Scientists of Stature

The link below is to the published version of the paper we posted on biorxiv in late 2017 (see blog discussion). Our results have since been replicated by several groups in academia and in Silicon Valley. Biorxiv article metrics: abstract views 31k, paper downloads 6k. Not bad! Perhaps that means the community understands now that genomic …

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Institute for Advanced Study: Genomic Prediction of Complex Traits (seminar)

Genomic Prediction of Complex Traits After a brief review (suitable for physicists) of computational genomics and complex traits, I describe recent progress in this area. Using methods from Compressed Sensing (L1-penalized regression; Donoho-Tanner phase transition with noise) and the UK BioBank dataset of 500k SNP genotypes, we construct genomic predictors for several complex traits. Our …

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Behold, the Super Cow

Hmm… how do they compute the Net Merit and GTPI? (But, but, what about all of that missing heritability?) See also Applied genomics: the genetic “super cow” Genomic prediction: no bull. Attention climate virtue signalers: more efficient cows produce less methane per liter of milk! Drink milk from genetically engineered cows :-) Tweet

23andme

I’m in Mountain View to give a talk at 23andMe. Their latest funding round was $250M on a (reported) valuation of $1.5B. If I just add up the Crunchbase numbers it looks like almost half a billion invested at this point… Slides: Genomic Prediction of Complex Traits Abstract: We apply methods from Compressed Sensing (L1-penalized regression; Donoho-Tanner …

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Natural Selection and Body Shape in Eurasia

Prior to the modern era of genomics, it was claimed (without good evidence) that divergences between isolated human populations were almost entirely due to founder effects or genetic drift, and not due to differential selection caused by disparate local conditions. There is strong evidence now against this claim. Many of the differences between modern populations …

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Genetic variation in Han Chinese population

Largest component of genetic variation is a N-S cline (phenotypic N-S gradient discussed here). Variance accounted for by second (E-W) PC vector is much smaller and the Han population is fairly homogeneous in genetic terms: …while we revealed East-to-West structure among the Han Chinese, the signal is relatively weak and very little structure is discernible …

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20 years of GATTACA (1997)

 A 20 year lag between science fiction and reality… not bad! Embryo selection, but no additional engineering: Geneticist (Blair Underwood): Keep in mind, this child is still you — simply the best of you. You could conceive naturally a thousand times and never get such a result … According to this discussion, an offer of …

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Asking for a Skeptic Friend

I sometimes get email from people asking, in one way or another, whether our long-term evolution experiment (LTEE) with E. coli provides evidence of evolution writ large – new species, new information, or something of that sort. I try to answer these questions by providing some examples of what we’ve seen change, and by putting …

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Genetics, Cognitive Ability, and Education (conversation with Cambridge PhD candidate Daphne Martschenko)

Genetics, Cognitive Ability, and Education (conversation with Cambridge PhD candidate Daphne Martschenko) Further conversation with Cambridge PhD candidate Daphne Martschenko concerning genetics of cognitive ability, implications for education policy, etc. See also earlier conversation: https://www.youtube.com/watch?v=YVqkvHpLfuQ Dunedin paper referenced in the video (polygenic score prediction of adult success for different SES groups): http://infoproc.blogspot.com/2016/09/genomic-prediction-of-adult-life.html Tweet

Speed, Balding, et al.: “for a wide range of traits, common SNPs tag a greater fraction of causal variation than is currently appreciated”

I recently blogged about a nice lecture by David Balding at the 2015 MLPM (Machine Learning for Personalized Medicine) Summer School: Machine Learning for Personalized Medicine: Heritability-based models for prediction of complex traits. In that talk he discussed some results concerning heritability estimation and potential improvements over GCTA. A new preprint on bioRxiv has the …

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Machine Learning for Personalized Medicine: Heritability-based models for prediction of complex traits (David Balding)

Highly recommended talk by David Balding on modern approaches to heritability, relatedness, etc. in statistical genetics. (I listened at 1.5x normal speed, which worked for me.) MLPM (Machine Learning for Personalized Medicine) Summer School 2015 Monday 21st of September Heritability-based models for prediction of complex traits by David Balding Complex trait genetics has been revolutionised …

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The tipping point

This is only the beginning. To serious people who read this blog, but may have been confused over the past 5+ years about things like missing heritability, genomic prediction, complex genetic architecture, gloomy prospects: isn’t it about time to consider updating your priors? Read all about it here. FT.com: Genetic scoring predicts how children do …

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Flipping DNA switches

The recently published SSGAC study (Nature News) found 74 genome-wide significant hits related to educational attainment, using a discovery sample of ~300k individuals. The UK Biobank sample of ~110k individuals was used as a replication check of the results. If both samples are combined as a discovery sample 162 SNPs are identified at genome-wide significance. …

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74 SNP hits from SSGAC GWAS

The SSGAC discovery of 74 SNP hits on educational attainment (EA) is finally published in Nature. Nature News article. EA was used in order to assemble as large a sample as possible (~300k individuals). Specific cognitive scores are only available for a much smaller number of individuals. But SNPs associated with EA are likely to …

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This is for PZ Myers

Scott Alexander (Slate Star Codex), Garrett Jones (Hive Mind), and Razib Khan (GNXP) alerted me (via Twitter) of this post by PZ Myers. Myers is both confused and insulting in his blog post, but I’ll refrain from ad hominem attacks, and just focus on the science. Myers seems to think that humans with much better …

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Genetic ancestry and brain morphology

Population structure — i.e., distribution of gene variants by ancestral group — is reflected in brain morphology, as measured using MRI. Brain morphology measurements can be used to predict ancestry. Strictly speaking, the data only show correlation, not genetic causation, but the most plausible interpretation is that genetic differences are causing morphological differences. One could …

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