Evolutionary Genetics
Short comment: Enough mathematical formalism to be technically illuminating, but not so much as to be opaque to the non-specialist.
Evolutionary Genetics
Short comment: Enough mathematical formalism to be technically illuminating, but not so much as to be opaque to the non-specialist.
Who are those Houston Gujus?
The figure to the left is a three dimensional representation of principal components 1, 2, and 3, generated from a sample of Gujaratis from Houston, and Chinese from Denver. When these two populations are pooled together the Chinese form a very homogen…
D.I.Y. population structure inference, part 1 of many
If you’ve been reading this weblog for a while you’ve seen many images like the one above. It comes from the 2008 paper Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation. The data set is from the Human Genome D…
A problem of aggregation of information
In a post below I regenerated the HGDP PCA plot you’ve probably seen around, except that I added my parents (and a few HapMap populations) into the plot. The PCA below was basically a visualization of the two largest independent dimensions of ge…
“Inadvertent” incest detection?
Ruchira and Randall Parker point me to a new story about routine genomics screens detecting first degree incest:
Beaudet wrote in the letter that “clinicians uncovering a likely incestuous relationship may be legally required to report it to chil…
“Inadvertent” incest detection?
Ruchira and Randall Parker point me to a new story about routine genomics screens detecting first degree incest:
Beaudet wrote in the letter that “clinicians uncovering a likely incestuous relationship may be legally required to report it to chil…
D.I.Y. PCA
Long time readers know that I have a fixation on people not taking PCA too literally as something concrete. Tonight I finally merged the HGDP data set with some of the HapMap ones I’ve been playing with, and tacked my parents onto the sample. I…
Swedes not so homogeneous?
Credit: David Shankbone
The more and more I see fine-scale genomic analyses of population structure across the world the more and more I believe that the “stylized” models which were in vogue in the early 2000s which explained how the worl…
Personal genomics around the web
Just some pointers. Dr. Daniel MacArthur has put up a guest post where I outline my own experience with personal genomics. Cool times that we live in. Also, Zack Ajmal has started posting higher K’s of HAP participants. He’s now in the second batch. My parents will be in the third. Lots of Tamils and […]
My genetic odyssey
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.
Counting beans the proper way
Apropos of several of my recent posts, The New York Times has an interesting article up, Counting by Race Can Throw Off Some Numbers. Basically it outlines the difficulty of enumerating different racial and ethnic groups for different purposes in a mor…
Inferring and visualizing patterns in genomic data
I’ve been playing around with ADMIXTURE and EIGENSOFT with the the HapMap data set along with a few friends & family merged into it. It is interesting to see how the intuitive inferences you make from ADMIXTURE bar plots differ somewhat from …
Why race will matter after we all get our full sequences
In my post “Health care costs and ancestry”, a commenter says:
“Race” is a concept that should have died with disco. I imagine it will soon be feasible for every patient to have their genome analysis included in their medical file and t…
Jacob’s Legacy: A Genetic View of Jewish History
Link to review: Jacob’s Legacy: A Genetic View of Jewish History.
Health care costs and ancestry
The Pith: In this post I examine the relationship between racial ancestry and cancer mortality risks conditioned on particular courses of treatment. I review research which indicates that the amount of Native American ancestry can be a very important …
Personal genomics in two dimensions
The Pith: In this post I take a different tack at genetic data visualization. Instead of bar plots, I show how genetic relationships can be explored using two dimensional spaces.
Last week I suggested that in some ways I had hit a wall of sharply reduc…
Does your twin have “rights” on your genomes?
Randall Parker asks, Genetic Privacy And Identical Twins:
Suppose you have a right to genetic privacy. You might believe you do. Suppose you have an identical twin. Suppose the identical twin decides to publish his (or her) genetic sequence on the web….
Your genome is mine! (?)
Guest blogging at Genetic Future Mischa Angrist has a post up critiquing the defense of the lack of disclosure of genetic/genomic information to research participants. Mischa begins:
Readers of Genetic Future, Genomics Law Report and Genomes Unzipped …
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…