PMC:4129407 / 8173-9253 JSONTXT

{"project":"2_test","denotations":[{"id":"25087609-23080122-2044419","span":{"begin":354,"end":356},"obj":"23080122"},{"id":"25087609-23762245-2044420","span":{"begin":568,"end":570},"obj":"23762245"},{"id":"25087609-23762245-2044421","span":{"begin":1078,"end":1080},"obj":"23762245"},{"id":"25087609-24656864-2044421","span":{"begin":1078,"end":1080},"obj":"24656864"}],"text":"To expand our HLA imputation protocol into HLA-like genes, we constructed a reference panel for imputation of MICA variants. We obtained classical four-digit MICA alleles for the subjects from a subset of the PsA data set (n = 1,046). These samples were not selected in any particular way. We obtained MICA amino acid sequences from the IMGT/HLA Database32 and the encoded MICA amino acid polymorphisms of the subjects, as well as the genotypes of MICA classical alleles and the genotyped SNPs in the MHC region. Using the constructed MICA reference panel and SNP2HLA,24 we imputed MICA variants for the other data-set collections. Imputed genotypes of the MICA alleles and MICA amino acid polymorphisms were extracted and merged into those obtained from HLA imputation mentioned in the previous section. We empirically assessed the accuracy of imputing MICA variants by additionally genotyping MICA in a subset of the subjects from the PAGE Immunochip data set (n = 104) and comparing concordances of the imputed and genotyped classical MICA variants as described elsewhere.24,26"}