Why siblings differ differently
The Pith: In this post I examine how looking at genomic data can clarify exactly how closely related siblings really are, instead of just assuming that they’re about 50% similar. I contrast this randomness among siblings to the hard & fast de…
My family’s Neandertal genes, ii
Last week I reported that it turns out that one of my siblings carry a possible Neandertal haplotype on the dystrophin gene. To review, it seems likely that ~3% of the average non-African’s genome is derived from Neandertal populations. But by an…
A genomic map of human variation, where we’re at
Zack has started exploring the K’s of his merged data set for HAP. A commenter suggests that:
As you have begun interpreting the reference results, let me make a friendly warning: you have to keep in mind that most of the reference populations of…
Harappa Ancestry Project, t-minus one day
Zack is going to post the first batch of results from HAP tomorrow. It looks like he’s going to be using mostly the merged HGDP, HapMap, SVGP, and Behar data set, supplemented by a second set which also merges the Xing et al. sample (the intersec…
“Asian” in all the right places
mtDNA haplogroup G1a2
The pith: In this post I examine the most recent results from 23andMe for my family in the context of familial and regional (Bengal) history. I also use these results to offer up a framework for the ethnognesis of the eastern Ben…
Harappa Ancestry Project, before the first wave
Zack has been posting his data sources, as well as how he filtered and formatted them, all this week. I assume that the first wave of results will be online soon. As of yesterday, this is what he had (I know he got some more today):
– Punjab 7
– Bengal…
Harappa Ancestry Project, before the first wave
Zack has been posting his data sources, as well as how he filtered and formatted them, all this week. I assume that the first wave of results will be online soon. As of yesterday, this is what he had (I know he got some more today):
– Punjab 7
– Bengal…
Neandertal (haplotype) in the family!
There is pretty much a 100% probability that I carry Neandertal origin genes, since I’m Eurasian. That being said, I hadn’t looked too closely into the matter in regards to my own genome, because the whole “which SNPs are Neandertal&#…
Visualizing variation, input → output
I have noted a few times that one thing you have to be careful about in two dimensional plots which show genetic variance is that the dimensions in which the data are projected upon are often generated from the data itself. So adding more data can chan…
Me, myself, and Myanmar
I have spoken of my somewhat atypical, for a South Asian, genetic results before. Recently Dienekes performed some cluster analysis which confirmed the initial findings, while adding a little detail: I am DOD075. The Southeast Asian component is modal in Malays, while the East Asian component is modal in the North Chinese. Vietnamese and Cambodians […]
Ron Bailey Unzipped
Over at Reason Ron Baily has an excellent piece up, I’ll Show You My Genome. Will You Show Me Yours? He reviews his results from two genotyping chips, and has placed his results online. I doubt readers of this weblog will learn anything that new, though the article might prove illuminating to friends & family. […]
On that Native American ancestor
Traces of Sub-Saharan African and Amerindian admixture in old stock European Americans:
Some people like to overestimate extra-European admixture in old stock Americans, while others take the position that it never happened. It did happen, and I can prove it, but certainly not to a great extent, otherwise I wouldn’t be bending over backwards to find […]
My Dodecad results
A few days ago Dienekes opened up the Dodecad project to a wider range of Eurasians. I decided to send my 23andMe sample to Dienekes ASAP, and the results came back today. I’m DOD075. Dienekes also just put up an explanation of the 10 ancestral components he’s generating from ADMIXTURE (along with tree-like representations of […]
The naked geneticists
John 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 […]
Genomes Unzipped – the naked sequence
Looks like Dr. Daniel MacArthur & company went and did it, go get their genotypes, or browse them online. This should be interesting. Since Dr. MacArthur’s wife has agreed to be a participant in some ways Tobias MacArthur is also part of the project by implication. To some extent the same is true of the […]
The confusions of genetic relatedness
Last spring I posted ‘Beyond visualization of data in genetics’ in the hopes that people wouldn’t take PCA too far in assuming that the method was a reflection of reality in a definite fashion. Remember, PCA visualizations are showing you two, and at most three, dimensions in genetic variation within the data set at any […]
Personal genomics & the state
Dr. Daniel MacAthur & Dan Vorhaus offer their takes on the recent hearings in Congress on the direct-to-consumer genomics industry, A sad day for personal genomics & “From Gulf Oil to Snake Oil”: Congress Takes Aim at DTC Genetic Testing. I guess I lean toward light regulation. I don’t think that DTC personal genomics will […]
“Unzipped,” not the film about Isaac Mizrahi
Just got notice of a new weblog, Unzipped, which I have added to my RSS feed. One of the primary contributors is Dr. Daniel MacArthur of Genetic Future (no, he’s not leaving ScienceBlogs!). Another is the always impressive Luke Jostins. Here’s their raison d’etre:
Welcome to Genomes Unzipped, a new group blog bringing together experts in […]
Project your own probability
By now you’ve probably stumbled onto Wired’s profile of Sergey Brin, and his quest to understand and overcome Parkinson’s disease through the illumination available via genomic techniques. I want to spotlight this section:
Not everyone with Parkinson’s has an LRRK2 mutation; nor will everyone with the mutation get the disease. But it does increase the chance […]