Heritability 501: LDSR-based H2…for the technically minded
http://www.NealeLab.is/blog/2017/9/14/heritability-501-ldsr-based-h2-in-ukbb-for-the-technically-minded Nice overview by @BMNeale lab HT @Sushant211
Nice blog post series explaining heritability.
http://www.nealelab.is/blog/2017/9/13/heritability-101-what-is-heritability
http://www.nealelab.is/blog/2017/9/13/heritability-201-types-of-heritability-and-how-we-estimate-it
The case of human nose shape & climate adaptation
http://journals.PLoS.org/plosgenetics/article?id=10.1371/journal.pgen.1006616 Comparing its Qst-Fst statistic w/ that for height & skin color
QT:{{”
“To address the question of whether local adaptation to climate is responsible for nose shape divergence across populations, we use Qst–Fst comparisons to show that nares width and alar base width are more differentiated across populations than expected under genetic drift alone. To test whether this differentiation is due to climate adaptation, we compared the spatial distribution of these variables with the global distribution of temperature, absolute humidity, and relative humidity. We find that width of the nares is correlated with temperature and absolute humidity, but not with relative humidity. We conclude that some aspects of nose shape may indeed have been driven by local adaptation to climate. However, we think that this is a simplified explanation of a very complex evolutionary history, which possibly also involved other non-neutral forces such as sexual selection.”
“}}
Thought-provoking calculations, perhaps suggesting that ever bigger association studies won’t yield useful results
https://twitter.com/joe_pickrell/status/875406448716632064
http://www.cell.com/cell/abstract/S0092-8674(17)30629-3
An Expanded View of Complex Traits: From Polygenic to Omnigenic
Evan A. Boyle
Yang I. Li
Jonathan K. Pritchard
DOI: http://dx.doi.org/10.1016/j.cell.2017.05.038
Common SNPs explain a large proportion (45%) of heritability for…height (85%)
http://www.Nature.com/ng/journal/v42/n7/abs/ng.608.html Cf 2010 GWASes could only explain 5%
Jian Yang,
Beben Benyamin,
Brian P McEvoy,
Scott Gordon,
Anjali K Henders,
Dale R Nyholt,
Pamela A Madden,
Andrew C Heath,
Nicholas G Martin,
Grant W Montgomery,
Michael E Goddard
& Peter M Visscher
Nature Genetics 42, 565–569 (2010) doi:10.1038/ng.608
QT:{{”
…conveniently implemented with a mathematically equivalent model that uses the SNPs to calculate the genomic relationship between pairs of subjects). Using this approach, we estimated the proportion of phenotypic variance explained by the SNPs as 0.45 (s.e. = 0.08, Table 1), a nearly tenfold increase relative to the 5% explained by published and validated individual SNPs
“}}
http://www.nature.com/ng/journal/v42/n7/abs/ng.608.html
Common SNPs explain a large proportion of the heritability for human height
Jian Yang,
Beben Benyamin,
Brian P McEvoy,
Scott Gordon,
Anjali K Henders,
Dale R Nyholt,
Pamela A Madden,
Andrew C Heath,
Nicholas G Martin,
Grant W Montgomery,
Michael E Goddard
& Peter M Visscher
Nature Genetics 42, 565–569 (2010) doi:10.1038/ng.608
QT:{{"
…conveniently implemented with a mathematically equivalent model
that uses the SNPs to calculate the genomic relationship between
pairs of subjects). Using this approach, we estimated the proportion
of phenotypic variance explained by the SNPs as 0.45 (s.e. = 0.08,
Table 1), a nearly tenfold increase relative to the 5% explained by
published and validated individual SNPs
"}}
Common SNPs explain a large proportion (45%) of heritability for…height (80%) http://www.Nature.com/ng/journal/v42/n7/abs/ng.608.html Vs ’10 GWAS SNPs could only expl. 5%
HTP discovery of novel developmental #phenotypes
http://www.nature.com/nature/journal/v537/n7621/full/nature19356.html New list of essential genes for the mouse, upping number to ~2900