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 3rd 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)).
Human omni2.5 8 beadchip array
Manufactured by Illumina
Sourced in Canada
The Human Omni2.5–8 BeadChip array is a high-throughput genotyping platform designed by Illumina. The array enables the simultaneous analysis of over 2.5 million genetic variants across the human genome. It is a tool used for various genomic research applications.
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Lab products found in correlation
2 protocols using human omni2.5 8 beadchip array
1
Measles Antibody and Cytokine Response
2
Copy Number Variation Analysis Protocol
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To estimate our method's ability to identify both true regions of copy-number changes and copy-neutral regions, we analyzed a subset of 16 samples from the validation set using the 2.3 million–feature Illumina Human Omni2.5–8 BeadChip array at the Princess Margaret Genomics Centre, Toronto, Canada (http://www.pmgenomics.ca ). Each sample was processed following the Illumina Infinium LCG assay protocol, hybridized to two BeadChips, stained as per Illumina protocol, and scanned on an Illumina iScan. The data files were quantified and normalized in the GenomeStudio version 2010.2 genotyping module using HumanOmni25-8v1-1_C.bpm manifest.
To call CNVs, data were exported from Genome Studio and uploaded into Biodiscovery Nexus v7.5 program. The significance threshold for segmentation was set at 1 × 10−8 and also required a minimum of three probes per segment and a maximum probe spacing of 1,000 between adjacent probes before breaking a segment. The log ratio thresholds for single-copy gain and single-copy loss were set at 0.13 and −0.23, respectively. Systematic GC wave correction was applied using Linear Correction with the HumanOmni2-5-8v1-1-C_hg19_illum_correction.txt file.
To call CNVs, data were exported from Genome Studio and uploaded into Biodiscovery Nexus v7.5 program. The significance threshold for segmentation was set at 1 × 10−8 and also required a minimum of three probes per segment and a maximum probe spacing of 1,000 between adjacent probes before breaking a segment. The log ratio thresholds for single-copy gain and single-copy loss were set at 0.13 and −0.23, respectively. Systematic GC wave correction was applied using Linear Correction with the HumanOmni2-5-8v1-1-C_hg19_illum_correction.txt file.
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