Bead express

Manufactured by Illumina

Sourced in United States

The Bead Express is a lab equipment product offered by Illumina. It is a versatile device designed for the efficient preparation and processing of bead-based samples. The core function of the Bead Express is to automate and streamline the sample preparation workflow, enabling users to consistently and reliably process their samples.

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Lab products found in correlation

Bovinehd beadchip, by Illumina (1 mentions) Bovinehd beadchip array, by Illumina (1 mentions)

Spelling variants of this product

Human Omni Express Exome Bead Chip Kit (3 citations) Bead Express platform (2 citations)

5 protocols using bead express

Genotyping of Non-HLA Variants in Type 1 Diabetes

Cited 3 times

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Individuals enrolled in DAISY were genotyped for selected non-HLA SNPs. Genotyping included the following methods: custom Taqman SNP genotype-based OpenArray platform (Applied Biosystems, Carlsbad, California, rs229541, rs2292239, rs7020673, rs2290400, rs4788084, rs11203203, rs3788013, and rs10517086), linear array or immobilized probe methods (as described by Mirel et al,^{26 (link)} INS23Hph1/rs689, rs2476601), and Illumina GoldenGate Beadexpress assays (rs12251307, rs11755527, and rs10509540). The methodology for the SNP collection, processing, and analysis in DAISY has been described previously.^{27 (link)–33 (link)}SNPs were selected for consideration in the current study if they were significantly (nominal P < .05) related to onset of T1D in previous DAISY publications and/or were included in the T1D genetic risk score model proposed by Winkler et al^{34 (link)} that was applied to the DAISY study population in Frohnert et al.^{30 (link)} SNPs selected for the analysis include the following: rs2476601 (PTPN22), rs689 (INS), rs11203203 (UBASH3A), rs3788013 (UBASH3A), rs229541 (C1QTNF6), rs10517086 (unknown), rs7020673 (GLIS3), rs12251307 (IL2RA), rs2292239 (ERBB3), rs2290400 (GSDMB), rs11755527 (BACH2), rs4788084 (IL27), and rs10509540 (RNLS/C10orf59) (Table S1).

Carry P.M., Vanderlinden L.A., Johnson R.K., Dong F., Steck A.K., Frohnert B.I., Rewers M., Yang I.V., Kechris K, & Norris J.M. (2020). DNA methylation near the INS gene is associated with INS genetic variation (rs689) and type 1 diabetes in the Diabetes Autoimmunity Study in the Young. Pediatric diabetes, 21(4), 597-605.

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Validating SNV Genotype Concordance

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We evaluated the genotype concordance between the SNVs and SNP panel genotype data of Gyr_1, Gyr_2, Girolando_1, Girolando_2, Girolando_3, and Guzerat_2 samples to verify and validate the quality of the identified SNVs. The genotype quality control (QC) was not carried out. A python script was used to compare the SNV calling to the Bovine HD BeadChip array (Illumina, San Diego, USA). The script stored the final report file output from the Illumina Bead Express software used with the BovineHD BeadChip and compared each called locus to its counterpart in the variant calling format (VCF) file containing the SNV calling from the whole-genome sequencing.

Stafuzza N.B., Zerlotini A., Lobo F.P., Yamagishi M.E., Chud T.C., Caetano A.R., Munari D.P., Garrick D.J., Machado M.A., Martins M.F., Carvalho M.R., Cole J.B, & Barbosa da Silva M.V. (2017). Single nucleotide variants and InDels identified from whole-genome re-sequencing of Guzerat, Gyr, Girolando and Holstein cattle breeds. PLoS ONE, 12(3), e0173954.

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ARDS Genetic Marker Profiling

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We extracted peripheral blood leukocyte DNA from 842 patients: 690 had ARDS, and 152 were classified as at-risk. We genotyped all markers using a multiplexed bead array assay run on a BeadExpress platform (Illumina, San Diego, California) as part of a larger study. We attained a genotyping call rate of 99.8%. We included 17 blinded internal replicates representing 2.0% of the sample set. The duplicate concordance rate was 99.6%. Because Caucasian patients represented the large majority of patients both locally and within ARDS Network data and there were very few non-Caucasian patients in the at risk cohort, we analyzed only samples from Caucasian patients to optimize the signal-to-noise ratio and avoid severe confounding by race.

Brown S.M., Grissom C.K., Rondina M.T., Hoidal J.R., Scholand M.B., Wolff R.K., Morris A.H, & Paine R I.I.I. (2014). Polymorphisms in key pulmonary inflammatory pathways and the development of acute respiratory distress syndrome. Experimental lung research, 41(3), 155-162.

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DNA Extraction and Genotyping Protocol

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DNA was extracted from white blood cells by a standard salting-out protocol [24 (link)]. DNA quality was assessed by absorption at 260 and 280 nm. Samples were aliquoted into 96 well plates for analysis. Genotyping for all selected SNPs, except rs1048943 and rs4646903, was carried out using the Illumina Bead Express platform that employs VeraCode technology (Illumina, San Diego, CA, USA). Rs1048943 and rs4646903 were genotyped by TaqMan™ assays (LifeTechnologies/Applied Biosystems, Carlsbad, CA, USA) in a 384 well plate format using an Applied Biosystems 7900 PCR system. About 7% of samples were run in duplicate for both SNP genotyping assays. Deletions in GSTM1 and GSTT1 were determined using TaqMan Copy Number Assays™ with RNase P as the control gene. Samples were run in triplicate and CopyCaller™ Software was used for determination of the copy number. The Bead Express for the genotyping was run by Dr. Robin J. Leach, Co-Director of the Genomics Resource Core of the University of Texas, Health Services Center, School of Medicine, San Antonio. The JAK2 V617F testing was completed by Dr. Mingjiang Xu at Mt. Sinai School of Medicine.

Gross-Davis C.A., Heavner K., Frank A.L., Newschaffer C., Klotz J., Santella R.M, & Burstyn I. (2015). The Role of Genotypes That Modify the Toxicity of Chemical Mutagens in the Risk for Myeloproliferative Neoplasms. International Journal of Environmental Research and Public Health, 12(3), 2465-2485.

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Retrospective Study of Pharmacogenomic Data

Cited 1 time

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Data from the years 2001 to 2018 were obtained from the Synthetic Derivative, a deidentified database of approximately 2.8 million patients derived from our institution’s electronic medical record, for a retrospective cohort study.(16 (link)) This study was approved by the institutional review board (number 190780), and formal patient consent was waived. CYP2C19 genotyping data were obtained from Vanderbilt’s PREDICT pharmacogenomics program, which utilized Thermo Fisher QuantStudio 7 TaqMan and Illumina BeadExpress microarrays, or MEGA genotyping platform, which utilized the Infinium Expanded Multi-Ethnic Genotyping Array.(16 (link), 17 (link)) All arrays were performed in the Vanderbilt Molecular Diagnostics Laboratory.

Patel P., Vimalathas P., Niu X., Shannon C.N., Denny J.C., Peterson J.F., Chitale R.V, & Fusco M.R. (2020). CYP2C19 Loss-Of-Function is Associated with Increased Risk of Ischemic Stroke after Transient Ischemic Attack in Intracranial Atherosclerotic Disease. Journal of stroke and cerebrovascular diseases : the official journal of National Stroke Association, 30(2), 105464.

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