Infinium omni 1m quad snp array

The genome-wide SNP typing was performed using the Infinium Omni 1M-Quad SNP array (Illumina; San Diego, CA) for the Rochester cohort, Illumina Human Omni2.5–8 BeadChip array for the US cohort, and Illumina Infinium HumanHap550v3_A or HumanHap650Yv3 BeadChip arrays for the San Diego cohort. Measles-specific neutralizing antibody and cytokine responses were quantified using a fluorescence-based plaque reduction microneutralization assay (PRMN) and ELISPOT/ELISA assays, as previously described (Haralambieva et al. 2011b (link)). Our humoral immune response phenotype, the 50% end-point titer (Neutralizing Doze, ND₅₀), was calculated using Karber’s formula and transformed into mIU/mL (using the 3^rd WHO international measles antibody standard), as described previously (Haralambieva et al. 2011b (link)). The variability of the PRMN assay, calculated as a coefficient of variation (CV) based on the log-transformed ND₅₀ values of the third WHO standard, was 5.7%, as previously published (Haralambieva et al. 2011b (link)).

Our HLA genotyping procedures are similar or identical to what we have previously published [5 (link), 11 ]. HLA class I A, B, and C typing was implemented using high-resolution SSP (sequence-specific primer) A, B, and C Unitray typing assays (Invitrogen), respectively. HLA class II typing was done with high-resolution DRB1-SSP, DQA1-SSP, DQB1-SSP, DPA1-SSP, and DPB1-SSP Unitray typing assays (Invitrogen). All PCR amplifications were completed on an ABI-377 (Applied Biosystems) and examined using MatchTools (Applied Biosystems) software. The genome-wide SNP typing for the Rochester cohort (n=706) was performed using the Infinium Omni 1M-Quad SNP array (Illumina, San Diego, CA). The genome-wide SNP typing for the San Diego cohort (n=1,012) was performed using the Infinium HumanHap550 BeadChip array (Illumina, San Diego, CA) for the self-declared Caucasian subjects, and the 650K Infinium HumanHap650Y SNP BeadChip array for the subjects indicating their race as either African-American or unknown [19 (link)].