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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Can Genius Be Genetically Engineered?

See you at the 92nd Street Y tomorrow (Thu, Mar 10, 2016, 8:15 pm)! With rapid advances in genome sequencing, genetic analysis and precision gene editing, it’s becoming ever more likely that embryo selection and genetic engineering could be used to optimize the intelligence of our future children. Although the complexities of genetics, the brain …

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Improved CRISPR–Cas9: Safe and Effective?

Two groups (Zhang lab at MIT and Joung lab at Harvard) announce improved “engineered” Cas9 variants with reduced off-target editing rates while maintaining on-target effectiveness. I had heard rumors about this but now the papers are out. See CRISPR: Safe and Effective? Nature commentary Genome Editing: The domestication of Cas9. High-fidelity CRISPR–Cas9 nucleases with no …

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Cognitive Genomics Interview

This is a discussion with Cambridge University PhD candidate Daphne Martschenko. Topics covered include: genetics of cognition, group differences, genetic engineering. The NYC roundtable on genius she mentions is here. Blog readers may also be interested in this event at the 92nd Street Y (Thu, Mar 10, 2016, 8:15 pm, Location: Lexington Avenue at 92nd …

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In vivo gene editing with CRISPR

Safe and Effective soon for humans? In vivo genome editing improves muscle function in a mouse model of Duchenne muscular dystrophyin vi Science DOI: 10.1126/science.aad5143 Duchenne muscular dystrophy (DMD) is a devastating disease affecting about 1 out of 5000 male births and caused by mutations in the dystrophin gene. Genome editing has the potential to restore …

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GCTA, Missing Heritability, and All That

Bioinformaticist E. Stovner asked about a recent PNAS paper which is critical of GCTA. My comments are below. It’s a shame that we don’t have a better online platform (e.g., like Quora or StackOverflow) for discussing scientific papers. This would allow the authors of a paper to communicate directly with interested readers, immediately after the paper …

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Nativity 2050

And the angel said unto them, Fear not: for, behold, I bring you good tidings of great joy, which shall be to all people. Mary was born in the twenties, when the tests were new and still primitive. Her mother had frozen a dozen eggs, from which came Mary and her sister Elizabeth. Mary had …

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Fear Not!

For relentless technological advance, powered by high g researchers, venture capitalists, capital markets, and government investment in basic research, continues to deliver a cornucopia of benefits to the average joe. (Note, however, that Moore’s Law itself has stalled out recently …) Tweet

Largest repositories of genomic data

This list of the largest repositories of genetic data appeared in the 25 September 2015 issue of Science. Note that the quality and extent of phenotyping varies significantly. 23andME SIZE: >1 million GENETIC DATA: SNPs This popular personal genomics company now hopes to apply its data to drug discovery (see main story, p. 1472). ANCESTRY.COM …

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No genomic dark matter

Let me put it very simply: there is NO genomic “dark matter” or “missing heritability” — it’s merely a matter of sample size (statistical power) to identify the specific variants that account for the total expected heritability. The paper below (see also HaploSNPs and missing heritability) suggests that essentially all of the expected heritability can …

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