Another evergreen reminder - ethnicity (or "race") is a process of self identification, often ticking a set of boxes, or gestalt assessment using visible characteristics of people (skin colour, hair type, clothes) by others. It is *not* a good representation of anyone's genetics.
The collapsing of ethnicity or race concepts as some sort of crude readout of genetics is plain wrong.
We can sometimes go the other way - genetic measurements in some places can predict the ethnicity box you will tick on a form - but we definitely can't predict your genetics from the box you tick.
For some aspects of ethnicity - notably skin colour - skin colour (like hair colour) has a genetic basis. However, skin colour is a small part of the human genome and also skin colour genetics is bamboozling complex
So - even in this well recognised physical attribute (skin colour) we can't even use this aspect of the box ticking to predict ("impute" would be the more formal term) genetics. If you want to use genetics, you have to ... measure genetics
Frustratingly geneticists do continue to use many ethnicity terms in their research as shorthand - eg, "Caucasian" and "African American", and it is common to talk about genetics for a particular "population" or "ancestry group"
It has taken me a while to work out what we are doing in these "population" groups. What we're not doing is handling genetic background effects. Rather we are navigating complex societal aspects using the fact we can predict ethnicity from genetics.
This is because humans are very social animals, and our social environment sets up many aspects of our life - from how much food and vitamins we have, to exercise, to how we access healthcare.
From a geneticists perspective these are all "environmental" (ie, non-genetic) factors, but they are our social environment. In complex societies, much of this is determined by this strange-when-you-think-about-it process of separating many aspects of society by ethnicity
We use this in everyday conversation ("Black British culture" and "White America") and some societies weave this through life in a deep way - the caste system in Hindu India. These are real parts of our society.
So when we do this "blob" in PC1/PC2 genetic space to select a subset of a cohort in a western society, we do this mainly to control (minimise) this social environment, and critically remove aspects of social environment that is confounded with drift of allele frequencies.
These "drifted" allele frequencies give rise to "genomic inflation" of our association tests (in some the tests are valid - but the causal link of association goes via this drift process, not the biological effect process we want to capture).
Importantly this process is *not* like laboratory mouse backgrounds, or even complex pedigrees in (say) diary cattle, where geneticists there don't use these techniques but rather more effective (and aggressive) linear mixed model techniques for the genetic background.
Ironically the slightly clumsy phraseology we use for this subsetting - "Caucasian" or "European American" or "Japanese" would be fine if one added the word "culture" or , if you want to be more abstracted, "social environment".
So - back to the starting point - divorce in your brain "ethnicity" and "human genetics". There are some aspects that link them (physical attributes, most notably skin colour) but these links are thin and not useful. They are different things.

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More from @ewanbirney

22 Nov
More musings on human genetics and race, but this time from a personal level to explain I think the different ways people "think about" racism and their role in it.
In this thread I am going to be critical about how many people think about broad structural racism/unconscious bias, but I will do this via critiquing my younger self, as it is super-hard to do this broadly without offending people; I can own offending myself :)
In my 20s I spent a fair bit of time in America and considered myself reasonably cool and trendy - worked hard at Cold Spring Harbor Laboratories, partied hard in NYC and Harvard, where I had friends.
Read 25 tweets
21 Nov
The ... level of self belief on Twitter is quite remarkable and apparently I don’t know much about the human genome or genetics. That’s me told ...
More seriously, conversations about ethnicity and race are loaded because it is both a big active part of many societies and discourse - most obviously US but many western countries (UK included of course) and >>
<< for many people this is a key part of their identity. There are shallow issues here -it is far too easy to use words that mean different things or for people to read strong motivational stances or inferences into statements
Read 9 tweets
21 Nov
A reminder and perspective on this COVID, mid November.
(context: I am an expert in genetics/genomics and computational biology research; I know experts in a variety of other domains; I have a COI as I am a long established consultant to Oxford Nanopore, which makes a new COVID test, LamPORE).
As ever, it is good to start with the overall perspective - SARS_CoV_2 is an infectious human virus which causes a nasty disease for a subset of people, often leading to death.
Read 23 tweets
17 Nov
Vaccine safety thread - briefing to journalists as much as anyone else as ever, and an offer.
Vaccines are safe. They are safe principally because of the extensive and multiple testing that happens before they are licensed, and that ultimately is due to 100,000s of people who volunteer for trials to assess and quantify safety. I am a scientist and one of these volunteers
"Safe" here of course can never mean never - strange things happen in life, healthcare and biology and like many things we do in life - crossing roads, going biking, drinking wine - we have constantly do things which are safe but have some small risk of something going wrong.
Read 14 tweets
15 Nov
Good case numbers in France, Germany yesterday and the Welsh firebreak definitely worked. (What a surprise - reducing person contacts slow transmission). Northern Ireland controlled well but plateauing high -another push needed
Need to see the impact of the English Nov lockdown - next week sometime one should see lower infection numbers after the 7 day ish incubation period from last Friday plus the test and reporting cycles.
Scotland’s Tiering scheme and particular the central belt work also has done well - though I suspect they want to achieve now more decrease in infection
Read 6 tweets
14 Nov
Right. Deep Breath. RT-PCR "false positives" and Ct numbers (again). tl;dr it is complex, but the RT-PCR testing systems deployed across the world are sound and the people who run them report positives are positives and little can be improved obviously.
Context: I am a genomics/genetics + computational biology expert. I know a large number of infectious disease testing experts. I have a COI in that I am a long established consultant for a company (ONT) that makes a new test here; this gives me additional insight
There a number of classes of false positives which don't concern the current debate (eg, sample swaps, lab contamination). To repeat an early point all the people I know in this are paranoid about this, test and check in a rather detailed way and these are looooow.
Read 22 tweets

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