There is such a wealth of information in this press release from the University of Pennsylvania titled Genetic Study Led by University of Pennsylvania and Cornell Clarifies African and African-American Ancestry. I’d like to focus on one aspect, namely one of the important advances: “A technique which can reliably distinguish African and European ancestry for any particular region of the genome in African-Americans.” How do they do that?

There are two key parts to doing this.

First the researchers needed a massive amount of genetic information about many individuals so that they could determine just what is African and European derived DNA. Instead of doing a massive amount of sequencing, they took advantage of microarray technology. This involved using a microscope slide with 500 000 spots of DNA stuck to it. The 500 000 spots correspond to 500 000 regions of the genome where we already know people have genetic variation (i.e. single nucleotide polymorphisms, that is, an A in some people but a T in others). When you put the DNA of an individual on that microscope slide it binds to those DNA spots (remember DNA likes to form double strands). The DNA is labeled with a fluorescent tag, so using scanners shows differences in binding at each spot. The differences in binding reveal the allele at that specific location (A or T, for example).

The key is having lots of information from lots of people. In this study they used 365 African-Americans, 203 West Africans from 12 populations and 400 Europeans from 42 countries.

The second key part is how to deal with all that information? The researchers used a data reduction technique called Principle Component Analysis. This is a great way of looking at a large amount of information in a way that makes sense. Basically what happens is that all the individuals are sorted by how similar their profiles are (those 500 000 pieces of information) and then mapped out in 2D. You can see the results for the West African populations on the right.

What’s nice, and also expected, is that different geographic populations group together on the PCA. That lends support to the technique, and tells us that the information they are working with can distinguish individuals in specific West African population. Imagine if you were given a DNA sample of an individual from one of those populations. You can analyse that DNA with a microarray and then plot that profile onto the PCA. It would tell you with some certainty where that individual was from. That’s exactly what the researchers set out to do with African Americans. The results of that plots are shown on the left.

That pink band across the top are all the individual African Americans. Some points fall clearly in the range of the West African populations, which others sit directly in the European populations. Which is where the press release is able to say: “People who identify as African-American may be as little as 1 percent West African or as much as 99 percent.”

(via Discovering Biology in a Digital World and Penn State Press Release)

Citation:

Katarzyna Bryc, Adam Auton, Matthew R. Nelson, Jorge R. Oksenberg, Stephen L. Hauser, Scott Williams, Alain Froment, Jean-Marie Bodo, Charles Wambebe, Sarah Tishkoff, and Carlos D. Bustamante. Genome-wide patterns of population structure and admixture in West Africans and African Americans. PNAS published online before print December 22, 2009, doi:10.1073/pnas.0909559107