has error rate of 10**-6. With error correct it's 10**-9 to 10**-12.

[mtlmtlmtlmtl]

Considering the current treatment in the worst cases(where more targeted treatments don't exist) is to blast the pasient with radiation and poison(chemotherapy) and hope it doesn't kill them, I'll take those odds.

[DrScientist]

Except a rogue bacteria won't just kill you, it could escape beyond you and kill millions.

Chemo/radiation only kills the patients it was given to ( not entirely true - if the treatment caused mutations in the germline and the patient subsequently had children, the effects of the treatment might be passed on - but still very limited ).

[mtlmtlmtlmtl]

Bacterial infections are generally very treatable though. Even when the bacteria aren't engineered. And especially when they are, because why would you leave any antibiotic resistance in an engineered bacterium?

Bacteria are the scariest when they've had the time to develop resistance to multiple different antibiotics.

Additionally, a bacterium that's engineered to be almost completely harmless evolving into a deadly strain in vivo is fairy unlikely in itself, especially if transcriptional errors can be reduced several orders of magnitude like GGP suggested.

Adding to that the option of hospitalisation or even home isolation to reduce risk of transmission, the risk of this resulting in some huge lethal epidemic must be pretty miniscule.

[pinkwinds]

Purposefully blocked for certain countries?

"The Amazon CloudFront distribution is configured to block access from your country."

[agumonkey]

what kind of math/cs/algorithmic skills do you think one should work on to get a job in this kind of company ?

[jghn]

There are two main flavors of jobs. For one you’ll want to be a phd in something like physics or math. For the other Amy standard software engineering background will do.

[crispycas12]

TBH I'm surprised how hard Illumina is already pushing Galleri as a product. Current ctDNA/cfDNA are imperfect for advanced cancers which should have a lot of shedding to begin with. Additionally CHIP is and outstanding issue. DNA methylation sequencing has promise but I feel more data would be needed to truly make diagnostic findings. So to see Illumina market it as a ready to go product is quite worrying. It may burn a lot of people