Elizabeth Warren carries Native American DNA – she’s running!

Since I’ve talked about this issue before, Warren releases results of DNA test:

There were five parts of Warren’s DNA that signaled she had a Native American ancestor, according to the report. The largest piece of Native American DNA was found on her 10th chromosome, according to the report. Each human has 23 pairs of chromosomes.

“It really stood out,” said Bustamante in an interview. “We found five segments, and that long segment was pretty significant. It tells us about one ancestor, and we can’t rule out more ancestors.”

He added: “We are confident it is not an error.”

The proportion of ancestry is not large. But it is clearly there. They compared to the Utah white and British European 1000 Genomes populations, which is a good standard for Old Stock Anglo-Americans. She’s clearly an outlier, with about an order of magnitude more “Native American” ancestry. So it’s unlikely to be some artifact.

There is some talk in the article about lack of reference populations. But remember, the key is to identify Native American ancestry, so all of this should coalesce back 10-15,000 years ago. Compared to the divergence from Northern Europeans, this is going to jump out against the genetic background.

So does Elizabeth Warren have Native American ancestry? 99% sure that that is a yes. Is she going to run? Well, I wouldn’t say 99%, but that seems likely too….

(I doubt she’ll do it, but it would be neat if she released her raw results)

Update: Here’s the technical report.

Update II: Some quick responses to comments. I’m going to address the genetic aspects. I’ll leave the cultural and political angles to others.

  • The analyst, who I know personally as well as by reputation, did exactly what I’d have expected he do with this data. So nothing atypical in terms of method/analytic pipeline. You can download and use the tools yourself!
  • The number of markers used in the analysis, 660,000, is a good number. Sufficient most definitely for the local ancestry analysis done here (and probably on some level necessary to gain a high level of confidence).
  • Some people wonder about the sample size of the reference population. Is the number sufficient? Yes, for the purposes of this analysis. For the scope of the questions asked. You aren’t looking for recent relatives, you are looking for a good representation of the genealogical networks from a given geography/ethnicity. The Utah whites are an industry standard sample set that is well known. The British data set in the 1000 Genomes is also pretty well known. Both seem representative of people of Northwest European heritage, a set of populations which are genetically very similar to each other.
  • People are asking about the robustness of this result. One thing you have to remember when comparing reference sets against an individual is that the genetic distance of the reference sets is important. Applying local ancestry to an individual of Dutch ancestry with training sets of Germans and English heritage is going to produce results, but the training sets themselves are going to overlap in some ways. Now, if you take someone with Dutch ancestry and do local ancestry for English vs. Javanese ancestry, then you’re going to get really clear results in comparison.
  • Some serious individuals are questioning the representativeness of the European panel and the Native American panel. As well as the lack of Siberian groups, who are closely related. But we know that Warren’s family background is such that a shift toward a Northeast Asian group is likely to be Native American. Not Chukchi. Further analysis could confirm, but the most likely hypothesis is that this is a woman of Northwest European ancestry with some Native American ancestry. Other models could fit these results. But those are not likely models in the first place (also, the PCA on Native American groups makes it likely that she is not Siberian, and she is not shifted to the northern groups).
  • A huge issue is that people are worried about the representativeness of the Native American groups. First, if you are looking for someone with indigenous North American ancestry, Mexican groups are sufficient. If anything this will reduce your power to detect, not produce false positives. Second, look at the plot, Warren’s haplotype is positioned between Canadian and Mexican natives: 
  • People are interpreting this local ancestry method, which assigns segments of the genome to particular populations with a probability, to the point estimates provided in most consumer genomics results. From what I can see, they assigned 0.4% of Warren’s genome as Native American. But 8% was not assigned. This is almost certainly mostly European, but some of it may be Native as well. Basically, the method here was less about assigning a specific proportion, and more about testing whether it was likely she had detectable indigenous American ancestry (she did), and, the range of periods in which that ancestry could have admixed into the Northern European genetic background. This is not comparable to the estimates you are getting from personal genomics tests.
  • One way you can try to assess whether these are artifactual is to compare an individual to populations of known ancestry and see the distribution of empirical results. Warren’s results are very atypical in comparison to Northern European reference sets. If this is a “false positive” due to the training sets, then you would expect the same type of problem to crop up when test out sample individuals.
  • Some are asking whether Warren is just a typical white American. You would need to do apples-to-apples comparisons. But my intuition is that she’s not. Most Old Stock white Americans probably have a genealogical relationship to Native Americans, but they may not have any segments of DNA because it is too far back. Warren is part of the minority of white Americans who have detectable Native American ancestry.

Basically, I think it is very likely that Warren has Native American ancestry. Follow-up analysis would probably just increase our confidence.

Open Thread, 10/15/2018

I pinned the above chart to my Twitter profile because I’m “trying to make it happen.” It was David Mittelman’s idea, and the data was courtesy of ISOGG, but putting it together as a graph has really brought home to people how the consumer genomic landscape has changed over the last half a decade.

The plot to the right, which shows a smoothed chart of the total number of kits over time, is also important.

I recorded a podcast for the Urbane Cowboys last week. It should go up today, so watch for it. I talked about a variety of topics, so I don’t know how it will drop in regards to editing.

Was talking to a friend about the importance of emotion in reasoning, or at least how emotion allows us to reason better. He asked about books, and Descartes’ Error came to mind. But I’ve read about critiques of its interpretation of the history of science and philosophy, though I think the big picture conclusion is probably still valid.

Will be at ASHG this week. Mostly I’m going to learn more about African genomics. Not as much on pop-gen as in previous years. If I approach your poster, don’t worry that I’m going to tweet or write about. Just be cool.

Noticed Tim Blanning’s massive survey of Frederick the Great is now less than $10 on Kindle. Because of the World Wars, I think we learn a lot less about Prussia from 1700 on than we otherwise would. Blanning’s The Pursuit of Glory: The Five Revolutions that Made Modern Europe: 1648-1815 is also excellent.

I’m listening to John Keegan’s A History of Warfare on Audible. To be honest I think I’m much better at reading than listening. This shouldn’t be surprising. In courses, I generally prefer to learn from the textbook as opposed to listening to lectures. And I have a lot of experience reading over my lifetime. Less so listening.

Xunzi: The Complete Text has been a difficult read for me. I’ve gone back and reread passages several times. It is definitely on the discursive side. That being said, I have come to a strange observation: Xunzi’s view of religion is similar to Ludwig Wittgenstein’s. Here from the Stanford Encylopedia of Religion:

He opposed interpretations of religion that emphasize doctrine or philosophical arguments intended to prove God’s existence, but was greatly drawn to religious rituals and symbols, and considered becoming a priest. He likened the ritual of religion to a great gesture, as when one kisses a photograph. This is not based on the false belief that the person in the photograph will feel the kiss or return it, nor is it based on any other belief. Neither is the kiss just a substitute for a particular phrase, like “I love you.” Like the kiss, religious activity does express an attitude, but it is not just the expression of an attitude in the sense that several other forms of expression might do just as well….

This seems similar to Xunzi’s belief that religious rituals were an important part of life, even if supernatural beings did not exist. Though Wittgenstein seems to have had some sort of fundamental mystical religious beliefs, whereas Xunzi was more of a naturalist.

The whale shark genome reveals how genomic and physiological properties scale with body size. Dim on comparative genomics. But I do like sharks.

Harvard and the Brigham call for more than 30 retractions of cardiac stem cell research. The medical science literature is going to yield a lot of problems sooner than later.

Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease.

The Democrats Have a Latino Problem Hispanic voters were supposed to be the party’s future. It’s not working out that way.

Jason Collin’s on global fertility projections.

Bayesian Estimation of Species Divergence Times Using Correlated Quantitative Characters.

Hidden ‘risk’ in polygenic scores: clinical use today could exacerbate health disparities.

Identity inference of genomic data using long-range familial searches. If they solve the Zodiac killer, forget about the worries.

Inferring Demography and Selection in Organisms Characterized by Skewed Offspring Distributions.

Adaptive walks on high-dimensional fitness landscapes and seascapes with distance-dependent statistics.

Existence and implications of population variance structure.

Megalakes in the Sahara? A Review.

On this week’s episode of The Insight we’re talking about the genetics of the Uralic peoples, and Finns in particular.

Have you been noticing more intrusive and stranger advertisements in the media? That’s because it’s in trouble. The whole sector. But you knew that.

On Eve of Harvard Bias Trial, Dueling Rallies Show Rifts Among Asian-Americans. The pro-Harvard Asians seem to have memorized zingers from Between the World and Me. They may be pro-social justice, but they’re still Asians, so no creativity!

The leisure class of the ancient world

The years before 1914 and the First World War are often termed the “first age of globalization” (with our current era the second). But that’s a little short-sighted view, even though arguably correct in some sense.

Books such as The Fate of Rome and The Fall of Rome: And the End of Civilization make it quite clear that Classical Antiquity achieved some level of globalization in its corner of Eurasia. At the other end of Eurasia, the Grand Canal also illustrates the importance of trade and economic interdependence in complex pre-modern societies.

But what has been made can be unmade. One of the major arguments in Framing the Early Middle Ages is that the decline in the social complexity of the early medieval period in Europe was due in part to the collapse of the whole fiscal apparatus of the Roman bureaucratic state. Some of these weak post-Roman states were really chiefdoms bound together with personalized rule. A process which advanced the furthest in Britain and the Balkans.

And yet during the first grat maximum of human civilization in the years after 0 international trade extended even beyond the bounds of specific imperium, from one end of Eurasia to the other.

The Roman Empire and the Indian Ocean: The Ancient World Economy and the Kingdoms of Africa, Arabia and India focus mostly on the international aspect of the trade. Much of it is concerned with the role of conspicuous consumption among elites in the Roman Empire in driving this trade, and so the bullion drain to the east. Silk, incense, ivory, and medicines were all imported in large quantities from the east. The state benefited in some sense through taxation, but the drain on specie was a constant consideration. It is well known that Roman coinage, sometimes modified, became the standard in the southern half of India in the first centuries AD.

In a stepwise fashion, East Roman traders pushed across the Indian ocean until in 166 we know that they reached the imperial court in China. This connection seems to have been made by following the trade routes which were already established by Indians into Southeast Asia. Roman geographers were familiar with the general shape of Peninsular Malaysia, as well as Java.

Because our records from China and the Roman Empire are very good, is easy to ignore the reality that a whole network of cities existed along the shores of the Indian ocean. These cities grew up around trade and acted as intermediaries for the demand for particular luxury goods which also pumped specie out of Roman mines. But the decades after the Antonine plague seems to have been defined by multiple regressions across Eurasia, as societies dependent and expecting trade faltered when local nodes collapsed and interrupted the flow.

A historical slice of evolutionary genetics

A few friends pointed out that I likely garbled my attribution of who were the guiding forces between the “classical” and “balance” in the post below (Muller & Dobzhansky as opposed to Fisher & Wright as I said). I’ll probably do some reading and update the post shortly…but it did make me reflect that in the hurry to keep up on the current literature it is easy to lose historical perspective and muddle what one had learned.

Of course on some level science is not as dependent on history as many other disciplines. The history is “baked-into-the-cake.” This is clear when you read The Origin of Species. But if you are interested in a historical and sociological perspective on science, with a heavy dose of narrative biography, I highly recommend Ullica Segerstrale’s Defenders of the Truth: The Battle for Science in the Sociobiology Debate and Beyond and Nature’s Oracle: The Life and Work of W.D. Hamilton.

Defenders of the Truth in particular paints a broad and vivid picture of a period in the 1960s and later into the 1970s when evolutionary thinkers began to grapple with ideas such as inclusive fitness. E. O. Wilson’s Sociobiology famously triggered a counter-reaction by some intellectuals (Wilson was also physically assaulted in the 1978 AAAS meeting). Characters such as Noam Chomsky make cameo appearances.

Segerstrale’s Nature’s Oracle focuses particularly on the life and times of W. D. Hamilton, though if you want that at high speed and max density, read Narrow Roads of Gene Land, Volume 2. Because Hamilton died before the editing phase, the biographical text is relatively unexpurgated. Hamilton also makes an appearance in The Price of Altruism: George Price and the Search for the Origins of Kindness.

The death of L. L. Cavalli-Sforza reminds us that the last of the students of the first generation of population geneticists are now passing on. With that, a great of history is going to be inaccessible. The same is not yet true of the acolytes of W. D. Hamilton, John Maynard Smith, or Robert Trivers.

Making what Harvard is about transparent

This is the future Edward Blum wants

In the 20th century version of the TV series Murphy Brown, there was an episode where three young American scholars were introduced. The big laugh was that they had very Chinese or Indian names. Though it’s probably politically incorrect today to depict it that way, the joke is that the best “American” scholars were not really American….

If you’re an Asian American who remembers the period before the 1990s, you know where I’m coming from. This was an America in black and white, and you were literally the Other if you were outside of those two boxes. People would be surprised that you spoke English without an accent, and inquire where you really came from. This still happens now and then, but back in the 1980s, it was pervasive. It was tradition. The children of the first post-1965 immigrants were not yet grown, so the majority of Asian American adults you saw and encountered were immigrants outside of a few areas, such as Hawaii and portions of the West Coast. In 1980 1.7% of the people residing in the United States were Asian American. Today nearly 7% are Asian American.

This is having an impact. The winners of spelling bees and science fair winners don’t “look like America” anymore.

And this is the major reason why the cultural elite is very upset about the scrutiny which admissions processes at top universities have been receiving. Consider this op-ed in The New York Times, A Damaging Bid to Censor Applications at Harvard. It concludes:

As a leader in higher education, Harvard is trying to change this through its modest consideration of race in admissions. Its goal is to create a diverse community of students who can engage with and learn from people who are different, and carry those experiences with them beyond the university.

Expressions of racial identity are part of the fullness of our humanity. It’s not possible to be blind to race. Pretending as though it is ensures we will forever be divided.

The op-ed is pretty measured and not particularly shoddy as far as it goes. This is the sort of message that the editors and reporters at The New York Times want to amplify. Call it the anti-Bari Weiss effect.

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An “in-fill” framework for the expansion of peoples in Europe: beakers, beakers everywhere!

In the 1970s A. J. Ammerman and L. L. Cavalli-Sforza argued for the validity of a model of Neolithic expansion of farmers into Europe predicated on a “demic diffusion” dynamic. This is in contrast to the idea that farming spread through the diffusion of ideas, not people. The formal theory is inspired by the Fisher wave model, but empirically just imagine two populations with very different carrying capacities due to their mode of production, farmers, and hunter-gatherers. In a Malthusian framework, the farmer carrying capacity in a given area of land might be ~10× greater than that of hunter-gatherers. Starting at the same initial population, the farmers will simply breed the hunter-gatherers out of existence.

As the farmers reaching their local carrying capacity, migration outward will occur in a continuous and diffusive process. For all practical purposes, the farmers will perceive the landscape occupied by hunter-gatherers as “empty.” This is due to the fact that hunter-gatherers often engage in extensive, not intensive, exploitation of resources. In contrast, even slash and burn agriculturalists leave a much bigger ecological footprint. They swarm over the land.

The beauty of the demic diffusion process is that that it’s analytically elegant and tractable. Families or villages engaged in primary production to “fill up” a landscape through simple cultural practices which manifest on the individual scale that allow for aggregate endogenous growth. And this model underlies much of the work by Peter Bellwood in First Farmers and Colin Renfrew’s theories about the spread of Indo-European langauges. You can call it the Walder Frey theory of history.

I didn’t really think deeply about this theory because I didn’t have much empirical knowledge until I read Lawrence Keeley’s War Before Civilization. In this book, Keeley observes that the archaeological record suggests that there was violent conflict between the first farmers and hunter-gatherers in northwestern Europe, near the North Sea. He reports that there seems to have been a broad front of conflict, presumably a prehistoric “no man’s land.” Not only that, but Keeley claims that the spread of agriculture stopped for a period. The barrier between hunter-gatherer occupation and farmer territory was not permeable. Not diffusion.

As a stylized fact, the demic diffusion framework treats all farmers as interchangeable and all hunter-gatherers as interchangeable. On the face of it, we know that this is wrong. But the assumption is that to a first approximation this axiom will allow us to capture the main features of the dynamics in question. This may be a false assumption. The fact is we know that some hunting and gathering populations can engage in intensive resource extraction and remain sedentary.

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Reflections on the biology of Homo calaquendi

For a while now I’ve been really haunted by a question about the verisimilitude of J. R. R. Tolkien’s world-building: what are the long-term social and biological consequences of the fact that the Eldar, the elves, are immortal?

Consider the fact that the elves are long-lived, and not particularly fecund. Even when they are, inter-general patterns are spotty. Fëanor had seven sons, but only one grandson! Today we have “helicopter parents”, always worried about the safety of their offspring. How would an elvish society ever flourish if parents are terrified about the risk of their few offspring dying prematurely?

The fact that elves even go to war is indicative of a very strange and alien psychology. If you had the opportunity for everlasting life, would you risk it in battle? Are elves courageous? Or do they just have high time-preference?

But for me, the bigger question is the psychology of Galadriel. At 7,000 years old she is one of the oldest creatures in Middle Earth, along with Gandalf, Sauron, Cirdan, and Glorfindel. Assuming 100 years that’s 70 human lifetimes. J. R. R. Tolkien is quite clear about her physical appearance. She is quite tall, with silver-gold hair. But her head is not particularly large. So the question presents itself: how does her long-term memory allocation work? We know she has a human cranial capacity.

If salient and emotionally resonant memories connected to excitement in the hippocampus are the ones banked, does that mean that Galadriel’s mind is brimming with incredibly vivid recollections? Shouldn’t she be depressed in the present, because the present is going to be so dull compared to her glittering memories of Aman, and the beauty and elegance of the First Age civilization of the Eldar?

Additionally, it seems clear that the Eldar don’t suffer from cognitive decline in the same way as humans. Does that mean perhaps that Galadriel’s intuitive abilities would be suprahuman? Both humans and elves are children of Eru Ilúvatar. There is no evidence from the legendarium that elves are orders of magnitude more gifted than humans in “system 2” thinking, that is, rational reflection. But in their grace and acuity in matters of perception are curious. Could be it be a function of acquired “system 1” faculties, as opposed to what they were born with?

Perhaps the fey grace of the Eldar is not a matter of their natural abilities, but a function of developmental psychology? If the 10,000-hour rule is a thing, how about the 100-generation rule?

Finally, the elvish recourse to writing strikes me as peculiar in light of their immortality. They seem to be primary producers and foragers who don’t engage in much trade, so accounting is not highly valued in all likelihood. And writing does not confer the gains of the advantage of immortality to an already immortal species.

Note: For those readers who suggest that this post may mean that I never have sex, I already have three children. That’s more than most elves!

The post-neutral human genome (the Kern-Hahn era)

If you have any background in evolutionary biology you are probably aware of the controversy around the neutral theory of molecular evolution. Fundamentally a theoretical framework, and instrumentally a null hypothesis, it came to the foreground in the 1970s just as empirical molecular data in evolutionary was becoming a thing.

At the same time that Motoo Kimura and colleagues were developing the formal mathematical framework for the neutral theory, empirical evolutionary geneticists were leveraging molecular biology to more directly assay natural allelic variation. In 1966 Richard Lewontin and John Hubby presented results which suggested far more variation than they had been expecting. Lewontin argued in the early 1970s that their data and the neutral model actually was a natural extension of the “classical” model of expected polymorphism as outlined by R. A. Fisher, as opposed to the “balance school” of Sewall Wright. In short, Lewontin proposed that the extent of polymorphism was too great to explain in the context of the dynamics of the balance school (e.g., segregation load and its impact on fitness), where numerous selective forces maintained variation. The classical school emphasized both strong selective sweeps on favored alleles and strong constraint against most new mutations.

And yet one might expect low levels of polymorphism from the classical school. The way in which the neutral framework was a more natural extension of this model is that even if most inter-specific variation, most substitutions across species, are due to selectively neutral variants, most variants could nevertheless be deleterious and so constrained. Alleles which increase in frequency may have done so through positive selection, or, just random drift. Not balancing forces like diversifying selection and overdominance.

The general argument around neutral theory generated much acrimony and spilled out from the borders of population genetics and molecular evolution to evolutionary biology writ large. Stephen Jay Gould, Simon Conway Morris, and Richard Dawkins, were all under the shadow of neutral theory in their meta-scientific spats about adaptation and contingency.

That was then, this is now. I’ve already stated that sometimes people overplay how much genomics has transformed our understanding of evolutionary biology. But in the arguments around neutral theory, I do think it has had a salubrious impact on the tone and quality of the discourse. Neutral theory and the great controversies flowered and flourished in an age where there was some empirical data to support everyone’s position. But there was never enough data to resolve the debates.

From where I stand, I think we’re moving beyond that phase in our intellectual history. To be frank, some of the older researchers who came up in the trenches when Kimura and his bête noire John Gillespie were engaged a scientific dispute which went beyond conventional collegiality seem to retain the scars of that era. But younger scientists are more sanguine, whatever their current position might be because they anticipate that the data will ultimately adjudicate, because there is so much of it.

With that historical context, consider a new paper, Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences:

Disentangling the effect on genomic diversity of natural selection from that of demography is notoriously difficult, but necessary to properly reconstruct the history of species. Here, we use high-quality human genomic data to show that purifying selection at linked sites (i.e. background selection, BGS) and GC-biased gene conversion (gBGC) together affect as much as 95% of the variants of our genome. We find that the magnitude and relative importance of BGS and gBGC are largely determined by variation in recombination rate and base composition. Importantly, synonymous sites and non-transcribed regions are also affected, albeit to different degrees. Their use for demographic inference can lead to strong biases. However, by conditioning on genomic regions with recombination rates above 1.5 cM/Mb and mutation types (C↔G, A↔T), we identify a set of SNPs that is mostly unaffected by BGS or gBGC, and that avoids these biases in the reconstruction of human history.

This is not an entirely surprising result. Some researchers in human genetics have been arguing for the pervasiveness of background selection, selection against deleterious alleles which effects nearby regions, for nearly a decade. In contrast, there are others who argue selective sweeps driven by positive selection are important in determining variation. Unlike the 1970s and 1980s these researchers don’t evince much acrimony, in part because the data keeps coming, and ultimately they’ll probably converge on the same position. And, the results may differ by species or taxon.

If you want a less technical overview than the paper, Kelley Harris has an excellent comment accompanying it. If you want to know what I mean by the Kern-Han era, it’s a joke due to the publication of The Neutral Theory in Light of Natural Selection.

Finally, some of you might wonder about the implications for demographic inference which preoccupies me so much on this weblog. In the big picture, it probably won’t change a lot, but it will be important for the details. So this is a step forward. That being said, the possibility of variable mutation rates and recombination rates across time and between lineages are also probably quite important.

Open Thread, 10/8/2018

Paul Romer won the Nobel. Not a big surprise. David Warsh’s Knowledge and the Wealth of Nations: A Story of Economic Discovery is pretty good. I recommend it. I would read it in concert with Hive Mind: How Your Nation’s IQ Matters So Much More Than Your Own and A Farewell to Alms: A Brief Economic History of the World (Warsh wrote a negative review of the second book and likely would not be a fan of the first).

Analyses of Neanderthal introgression suggest that Levantine and southern Arabian populations have a shared population history. Bigger Yemeni data set. Yemeni and Levantine populations seem quite similar….

As you may not know Google+ was finally given an explicit sunset schedule. Google tried twice to tackle Facebook but failed both times. But it turns out that Facebook may never have a successor. A centralized social-graph has weaknesses, and younger cohorts seem to be creating segmentation. Their parents are on Facebook, so they have a nominal Facebook account. But the real action is on other platforms.

Life on the Dirtiest Block in San Francisco. Having drinks with friends at the top of hotels and high rise condominium complexes makes you forget that far below the homeless have come out and taken over the night.

Why most narrative history is wrong. First, this seems to be more about ‘popular’ history today, and the mainstream of past history. One reason contemporary academic history is so boring for most people is that it resists grand narrative temptation.

With that being said, this is more of an indictment on modern journalism.

Quantifying how constraints limit the diversity of viable routes to adaptation.

A Simulation-Based Evaluation of Total-Evidence Dating Under the Fossilized Birth-Death Process.

Expanded Pre-Implantation Genomic Testing.

Fudged statistics on the Iraq War death toll are still circulating today. Do you remember this debate more than ten years ago? I do. The very assertion of these numbers distorted the discourse. This was just a prefiguring of the media landscape today. It’s mostly propaganda.

Phylogeny, ancestors and anagenesis in the hominin fossil record.

The genetic relationship between female reproductive traits and six psychiatric disorders.

In case my Twitter account gets deleted, remember you can subscribe to my RSS or follow my Facebook page.

ASHG Meeting next week.

Max Boot is making the rounds promoting his new book, The Corrosion of Conservatism: Why I Left the Right. I haven’t read the book, but having listened to him on various podcasts, one thing that annoys me about this guy: his faction of maximalist neoconservatives and war-hawks in the post-9/11 era were cheering on the mass psychosis which led to this nation backing multiple military adventures. In particular, I’m talking about the invasion of Iraq, which cost $2 trillion dollars, 4,500 American soldiers’ lives, and hundreds of thousands of Iraqi lives.

Instead of starting in 2015, he should start in 2003.

The population genetic structure of China (through noninvasive prenatal testing)

This week a big whole genome analysis of China was published in Cell, Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History. The abstract:

We analyze whole-genome sequencing data from 141,431 Chinese women generated for non-invasive prenatal testing (NIPT). We use these data to characterize the population genetic structure and to investigate genetic associations with maternal and infectious traits. We show that the present day distribution of alleles is a function of both ancient migration and very recent population movements. We reveal novel phenotype-genotype associations, including several replicated associations with height and BMI, an association between maternal age and EMB, and between twin pregnancy and NRG1. Finally, we identify a unique pattern of circulating viral DNA in plasma with high prevalence of hepatitis B and other clinically relevant maternal infections. A GWAS for viral infections identifies an exceptionally strong association between integrated herpesvirus 6 and MOV10L1, which affects piwi-interacting RNA (piRNA) processing and PIWI protein function. These findings demonstrate the great value and potential of accumulating NIPT data for worldwide medical and genetic analyses.

In The New York Times write-up there is an interesting detail, “This study served as proof-of-concept, he added. His team is moving forward on evaluating prenatal testing data from more than 3.5 million Chinese people.” So what he’s saying is that this study with >100,000 individuals is a “pilot study.” Let that sink in.

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