Samples were genotyped for rs12143842 using 5 different platforms: Illumina Infinium Global Screening Array; Affymetrix Genome‐wide Human SNP Array 6.0; Agena Biosciences MassARRAY; Applied Biosystems Taqman real‐time polymerase chain reaction; and Illumina TruSeq sequencing. All genotyping and sequencing were performed according to the manufacturer's instructions. Quality control was performed separately on each data set before merging. Data set and quality control information are summarized in Table S1 . Overlapping samples between platforms were used to evaluate the accuracy of the genotyping (reported in Table S2 ). Using 1576 samples run on multiple platforms, 1957 pairwise comparisons were performed demonstrating a >99.9% concordance rate between the genotyping platforms. After exclusions, the study population included 2282 individuals with SCD and 3561 Finnish controls.
Massarray
Manufactured by Thermo Fisher Scientific
Sourced in United States
The MassARRAY is a high-throughput genotyping platform designed for efficient and accurate analysis of genetic variations. It utilizes matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry technology to detect and analyze single nucleotide polymorphisms (SNPs) and other genetic markers.
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Lab products found in correlation
2 protocols using massarray
1
Genotyping Accuracy Across Multiple Platforms
2
Tagging Circadian Clock Genes
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Based on publicly available HapMap-CEU data (Release #28; http://hapmap.ncbi.nlm.nih.gov/index.html.en ) and the tagger function of Haploview 4.2 (http://www.broadinstitute.org.haploview/haploview ), we identified 121 SNPs tagging all common SNPs (minor allele frequencies ≥ 0.05) in the ARNTL, ARNTL2, CLOCK, CRY1, CRY2, PER1, PER2, PER3, and TIMELESS loci (gene regions and up to 5 kb of 5’- and 3’-flanking regions) with an r² ≥ 0.8. Information about the genomic localisation of the tagging SNPs is given in S1 Table . For genotyping, DNA was isolated from whole blood using a commercial kit (NucleoSpin, Macherey & Nagel, Düren, Germany). The tagging SNPs were genotyped by mass spectrometry (massARRAY, Sequenom, Hamburg) and the manufacturer’s iPLEX software, and SNPs that resisted massARRAY’s multiplex design were genotyped with TaqMan assays (Applied Biosystems, Foster City, CA, USA). Eleven SNPs were excluded from further analyses due to failure to achieve Hardy-Weinberg equilibrium (p < 0.05). The genotyping results including call rates, minor allele frequencies, and p-values for Hardy-Weinberg equilibrium are given in S1 Table . The 110 tagging SNPs that were followed-up in association analyses covered 76% of common SNPs in ARNTL, 79% in ARNTL2, 99% in CLOCK, 97% in CRY1, 100% in CRY2, 86% in PER1, 83% in PER2, 56% in PER3, and 100% in TIMELESS.
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