HLA Completion

[…] using hla allele frequency (af) and linkage disequilibrium (ld) data from the same cohorts. all hla haplotypes were confirmed using the same published probabilistic method used for the homer cohort (hla completion web tool, http://boson.research.microsoft.com/hla/). only 72 (of 6392, 1.12%) missing hla-a or hla-c types were imputed due to pcr/sequencing failure at these loci or lack of sample […]

[…] (c*17:01 in the analysis, encompassing c*17:01/c*17:02/c*17:03), and c*04:01:01g (c*04:01 in the analysis, encompassing c*04:01/c*04:09n), among others. all hla haplotypes were confirmed using the hla completion web tool (available at http://boson.research.microsoft.com/hla/) (). additionally, a total of 33 hla-a or hla-c types that failed amplification or sequencing were imputed using […]

[…] kits (secore a, b and cw locus sequencing kits, thermo fisher scientific, waltham, ma). allele assignments were made with utype v6.0 (thermo fisher scientific). ambiguities were resolved using the hla completion tool available on-line []., we performed mann-whitney u tests (stata/se v12, statacorp, college station, tx) to look for associations between the presence/absence of all hla class […]

[…] typing was performed using sequence-based methods [] and imputed where necessary to high resolution using a machine learning algorithm ([]; http://research.microsoft.com/en-us/projects/bio/mbt.aspx#hla-completion). hiv-1 sequences from cohorts where rebs allow public sequence deposition have been deposited in genbank: accession numbers are gag (kj869442 - kj869609), protease-rt (kj869900 - […]

[…] learning algorithm trained on a dataset of complete high resolution hla-a, b and c types from >13,000 individuals with known ethnicity (; http://research.microsoft.com/en-us/projects/bio/mbt.aspx#hla-completion) and assigned the highest-probability allele combination. hla types could not be imputed when data were missing from more than one locus., gag and nef sequences were annotated […]