Tag: Genomes Unzipped

Poll on personal genomics

By Razib Khan | September 14, 2011 10:08 pm

Genomes Unzipped points me to a Nature survey on personal genomics for scientific researchers. With price points down to $200 or so many scientists have been at least genotyped. Though it varies by domain. Many molecular biologists seem intrigued by the novelty of personal genotyping services. In contrast, in a room of a dozen or so population geneticists and the like nearly half are liable to have already gone through some service.

All that being said, I haven’t heard from people who want to make their genotype public in a long, long, time. Has the steam run out of that project? You might hear from me again with a subtle twist on this in the near future.

CATEGORIZED UNDER: Personal Genomics

My genetic odyssey

By Razib Khan | February 10, 2011 9:49 am

I have a guest post at Genomes Unzipped, summarizing what I’ve found via ancestry analysis over the past 6 months with the results from 23andMe. It is in many ways a brief overview of the detailed posts which you’ve see in this space.

CATEGORIZED UNDER: Genetics

"Genome blogging"

By Razib Khan | December 15, 2010 12:06 pm

Nature profiles Dodecad, the Pickrell Affair, and the emergence of amateur genomicists in a new piece. Interestingly David of BGA is going to try and get something through peer review. In particular, the relationship of Assyrians and Jews.

So we have Genomes Unzipped, Dodecad, and BGA. What next? Who next? I hope Dienekes doesn’t mind if I divulge the fact that the computational resources needed to utilize ADMIXTURE as he has is within the theoretical capability of everyone reading this post. Rather, the key is getting familiar with PLINK and writing some code to merge data sets. After you do that, to really add value you’d probably want to get raw data from more than what you can find in the HGDP, HapMap and other public resources.

But here I make an open offer: if you start a blog or a project which replicates the methods of Dodecad and BGA I’ll link to you and promote you. When Dienekes began Dodecad I actually started to play around with the data sets in ADMIXTURE, but I’ve personally held off until seeing what he and David find. What their pitfalls and successes might be. Here’s to 2011 being more interesting than we can imagine!

Update: Already had a friend with a computational background contact me about doing something on South Asian genomics. So again: if you get a site/blog set up, and start pumping out plots, I will promote you. In particular, if you need 23andMe raw data files of geographical region X it might be useful to try and get the word out via blogs and what not.

CATEGORIZED UNDER: Blog, Genomics

Eurogenes 500K SNP BioGeographicAncestry Project

By Razib Khan | November 23, 2010 12:11 am

Since I have been promoting the Dodecad Ancestry Project, it seems only fair to bring to your attention Eurogenes 500K SNP BioGeographicAncestry Project. The sample populations are a bit different from Dodecad, but again ADMIXTURE is the primary tool. But the author also makes recourse to other methodologies to explore more than simply population level variation. For example, his most recent post is Locating and visualizing minority non-European admixtures across our genomes:

Imagine, for example, a white American carrying a couple of tiny segments of West African origin, from an ancestor who lived 250 years ago, and an eastern Finn with no Asian ancestors in the last 4000 years or more. If we run an inter-continental ADMIXTURE analysis with these two, it’s very likely the American will score 100% European, while the eastern Finn will probably come out around 9% North and East Asian due to really old Uralic influence.

That sort of thing isn’t a huge problem when comparing the genetic structure of populations. Obviously, overall, eastern Finns rather than white Americans are genetically closer to North Asians, and that’s basically what ADMIXTURE picks up. However, if the focus is also on individuals, this certainly can become an issue. Our hypothetical American might be aware of that African ancestor, with solid paperwork backing up their genealogical connection, but he’s pulling his hair out because nothing’s showing up via genetic tests.

So let’s take a look at a real life example of how RHHcounter can pick up segments of potentially recent Sub-Saharan African origin…

euras1
Olivia Munn & Uyghur woman

The basic issue here is that in terms of genomic variation old admixture looks different from new admixture. Someone who is a first generation Eurasian, with a Chinese and European parent, may be about the same ancestral mix proportionally as a Uyghur. They would resemble a Uyghur on STRUCTURE and be placed within that cluster on a PCA chart (this is what happens in 23andMe). But, the Uyghur “Eastern” and “Western” genetic heritage has been reshuffled to a great extent by recombination over the past 1,000-2,000 years. In contrast, a first generation Eurasian will have huge swaths of their genome which are Eastern or Western on alternating strands (from their respective parents). In population genetic language a group of first generations hybrids would be exhibit a lot of linkage disequilibrium (LD). In a panmictic hybrid population LD will decay due to recombination, which breaks apart the distinctive allelic associations inherited from the parental populations.

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CATEGORIZED UNDER: Genetics, Genomics

The layers and fault-lines of genes

By Razib Khan | November 11, 2010 4:04 pm

800px-Cross-cutting_relatio

At Genomes Unzipped Luke Jostins elaborates on how the genetic facts he now has about his paternal lineage change how he views his own personal history:

… my father’s father is Latvian, and the N1 haplogroup is not rare in the Baltic regions. In fact, the subgroup, N1c1, is more common in parts of Eastern Europe than it is in Asia.

Initially, this seemed to play nicely into a part of our ancient family history. There is a folk history, relayed to me be my Dad and my uncle Johnny, that Jostins blood may contain traces of Mongolian. The justification for this is that in around 1260, just before the civil war caused the Mongol Empire to die back in Europe, the Empire extended all the way to the Baltic States. It was at this point, my fellow N1c1-bearers hypothesise, that Mongolian DNA entered the Jostins line.

Unfortunately on closer inspection this tale is not really supported by the DNA evidence. The famous Mongol Expansion haplogroup is actually C3, which is the modal haplogroup of Mongolians. In contrast, N1c1 has existed in Europe for thousands of years, and is far to old and too wide-spread to represent a recent expansion.

dnanlargergTo the left is a frequency map of the concentration of N1c1. Based on the current distribution, and the diversity being modal in the East Baltic, one has to be skeptical of a simple east-west model. Interestingly the frequency difference of this haplogroup between Finland and Sweden is very high. Also, branch of N1c1 seems to be found among the Rurikids of Russia. This was the ruling dynasty of the Rus, a people who originally seem to have been ethnic Scandinavians from Sweden. Eventually they ruled over a polyglot state of Finns, Slavs and Scandinavians, and submerged their own identity with that of the Slavic peasants. In this they followed the example of the Bulgars, who were ethnically distinctive from their Slavic subjects, but were totally absorbed excepting that their ethnonym persisted. There is some evidence that the Serbs are a similar case, an Iranian group which was eventually absorbed into the South Slav substrate.

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CATEGORIZED UNDER: Genetics, Genomics

The naked geneticists

By Razib Khan | October 12, 2010 2:44 am

Girl_hands_out_flyer_at_Loveparade_03John Hawks, Genomes unzipped, unzipped:

What I wonder is, how much will personal genomics be like nude beaches? I mean, it’s been a long time since the first nude beaches, but most people don’t take advantage of the opportunity. Clearly, there’s variation in different countries! But most people neither feel compelled to see others’ data nor feel comfortable sharing their own.

Well, they used the word unzipped, not me!

Obviously John had his tongue-firmly-planted-in-cheek, but I have wondered about this. How deep is the impact of personal genomics going to be for individuals? If a person gets their genome sequenced and has a list of odds ratios in front of them are they going to bone up on the statistical genetic subtleties of the face value?

That is where genetic counselors come in. The necessity of interpretative experts highlights the difference between nude beaches and personal genomics: personal genomics has more potential societal impact. I know of the nudist/naturist phenomenon only tangentially, but it strikes me as similar to the broader New Age health movement. The focus is on individual health returns.  A colon cleanse simply does not have much of broader social effect. Yes, lest my nudist readers strike me down I do understand that there are purported positive social externalities, but set next to personal genomics nudism still strikes me as a fundamentally more individual activity whose benefits redound to the naked individuals, and not the broader clothed society. It does not pick my pocket nor break my leg if my neighbor is a weekend nudist. It is of no concern of mine (in contrast, my experience with public nudity is that it is generally disruptive when unexpected).

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CATEGORIZED UNDER: Biology, Genomics
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Gene Expression

This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!
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