We performed single nucleotide polymorphism (SNP) genotyping by using an Illumina Asian Screening Array-24 v1.0 BeadChip, following the Illumina Infinium HTS Assay protocol (Illumina, San Diego, CA, USA). The array platform contained 659,184 SNPs probes across the genome. We applied standard SNP quality control filters to exclude SNPs with a low call rate of <98%, a missing genotype rate per individual of >10%, a missing genotype rate per SNPs of >5%, gender inconsistency based on the heterozygosity rate of the X chromosome (maleTh =0.8, femaleTh =0.2), Hardy-Weinberg equilibrium test (P<1E-06), minor allele frequency (MAF) of each SNP of <0.01, and genome-wide estimates of identity-by-descent (pihat) ≥0.185 (3rd generation). We were left with 443,063 variants after quality control.
Infinium hts assay protocol
Manufactured by Illumina
Sourced in United States
The Infinium HTS Assay protocol is a high-throughput genotyping solution from Illumina. It is designed to analyze genetic variations across the genome. The protocol utilizes Illumina's proprietary bead array technology to generate reliable and accurate genotyping data from DNA samples.
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2 protocols using infinium hts assay protocol
1
Genome-wide SNP Genotyping and Quality Control
2
Spanish Population Genomic DNA Genotyping
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The discovery phase samples were genotyped with the Axiom Spain Biobank Array (Thermo Fisher Scientific) following the manufacturer’s instructions in the Santiago de Compostela Node of the National Genotyping Center (CeGen-ISCIII; http://www.usc.es/cegen ). This array contains 757 836 markers, including rare variants selected in the Spanish population. Genomic DNA was obtained from peripheral blood and isolated using the Chemagic DNA Blood100 kit (PerkinElmer Chemagen Technologies GmbH), following the manufacturer’s recommendations.
For the second phase study samples, a total of 250 ng of DNA was processed according to the Infinium HTS assay Protocol (Part # 15045738 Rev. A, Illumina), including amplification, fragmentation and hybridization using the Global Screening Array Multi-disease v3.0. This array contains a total of 730 059 markers and was scanned on an iScan platform (Illumina, Inc.). Clustering and genotype calling were performed using Genome Studio v2.0.4 (Illumina, Inc.).
For the second phase study samples, a total of 250 ng of DNA was processed according to the Infinium HTS assay Protocol (Part # 15045738 Rev. A, Illumina), including amplification, fragmentation and hybridization using the Global Screening Array Multi-disease v3.0. This array contains a total of 730 059 markers and was scanned on an iScan platform (Illumina, Inc.). Clustering and genotype calling were performed using Genome Studio v2.0.4 (Illumina, Inc.).
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