Sharing this in case it's useful: I find that students often have a hard time conceptualizing quantitative parameters in genomics and popgen
Here's a cheat-sheet I put together for teaching. It's also part of a textbook I have been writing on human genetics (more on that below)
It's a pity that All of Us used UMAP to visualize ancestry variation in their new marker paper, out today in Nature.
The UMAP algorithm, by design, exaggerates the distinctiveness of the most frequent ancestries, a message that can be misinterpreted by the public.
Two new chapters from my open-access textbook in human population genetics are now online:
- Population structure: I. Ancestry estimation
- Population structure: II. More about admixture
web.stanford.edu/group/pritchar…
I was thinking about how a paper that has been on bioRxiv for a year got massive attention on here when it came out in Nature this week. To me this shows that our community still needs to do more to promote and disseminate the great work in preprints.
Today marks the 25th anniversary of Neil Risch and Kathleen Merikangas' classic 2-page paper that articulated GWAS as the future of human genetics. A short thread.
www-leland.stanford.edu/~huatang/gene2…
Two new chapters from my free online book in human genetics out this weekend!
These complete Part 3 of the book, on human population structure and history:
3.3: Inferring human prehistory from genetic data [this thread]
3.4: Ancient DNA [next thread]
web.stanford.edu/group/pritchar…
Delighted to share our latest work, on ancient DNA of individuals from in and around Rome, spanning the last 12,000 years. At its peak Rome was the largest city of the ancient world with 1M inhabitants, controlling an empire of 70M people
science.sciencemag.org/content/366/64…
Our new work on understanding the architecture of complex traits "Trans effects on gene expression can drive omnigenic inheritance" is out today
cell.com/cell/fulltext/…
Great collaboration with @XuanyaoLiu@yang_i_li
Modern GWAS can identify 1000s of hits but it can be hard to turn this into biological insight. What key cellular functions link genetic variation to disease?
I'm excited to present our new work combining associations + Perturb-seq to build interpretable causal graphs! A🧵
Two new chapters from my free online book in human genetics out this weekend!
These complete Part 3 of the book, on human population structure and history:
3.3: Human prehistory [separate thread]
3.4: Ancient DNA: a genetic time capsule [this thread]
web.stanford.edu/group/pritchar…
Our work on genetic architecture of molecular traits is out now: elifesciences.org/articles/58615
We studied GWAS of urate, IGF1 and testosterone-chosen because much is already known about their biology. Eg for testosterone we see clear enrichment of GWAS hits in the biosynthesis pathway
I share my surname with Stanford's QB coach, so I regularly get emails from football recruits (unlike my lab applications these list hand-size).
But this is something new. Do we need an offensive graduate assistant? Wants to be promoted from offensive intern. How offensive?
Our latest: "GWAS of three molecular traits highlights core genes and pathways alongside a highly polygenic background": biorxiv.org/content/10.110…
We use urate, IGF-1, and testosterone as model molecular traits to learn general principles about the architecture of complex traits.
