Iain Mathieson
@mathiesoniain.bsky.social
Converse is people using the term "experiment" to describe some kind of data analysis.
October 23, 2025 at 12:47 PM
Converse is people using the term "experiment" to describe some kind of data analysis.
And Mary-Claire
October 18, 2025 at 9:33 PM
And Mary-Claire
Well I suppose specifically for a developmental trait like this I might think that the environmental assumptions of the twin study design would be violated - i.e. twins share more of the relevant (in utero) environment than sibs, leading to an overestimate of h2.
October 18, 2025 at 1:57 PM
Well I suppose specifically for a developmental trait like this I might think that the environmental assumptions of the twin study design would be violated - i.e. twins share more of the relevant (in utero) environment than sibs, leading to an overestimate of h2.
I don't think this really makes sense though; it's like how anthropologists sometimes talk about things like "potential height" which is the height you would reach if you had perfect nutrition. But it's not a phenotype.
October 17, 2025 at 10:38 PM
I don't think this really makes sense though; it's like how anthropologists sometimes talk about things like "potential height" which is the height you would reach if you had perfect nutrition. But it's not a phenotype.
Indeed, rates of right-handedness were increased by [an environment] in which people were forced to write right-handed.
October 17, 2025 at 1:27 PM
Indeed, rates of right-handedness were increased by [an environment] in which people were forced to write right-handed.
I mean if someone is forced to the point where they use their right hand all the time, are they not right-handed?
October 17, 2025 at 1:25 PM
I mean if someone is forced to the point where they use their right hand all the time, are they not right-handed?
Yeah, those are always inflated
October 17, 2025 at 1:24 PM
Yeah, those are always inflated
Also I don't believe the heritability is 25%. UKB SNP heritability is less than 2%.
October 17, 2025 at 1:22 AM
Also I don't believe the heritability is 25%. UKB SNP heritability is less than 2%.
It's still environment, even if it's not practically measurable! Also, handedness can modified [by changing the environment].
October 17, 2025 at 1:19 AM
It's still environment, even if it's not practically measurable! Also, handedness can modified [by changing the environment].
Not sure the individual variation is the issue; it looks like they see it in most samples but I wonder whether there could be an off-target effect in the PCR step. Would want to check whether the putative mutant reads are enriched for mismatches.
September 12, 2025 at 2:52 PM
Not sure the individual variation is the issue; it looks like they see it in most samples but I wonder whether there could be an off-target effect in the PCR step. Would want to check whether the putative mutant reads are enriched for mismatches.
The only bit of the ARG you own is your terminal branch.
August 2, 2025 at 3:00 AM
The only bit of the ARG you own is your terminal branch.
We'll have to fix that!
July 31, 2025 at 12:59 PM
We'll have to fix that!
I don't know if it's better. They can certainly phase better, and this suggests they have access to UKB data: www.ukbiobank.ac.uk/projects/hig.... Plus they have in-house non-EUR panels (e.g. www.nature.com/articles/s42...)
July 30, 2025 at 2:36 AM
I don't know if it's better. They can certainly phase better, and this suggests they have access to UKB data: www.ukbiobank.ac.uk/projects/hig.... Plus they have in-house non-EUR panels (e.g. www.nature.com/articles/s42...)
Yes seems so, at least a couple of months ago I was able to download imputed data.
July 29, 2025 at 9:53 PM
Yes seems so, at least a couple of months ago I was able to download imputed data.
True, I mean I guess that [people imputing their own genomes] is exactly what they don't want people doing. Also 23andMe gives you imputed data, possibly better than TopMed imputation anyway?
July 29, 2025 at 12:56 PM
True, I mean I guess that [people imputing their own genomes] is exactly what they don't want people doing. Also 23andMe gives you imputed data, possibly better than TopMed imputation anyway?
Maybe because they don't want people trying to split up their samples over many small jobs. If you just have one, I guess just add in 19 samples from 1000 Genomes?
July 29, 2025 at 1:21 AM
Maybe because they don't want people trying to split up their samples over many small jobs. If you just have one, I guess just add in 19 samples from 1000 Genomes?
He chose.... poorly
July 24, 2025 at 3:41 PM
He chose.... poorly
I find Figure 7 more informative about the route than Figure 1
July 24, 2025 at 2:10 PM
I find Figure 7 more informative about the route than Figure 1
I think it makes very little difference - the high LD regions are small (and don't obviously have different patterns of cross-individual differences), so won't have much effect on the genome-wide differences.
July 23, 2025 at 4:33 PM
I think it makes very little difference - the high LD regions are small (and don't obviously have different patterns of cross-individual differences), so won't have much effect on the genome-wide differences.
In practice the main use of LD pruning seems to be removing high ("long-range") LD regions that otherwise show up as individual PCs (e.g. see Fig1 etc here: academic.oup.com/bioinformati...). In some sense those are still "real" structure in the ARG, but it's kind of undesirable for some analyses.
July 22, 2025 at 5:50 PM
In practice the main use of LD pruning seems to be removing high ("long-range") LD regions that otherwise show up as individual PCs (e.g. see Fig1 etc here: academic.oup.com/bioinformati...). In some sense those are still "real" structure in the ARG, but it's kind of undesirable for some analyses.
I think you could probably bias it one way or another depending on how you do the LD pruning (LD in which population?). I think of it as like you're changing the relative weighting of different parts of the ARG.
July 22, 2025 at 5:50 PM
I think you could probably bias it one way or another depending on how you do the LD pruning (LD in which population?). I think of it as like you're changing the relative weighting of different parts of the ARG.
So |EUR-YRI| can be < |YRI-X| for some other African population X, due to structure within Africa. |EUR-YRI| can be < |YRI-YRI| for some PCs but if you sum the distances across enough PCs, weighting them appropriately, it will always be larger.
July 21, 2025 at 3:37 AM
So |EUR-YRI| can be < |YRI-X| for some other African population X, due to structure within Africa. |EUR-YRI| can be < |YRI-YRI| for some PCs but if you sum the distances across enough PCs, weighting them appropriately, it will always be larger.
I see, but to the original point that's not how PCA works. I don't think |EUR-YRI| is ever going to be less than |YRI-YRI| in PC space – again YRI-YRI can coalesce before the split. Of course if you only look at the first 2 (or first N) PCs, it can be, but that just depends on sampling.
July 21, 2025 at 3:37 AM
I see, but to the original point that's not how PCA works. I don't think |EUR-YRI| is ever going to be less than |YRI-YRI| in PC space – again YRI-YRI can coalesce before the split. Of course if you only look at the first 2 (or first N) PCs, it can be, but that just depends on sampling.
They are not measuring pairwise differences. If I understand their figure 4A, if one individual is 0/0 and another is 1/0 then they count that as S=1. But If the second individual is 1/1 then they also count that as S=1 (not S=2). So they undercount differences in individuals with low heterozygosity
July 21, 2025 at 1:59 AM
They are not measuring pairwise differences. If I understand their figure 4A, if one individual is 0/0 and another is 1/0 then they count that as S=1. But If the second individual is 1/1 then they also count that as S=1 (not S=2). So they undercount differences in individuals with low heterozygosity