LEAVING ACADEMIA

Although I did not manage to secure the funding needed to establish my own research group, I am grateful for what I’ve learned in academia.

*I am now beginning a new chapter*, joining a very early startup in France working on detecting cancer from DNA circulating in the blood.

But you shouldn’t use only 2 PCs to compute the distance 😉

I probably won't have time to make a video out of this.

But the materials are available online, and should be pretty self-explanatory.

Hope this is useful to some people.

privefl.github.io/statgen-cour...

Next week, I'm teaching a **Statistical Human Genetics course using R**; would be of interest if I try to record it to make it available as a Youtube video?

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Yes, but the sample sizes are quite small there.

Thanks!

I actually use a few people from the 1000G as well, to get a few more people from Finland, Japan, and South America.

In the future I would like to also add the Papuan from the SGDP.

✅ In this paper, I used the UK Biobank to define 18 reference worldwide populations, and provided a method to easily infer ancestry proportions of individuals from your study more accurately.

Please have it a try!

Paper: doi.org/10.1093/bioi...
Tutorial: privefl.github.io/bigsnpr/arti...

👀 I still see many papers using the 1000G data to infer ancestry proportions of individuals in their respective studies.

❌ But I argue that the 1000G is not doing a very good job at covering well the worldwide populations.

Not sure. I think someone provided some VCF -> bed -> BGEN conversion.
Not sure what is this DRAGEN.

Did they update the BGEN files they provide?
Initially they were missing 30% of variants.

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Genetic PCs rarely provide large % of variation, but I don’t think it means they’re not useful.

Try to look at the loadings if possible.

Are there any peaks?
Cf. privefl.github.io/bigsnpr/arti...

I meant the looking of the PC scores.
Did you look at the PC loadings?

The PCA is indeed a bit odd; are you sure you’re not capturing LD instead of population structure?

My standing « desk », by the fireplace 😊

Sinner