Genotyping was completed at the Center for Applied Genomics at CHOP, as previously described by Sleiman et al.14 (link). The samples were genotyped on the Illumina HumanHap550 or HH610. Standard quality control parameters were applied. Samples with chip-wide genotyping failure rate <5% were excluded from the study, as were SNPs with minor allele frequencies of <1%, genotyping failure rates of greater that 2% and Hardy-Weinberg P-values <1 × 10−6. Smartpca, a part of the EIGENSTRAT package, was used on 100,000 random autosomal SNPs in linkage equilibrium to compute principal components on the dataset, thereby determining genetic ancestry. K means clustering was used to cluster the patient samples into four continental ancestry group clusters using the kmeans package in R. These ancestry groups included Caucasian, African (including African American), Asian, and Native American/Hispanic. A risk allele was defined as a genetic variation in the gene that increased the probability of having EoE14 (link). RS3806932 was the TSLP SNP that was previously identified as being associated with EoE by Rothenberg et al. and was the TSLP risk allele that was assessed in this study1 (link).
Hh610
Manufactured by Illumina
The HH610 is a laboratory instrument designed for DNA and RNA quantification. It utilizes fluorescent dye-based detection methods to accurately measure the concentration of nucleic acid samples. The HH610 provides reliable and precise measurements to support various genomic research and molecular biology applications.
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Lab products found in correlation
3 protocols using hh610
1
Genotyping for Eosinophilic Esophagitis Risk
2
Genome-wide Association Study Quality Control
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The discovery samples were genotyped on either the Illumina HumanHap550, HH610 and the replication samples were genotyped on the Illumina HumanOmni Express-12v1 arrays at the Center for Applied Genomics at CHOP.
Standard quality control parameters were applied to the dataset, samples with chip-wide genotyping failure rate < 5% were excluded. SNPs with minor allele frequencies of < 1%, genotyping failure rates of greater that 2% and Hardy-Weinberg P-Values less that 1×10−6 were excluded from further analysis.
Genetic ancestry was determined by computing principal components on the dataset using smartpca, a part of the EIGENSTRAT package, on 100,000 random autosomal SNPs in linkage equilibrium. Samples were clustered into 4 Continental ancestry groups (Caucasian, African including admixed African-American, Asian and native American / admixed Hispanic) by K-means clustering using the kmeans package in R.
Standard quality control parameters were applied to the dataset, samples with chip-wide genotyping failure rate < 5% were excluded. SNPs with minor allele frequencies of < 1%, genotyping failure rates of greater that 2% and Hardy-Weinberg P-Values less that 1×10−6 were excluded from further analysis.
Genetic ancestry was determined by computing principal components on the dataset using smartpca, a part of the EIGENSTRAT package, on 100,000 random autosomal SNPs in linkage equilibrium. Samples were clustered into 4 Continental ancestry groups (Caucasian, African including admixed African-American, Asian and native American / admixed Hispanic) by K-means clustering using the kmeans package in R.
3
Genome-wide Association Study Quality Control
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