dvdt

We used a law firm. The paperwork was quite straightforward because our attorney managed it.

BillionToOne (YCS17) | Staff/Senior Software Engineer | Remote (US) or Onsite (Menlo Park CA) | www.billiontoone.com

BillionToOne develops innovative diagnostics tests that can affect the lives of millions of patients. Our QCT technology platform improves the resolution of cell-free DNA testing by >1000x fold and enables novel tests for both prenatal and oncology care. We've raised over $30M and have launched multiple clinical products in the past 2 years, including an FDA authorized COVID-19 test.

We are hiring a senior engineer (5+ years experience) to build internal APIs, bioinformatics procecessing pipelines, laboratory automation tools, and help manage CI/CD. We use python, django, rabbitmq, circleci, dbt, postgres, heroku, aws, and a variety of other tools.

If you have experience in full stack web development, love seeing your work positively affect your colleagues, and thrive in a fast-paced entrepreneurial environment, this could be a great opportunity for you.

Please contact me directly at [email protected] if interested.

I completely agree with the point about integrated REPL/IDE, and wanted to share some of the combinations I have used in the past, since it can be a concrete getting started point for those who are curious. Some of these are not literally repls, but IMO give a similar experience.

- ClojureScript with Figwheel and the web browser

- Clojure with Emacs Cider, Clojure with Cursive

- R and Rstudio

- Matlab

- ipython jupyter notebook

- Pycharm debug breakpoints that are triggered by unittests (Running the unittest to initiate a python repl at the breakpoint)

A turn around time of 24-36 hours should be easily achievable for the performing lab, depending on the time of day the specimen arrives (morning vs afternoon). It takes about 1 hour for the initial RT-PCR amplification, and sequencing takes about 12 hours.

Our technique would still be affected by shortages in specimen collection (like swabs).

Purely speculative, but I think if swabs remain an issue for too long, alternatives could start coming online, such as even using qtips + saline (no idea if it works, it's just an example). The current swab + Universal / Viral Transport Medium combo is optimized for flexibility; it is designed to work across a very broad range of viruses and bacteria that have different viral loads and shedding characteristics. The current pandemic is pretty much COVID-19 only, so I think it's a priori feasible that a specimen collection procedure can be found that uses common materials. We did try early on to see if saline or other buffers affected the performance of the assay, and it worked fine in those conditions.

We use fairly standard chemicals. I haven't heard from our suppliers about shortages for the chemicals we use. Chemicals and enzymes tend to be relatively fast to scale up for bulk manufacturing.

There's always manufacturing risk that a product will not work as expected. In fact, the first COVID-19 test developed by the CDC did not work as expected, and this delayed testing by several weeks. We de-risk this as much as possible by performing experiments as early as possible, akin to the fail fast mentality of checking for the highest risk failure modes first. Since we don't have a national healthcare system in the US, the manufacturer takes on the vast majority of the risk of a defective product.

Thanks!

The Abbott machines are point-of-care devices that typically sit in doctor's offices. One really interesting use case I've heard of for the Abbott machines is to test all OB patients who are coming in to the clinic for routine care to make sure that they are COVID-19 negative. This allows the clinical staff to conserve PPE and use less burdensome precautions.

I think that where the Abbott machines might hit a wall is that they are one at a time, and they require Abbott's consumable test cartridge and device to run (think printer ink / printer). I don't have any firsthand knowledge, but I would anticipate that it is difficult to scale-up manufacturing of the devices rapidly enough to keep pace with the pandemic growth.

We absolutely need contact tracing to find everybody who needs to be tested. We're not working on scaling up contact tracing, but I think several people in the tech community are working on making that easier to perform at scale.

"When you’re fundraising, it’s AI When you’re hiring, it’s ML When you’re implementing, it’s linear regression"

The core of our machine learning is Ax=b :grins:

More seriously, the main reason why traditional sanger sequencing can't be used for COVID-19 testing is because it would be unclear whether a lack of signal is truly due to lack of virus, or if it is just because the assay failed (happens all the time!)

What we've done is introduce a reference sequencing signal that is biochemically very similar to viral RNA, but produces a distinct vector of electrical signals that is different from the signals emitted by viral RNA. Since we know what both the reference and viral signals look like, we can perform linear regression analysis to fit the linear combination of viral and reference signals that best match our data.