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Techniques to infer admixture using genome-wide autosomal DNA 2
Published on May 31, 2022 28 min
A selection of talks on Biochemistry
The ERK1/2 MAPK cascade
- Prof. Melanie H. Cobb
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Amino acid conjugation: mechanism and enzymology
- Dr. Kathleen Knights
- Flinders University, Australia
Next, we'll talk about the program GLOBETROTTER, which similarly can identify and date admixture assuming a pulse model. As can a more efficient, recently released program called fastGLOBETROTTER.
I'll describe the intuition of this approach briefly on this slide. These programs use a technique called chromosome painting that takes in individuals genetic variation data, such as h_4 here, at a five SNP sequence and compares it to those from a set of surrogate populations represented here by different colors, h_1, h_2 and h_3. Here, h_4 matches the first two SNPs to h_1. The last three you see can match h_2. We color or paint h_4 to show this matching. GLOBETROTTER and fastGLOBETROTTER use the program CHROMOPAINTER to do this painting. According to this, it looks like h_4 is a mixture of the populations represented by h_1 and h_2, with one block of SNPs inherited from the blue population and the other block from the red population. The programs then measure how the correlation amongst these blocks decays with genetic distance between the blocks. The decay should follow an exponential distribution with rate equal to when the admixture occurred. This is quite similar to the approach of ALDER/MALDER. But in contrast, these programs incorporate haplotype information in the way that they consider blocks of contiguous SNPs, rather than analyzing each SNP independently. This can increase power in certain situations.
Running GLOBETROTTER, with fastGLOBETROTTER run in a nearly identical way, requires three steps. First, another program that I had previously mentioned, CHROMOPAINTER, which is described in Lausanne et al. 2012, has to be run twice. The first time it is run to paint sampled individuals from surrogate populations against each other. The second time is to paint sampled individuals in the admixed target population against the surrogates. We then run GLOBETROTTER or fastGLOBETROTTER using the combined results from steps 1 and 2. To run this, first extract the files in both of these programs and compile them using their provided instructions.