Ambry Genetics and PRS “equity”
A few people shared with me some screenshots from a message from Ambry Genetics regarding polygenic risk scores (click to enlarge). From what I can gather this seems to indicate […]
Problems in PRS?
Variable prediction accuracy of polygenic scores within an ancestry group: Fields as diverse as human genetics and sociology are increasingly using polygenic scores based on genome-wide association studies (GWAS) for phenotypic prediction. However, recent work has shown that polygenic scores have limited portability across groups of different genetic ancestries, restricting the contexts in which they […]
Not happening at genomic speed: diversification of GWAS panels
One of the things that is evident and the norm when you are interested in genetics and genomics is that things happen fast. There are some sciences which proceed at a normal and conventional pace. But, because genomics is fundamentally driven by the …
Cystic fibrosis as the sickle-cell anemia of the north
Cystic fibrosis is one of those ‘classical’ recessive diseases you learn about in medical genetics. It’s frequent enough that doctors will always be interested in it, and its inheritance pattern is relatively simple, following a rough Mendelian pattern of recessive expression. The reality is a little more complicated than that though, as there are different […]
Crohn’s disease is about barely keeping you alive
The Pith: Natural selection is a quick & dirty operator. When subject to novel environments it can react rapidly, bringing both the good and the bad. The key toward successful adaptation is not perfection, but being better than the alternatives. T…
You are a mutant!
The Pith: You are expected to have 30 new mutations which differentiate you from your parents. But, there is wiggle room around this number, and you may have more or less. This number may vary across siblings, and explain differences across siblings. …
Who are those Houston Gujus?
The figure to the left is a three dimensional representation of principal components 1, 2, and 3, generated from a sample of Gujaratis from Houston, and Chinese from Denver. When these two populations are pooled together the Chinese form a very homogen…
Health care costs and ancestry
The Pith: In this post I examine the relationship between racial ancestry and cancer mortality risks conditioned on particular courses of treatment. I review research which indicates that the amount of Native American ancestry can be a very important …
Every variant with an author!
I recall projections in the early 2000s that 25% of the American population would be employed as systems administrators circa 2020 if rates of employment growth at that time were extrapolated. Obviously the projections weren’t taken too seriously, and the pieces were generally making fun of the idea that IT would reduce labor inputs and […]
The “how” of cystic fibrosis through the “why”
It’s just a fact that contemporary human evolutionary genetics has relied upon its potential insights into disease to generate funding, support and interest. I don’t think that this is much of a silver lining when set next to the suffering caused by disease, but it’s a silver lining nevertheless. Therefore findings which would be of […]
Heterozygote advantage in resistance to tuberculosis
The lta4h Locus Modulates Susceptibility to Mycobacterial Infection in Zebrafish and Humans:
Exposure to Mycobacterium tuberculosis produces varied early outcomes, ranging from resistance to infection to progressive disease. Here we report results from a forward genetic screen in zebrafish larvae that identify multiple mutant classes with distinct patterns of innate susceptibility to Mycobacterium marinum. A hypersusceptible […]