Interpreting rare private mutations is one of the next challenges in human genetics. Some ideas for interpreting them include downstream studies with functional assays, e.g. see Robert Plenge’s keynote lecture at the Variant to Function symposium dissecting the functional consequences of TYK2 ultra rare variants.
We built an AI agent that integrates literature to interpret the consequences of newly identified variants from whole-genome sequencing data.
Spherical harmonics are a family of mathematical functions that describe patterns on the surface of a sphere. They are widely used in physics, computer graphics, and geomathematics.
Here, we present new approaches to detect localized genetic effects using spherical harmonics. The write-up is on bioRxiv – we have simulations and apply the framework to FinnGen coding dataset.
If you want to read how spherical harmonics are used for testing against the null of multivariate normality, please see the write-up below.
In my lab we developed Global Biobank Engine to support the visualization and search of genetic association results from UK Biobank. Prof. Euan Ashley called it the Google Maps of the Genome in his book. Global Biobank Engine’s design was inspired by the ExAC browser, which summarized exome sequencing data from over 100k individuals.
Now, there are multiple browsers online including from Finland, the FinnGen browser, which makes available results from their analysis of genetic integrated with medical record data from 500k Finns.
With the release of the ChatGPT Atlas browser we can now automate some of the process of exploring therapeutic hypotheses guided by human genetics, our North Star.
Here, I show you how I used ChatGPT Atlas with AI agent mode to explore these browsers and come up with therapeutic hypotheses. The AI agent does the work itself. It’s an exploration, but interesting nonetheless. I’m impressed with its capabilities. It took 11 minutes while I drank coffee and listened to music. BTW, the make no mistakes prompt is in jest.
