Onur

Working on latest technology is cool!

Currently, I am trying to wrap up my PhD where I analyzed single cell multi-omics data. It is cool, very cool indeed. You get to learn many new insights, be at the cutting-edge of science and discover.

Yet, the usefulness of a technology proves itself with time. Take neural networks for example. Almost everybody who worked on image processing or natural language processing realized its potential in 2012 when AlexNet came out. Still, it took almost a decade for everyone to notice its potential.

Today, single-cell or spatial transcriptomics are the cutting-edge technologies for analyzing data from cells, but if you go back a little bit, like a decade ago, bulk sequencing was living its golden age. Now, the hype is definitely not there anymore for bulk sequencing.

But… realistically bulk sequencing is incredibly useful. Why?

It’s cheaper, informative, robust, and people have done A LOT of it and to be honest people really don’t care about it.

But, the realization should have been upon us by now. Data is power and bulk data is mostly lying there for us to realize its potential!

Our latest paper on leukemia was the turning point for me (maybe a bit more than it should), but it honestly made me realize how this can be useful for the patients.

This is what I call “The holy grail of AML”.

More than 1200 AML patients’ data is lying on this map. First, you don’t really feel the magic. But if you look at the numbers the image becomes clearer. There is estimated to be ~21,000 AML patients in the entire United States, so this map includes almost a month of patients of an entire country!

And this is just the beginning. There will be more patients added to this map, it will surely be bigger and bigger.

Okay… but why should we care about this?

Let’s imagine an AML patient in a rural place of the US. Patient comes in to the hospital, the standard diagnostic is run, but you find nothing, maybe a weird fusion? Then patient is forwarded to a bigger state with a bigger hospital. A lot of tests are run, patient is tired, closest people to the patient are tired, thousands of dollars are wasted.

What if there was a way to check thousands of samples from previously analyzed patients… and compare this new patient with the existing database. Then… maybe then, you could actually see that this weird fusion is enriched for previously analyzed patients that share similar characteristics with this patient. Hmm.

I think, it’s time for us to cast the stone and make this a reality. Many cool people are working on it to make this a reality. I would like to be one of them and that’s what I am working on right now. I think, it is time for bulk sequencing to shine.

We’re almost there and it definitely feels like magic ✨

– Onur