Genomic DNA was extracted from blood or saliva samples of study participants (n = 1,211). FLG variants R501X, 2282del4, and S3247X were genotyped using GoldenGate Genotyping Assays on the BeadXpressVeracode platform (Illumina, Inc, SanDiego, CA, USA) per Illumina’s protocol. Individuals carrying the minor allele for at least one of the FLG variants R501X, 2282del4, or S3247X were classified as having filaggrin haploinsufficiency. Detailed information on FLG genotyping is provided by Ziyab et al.17 (link). Single nucleotide polymorphisms (SNPs; n = 13; rs8832, rs1110470, rs1805011, rs1805012, rs2057768, rs3024604, rs3024622, rs3024676, rs3024685, rs4787423, rs6498012, rs12102586, and rs16976728) spanning the genomic region of IL4R gene were selected for genotyping based on a tagging scheme aiming to capture common/functional genetic variants that are related to allergic conditions across the IL4R gene18 (link) (see Supplementary Methods online for detailed information on genotyping).
Beadxpressveracode platform
Manufactured by Illumina
Sourced in United States
The BeadXpressVeracode platform is a high-throughput genotyping system designed for large-scale genomic analysis. It utilizes bead-based technology to perform multiplexed genetic assays, enabling the simultaneous analysis of multiple genetic markers in a single reaction. The platform provides a flexible and efficient solution for researchers and clinicians seeking to conduct comprehensive genomic studies.
Automatically generated - may contain errors
8 protocols using beadxpressveracode platform
1
Genotyping FLG and IL4R variants
2
Genotyping of Filaggrin Variants
3
Genotyping FLG Null Variants
4
Prenatal and Early Life Factors Affecting Eczema
5
Genetic Analysis of Asthma and Allergies
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A whole population birth cohort was established in the Isle of Wight, UK, in 1989 to prospectively study the natural history and etiology of asthma, eczema, and allergic conditions. A total of 1,456 children were followed up at 1, 2, 4, 10, and 18 years, as described elsewhere [15 (link)]. Blood or saliva samples were collected at the ages of 10 and 18 years for genetic analysis.
In the IOW cohort, DNA was measured using Illumina Infinium HumanMethylation450 BeadChips (Illumina, Inc., San Diego, CA, USA), as previously described [15 (link)]. The TNFα SNPs rs1800610 (an intron variant) was determined using Golden Gate Genotyping Assays (Illumina, Inc., San Diego, CA, USA) on the Bead Xpress Veracode platform (Illumina, Inc., San Diego, CA, USA). In brief, samples were fragmented and hybridized to the pool of allele-specific primer sets. Following an extension/ligation reaction, the samples were then hybridized to the Veracode bead pool and processed on the BeadXpress reader. Data were analyzed using the genotyping module of the GenomeStudio software package (Illumina, Inc., San Diego, CA, USA). The quality threshold for allele determination was set at a GenCall score 0.25 (scores #0.25 were ‘no calls’) with 98.3% and retained for further analysis.
In the IOW cohort, DNA was measured using Illumina Infinium HumanMethylation450 BeadChips (Illumina, Inc., San Diego, CA, USA), as previously described [15 (link)]. The TNFα SNPs rs1800610 (an intron variant) was determined using Golden Gate Genotyping Assays (Illumina, Inc., San Diego, CA, USA) on the Bead Xpress Veracode platform (Illumina, Inc., San Diego, CA, USA). In brief, samples were fragmented and hybridized to the pool of allele-specific primer sets. Following an extension/ligation reaction, the samples were then hybridized to the Veracode bead pool and processed on the BeadXpress reader. Data were analyzed using the genotyping module of the GenomeStudio software package (Illumina, Inc., San Diego, CA, USA). The quality threshold for allele determination was set at a GenCall score 0.25 (scores #0.25 were ‘no calls’) with 98.3% and retained for further analysis.
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Filaggrin Haploinsufficiency Genotyping
7
Filaggrin Genotyping for Haploinsufficiency
8
Genetic Variation Analysis of HPV Receptor Genes
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The Haploview software 4.2 (Mark Daly' s lab of Broad Institute, Cambridge, MA, Britain) was used to analyze the tagSNPs and haplotype block based on the CHB (Chinese Han Beijing) population data of HapMap (HapMap Data Rel 27 PhaseII +III, Feb09, on NCBI B36 assembly, dbSNP b126 (International HapMap Project), a total of 96 SNPs in 8 HPV receptor and associated genes (EGFR, PPIB, HSPG2, FGFR2, FURIN, ITGA6, TSPAN1 and SDC2) were genotyped. Validated tagSNPs were selected with a MAF > 5% in the HapMap Asia population. SNPs that satisfied the following criteria were considered for detection: 1) tagSNPs were preferentially selected, 2) those SNPs were previously reported to be frequent in Chinese population (http://www.ncbi.nlm.nih.gov/snp ). The total genomic DNA was extracted from the cervical exfoliated cells using KoningTM Mutisource Genomic DNA Extration Kit-Mini and PureLink® Genomic DNA Kits (invitrogen). The DNA concentration was detected, agarose gel eletrophoresis was run and the final concentration was quantified to 50 ng/μl. All the SNPs were genotyped by Illumina BeadXpress VeraCode platform (USA), according to the manufacturer's protocol.
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