Category: Genomics
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Reconstructing a generation unsampled
In the near future I will be analyzing the genotype of an individual where all four grandparents have been typed. But this got me thinking about my own situation: is there a way I could “reconstruct” my own grandparents? None of them are living. The easiest way to type them would be to obtain tissue…
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Between the desert and the sea
Zinedine Zidane, a Kabyle There is a new paper in PLoS Genetics out which purports to characterize the ancestry of the populations of northern Africa in greater detail. This is important. The HGDP data set does have a North African population, the Mozabites, but it’s not ideal to represent hundreds of millions of people with…
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More on the “missing heritability” and epistasis
Please see Luke Jostins’ posts at Genetic Inference and Genomes Unzipped. Update: Steve Hsu weighs in. He read the supplements! Mad props.
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The last word on dog genesis is not nigh!
In my post below Rob commented: Surely the genetic evidence is pointing towards a single domestication event (see http://news.sciencemag.org/sciencenow/2011/11/new-data-fuels-dogfight-over-the.html?ref=hp) My general response is not to accept the latest press release about the genetic origin of dogs. I keep track of the literature and it’s rather fluid. For example, I woke up this morning, and this…
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Lactose intolerant when you shouldn’t be
Milk, it does a body good (or not): I’ve discussed this before earlier this year, when we got our results back (my husband, children, in-laws, parents, siblings… etc have all done genomic scans), two results came back that surprised us but proved true. My mother-in-law and husband were likely lactose intolerant. When I pointed that…
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How to reconstruct the Indo-Europeans
As must be obvious, I think now that the spread of Indo-European languages had some demographic impact. It wasn’t analogous to the spread of English to Jamaica, or the existence of French as an official language in Congo-Brazzaville. Because of this, I now believe it is possible in the near future that scientists will reconstruct…
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The history and geography of genomes
A new paper in PloS Genetics sheds some light on issues which we were already familiar with through conventional history, Ancestral Components of Admixed Genomes in a Mexican Cohort. What we already know: Mexicans and people of Mexican descent predominantly derive from an admixture event(s) between Europeans and Amerindians, with a minor African component. The…
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Out of the agricultural hearths
Dienekes has an important post up, The womb of nations: how West Eurasians came to be. He outlines a scenario where a rapid expansion of a farming population has overlain much of Western Eurasia, atop aboriginal substrata. A few years ago you’d have laughed at such a model, mostly due to the authority of archaeologists…
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Most Reported Genetic Associations with General Intelligence Are Probably False Positives
The title says it all, and I yanked it from a paper that is now online (and free). It’s of interest because of its relevance to the future genetic understanding of complex cognitive and behavioral traits. Here’s the abstract: General intelligence (g) and virtually all other behavioral traits are heritable. Associations between g and specific…
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Peeling the population genetic Indian onion
There’s a new paper in The American Journal of Human Genetics, Shared and Unique Components of Human Population Structure and Genome-Wide Signals of Positive Selection in South Asia. It’s free, so go read it. I don’t have time to comment in detail, but I did read the paper, and I want to mention a few…
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Cancer Genome Atlas Research Network Symposium videos online
They’re here. The “War Against Cancer” has been stalling for a while now. Is this going to make a difference? I hope so, but I don’t know….
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Introducing “genoeconomics”
A new paper (open access) in The Journal of Economic Perspectives, Molecular Genetics and Economics. The authors introduce the term “genoecomics.” They start out with the proposition that the intersection of genomics and behavioral economics suffers from 1) the study samples are way too small, 2) there’s a publication bias toward false results. It’s a…
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Thoughts on the $1,000 genome, circa 2007
You’ve probably read Andrew Pollack’s DNA Sequencing Caught in Deluge of Data, by now. This section caught my eye: “The cost of sequencing a human genome — all three billion bases of DNA in a set of human chromosomes — plunged to $10,500 last July from $8.9 million in July 2007, according to the National…
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But it still adapts!
Dienekes and Maju recently pointed to a paper, Contrasting signals of positive selection in genes involved in human skin color variation from tests based on SNP scans and resequencing, in Investigative Genetics. Skin color is an interesting trait because it’s one of the big “wins” in human genomics over the past 10 years. To a great…
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A consideration of Pacific Biosciences
I went to a seminar where a Pacific Biosciences representative was presenting recently. Along with others I arrived early because we thought it would be rather crowded. Not so much. Has the bubble burst? Zoom in to the last year….
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On structure, variation, and race
I noticed yesterday that Andrew Sullivan, Ta-Nehisi Coates, and a cast of others were having a roiling debate on race and I.Q. My name came up in several comment threads on various issues. I’m aware of this because I have Google Alerts set for my name. I don’t have the time or energy to get immersed…
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Genetic Creationism
Carl Zimmer points me to a piece in a publication called GeneWatch, The Crumbling Pillars of Behavior Genetics. I won’t quote from it because it’s kind of a tired rehash of the confusions and misrepresentations found in The Great DNA Data Deficit: Are Genes for Disease a Mirage?, thoroughly refuted by Luke Jostins and Dan…
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More than models
Slate recently had a series up on the use of mice as “model organisms.” In particular, it put the spotlight of some limitations of extrapolating from a mouse to a man (or other species). This is in some ways biology’s “WEIRD” problem. There are always going to be obvious reasons why we’d want to use…
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When trees turn into brambles
Genetics is powerful. The origins of the field predate Gregor Mendel, and go further back to plain human common sense. Crude theories of inheritance in the 19th century gave way in the early 20th to Mendelism, which happens to be a very powerful formal system for predicting the patterns of transmission of information from generation…