In the part II of my experimental analysis, we are going to discuss a promising alternative to the standard ADMIXTURE analysis. This alternative is the combination of STRUCTURE and LAMP analysis.
LAMP (Local Ancestry in adMixed Populations) is a software for the inference of locus-specific ancestry in recently admixed populations(
Sriram Sankararaman, Srinath Sridhar, Gad Kimmel and Eran Halperin, Estimating Local Ancestry in Admixed Populations, The American Journal of Human Genetics, Volume 82, Issue 2, 290-303, 2008). LAMP computes the ancestry structure for overlapping windows of contiguous SNPs and combines the results with a majority vote.Basically, LAMP allows to reconstruct fine-scale chromosomal patterns of admixture and visualize them in a manner, which is similiar to 23andme's Ancestry Painting.
The input genotype file for LAMP can be easily converted from PLINK by running plink --recodeA command, removing first line and first six columns of output file and replacing NA with "-1". For my dirty and quick experiment with LAMP i used 8271 SNPs from Chr.22, which i converted to LAMP and STRUCTURE input formats. Since the LAMP algorithm for P>2 requires estimated allele frequencies for all populations in dataset, i first ran on my dataset the Bayesian clustering algorithm
STRUCTURE еo estimate ancestral allele frequencies and assess admixture proportions within and among populations in my dataset (Russians, Orcadians, Romanians, Hungarians, Belorussians and Lithuanians). I also included the following participants of my project:
| V161 |
| V162 |
| V163 |
| V164 |
| V165 |
| V201 |
| V202 |
| V166 |
| V167 |
| V168 |
| V169 |
| V170 |
| V171 |
| V172 |
| V173 |
| V174 |
| V175 |
| V176 |
| V177 |
| V178 |
| V179 | | | | | | | |
The results of this simplified STRUCTURE run (same as unsupervised ADMIXTURE analysis) for Chr.22 are included in Google spreadsheet:
After estimating ancestral allele frequencies (gprob1, gprob2, grpob3, grpob4 etc.) i entered the recombination rate, the number of generations/individuals to analayze allele frequencies, and estimated alpha values (the rest of options remained unchanged). Then I used LAMP to reconstruct for each individual in our data set, segments of different ancestry across Chr.22 in all admixed and putative source population individuals.
The visualization of ancestral segments
Interesting stuff...I am V179...the c3/c5 most resembles V175....who is....? ( Names not necessary, what is your background?)
ReplyDeleteI am curious as to how you match the LAMP results back with the SNP identifying information? I have been running LAMP but it seems silly that you strip out all of the identifying information for both the individuals and the genetic variants prior to the run. Combined with LD pruning during the run, it seems like this makes it very difficult to match the results back up to the identifiers.
ReplyDeleteBen,
ReplyDeleteThis was my first experiment with LAMP, i would suggest you tocomment on my recent experiment with LAMP
http://magnusducatus.blogspot.com/2011/05/experimental-test-iii-deconstructing.html