HLA Completion: New method

Oct 13, 2008 at 5:18 PM

We've replaced the HLA Completion tool with a new method based on 

Listgarten J, Brumme Z, Kadie C, Xiaojiang G, Walker B, et al. 2008 Statistical Resolution of Ambiguous HLA Typing Data. PLoS Computational Biology 4(2): e1000016 doi:10.1371/journal.pcbi.1000016

(paraphrasing the abstract)
The new method improves upon the Expectation-Maximization (EM)-based approaches currently used within the HLA community. Our improvements are achieved by using a parsimonious parameterization for haplotype distributions and by smoothing the maximum likelihood (ML) solution. These improvements make it possible to scale the refinement to a larger number of alleles and loci in a more computationally efficient and stable manner. We also show how to augment our method in order to incorporate ethnicity information (as HLA allele distributions vary widely according to race/ethnicity as well as geographic area).

- Carl