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Infinium coreexome 24 beadchip

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The Infinium CoreExome-24 BeadChip is a high-throughput genotyping array designed by Illumina. It provides comprehensive genome-wide coverage of common and rare variants across the human genome. The BeadChip contains probes for over 547,000 genetic markers and is suitable for a wide range of genetic research applications.

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Lab products found in correlation

Dispase, by Thermo Fisher Scientific (1 mentions) Dmem f12, by BD (1 mentions) Matrigel, by BD (1 mentions) Mtesr1 media, by STEMCELL (1 mentions) Abi 7700 sequence detection system, by Thermo Fisher Scientific (1 mentions) Kasp genotyping platform, by LGC (1 mentions) Axiom lat1 array, by Thermo Fisher Scientific (1 mentions) Dneasy blood and tissue kit, by Qiagen (1 mentions)

6 protocols using infinium coreexome 24 beadchip

1

Genetic Variants Associated with NAFLD

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Buffy coat samples were used to extract DNA, and DNA samples were genotyped using a genome-wide SNP assay (Infinium CoreExome-24 BeadChip, Illumina, San Diego, CA, USA). Genetic information for four SNPs were extracted from the initial database: PNPLA3-rs738409 (C > G), TM6SF2-rs58542926 (G > A), MBOAT7-rs641738 (G > A) and GCKR-rs780094 (G > A). All SNPs satisfied the Hardy–Weinberg equilibrium (HWE), had a minor allele frequency > 5%, and were successfully genotyped in our sample (SNP call rate ≥ 98%). Nine individuals were removed from genetic analyses due to low genotyping rate (sample call rate ≥ 95%). Genetic variants’ information and genotype distribution in NAFLD/control groups and lean/non-lean NAFLD groups are presented in the Supplementary File (Tables S1–S3).
Kalafati I.P., Dimitriou M., Revenas K., Kokkinos A., Deloukas P, & Dedoussis G.V. (2023). TM6SF2-rs58542926 Genetic Variant Modifies the Protective Effect of a “Prudent” Dietary Pattern on Serum Triglyceride Levels. Nutrients, 15(5), 1112.
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2

Characterization of iPSC Lines from PMSE Subjects

Cited 3 times
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Stem cell colonies were maintained at 37°C, 5% CO2, in mTeSR1 media (Stemcell Technologies, Vancouver, British Columbia, Canada), on tissue culture plates pre-coated with Matrigel (1:100 dilution in DMEM/F12, BD Biosciences, San Jose, California, USA). iPSCs were passaged every 4–7 days using Dispase (Thermo Fisher Scientific, Waltham, Massachusetts, USA). Cultures were confirmed myco-plasma negative via periodic testing with a PCR-based assay. Each line used for experiments had expression of pluripotency markers (NANOG, OCT3/4, SSEA, SOX2) (Dang et al., 2020 (link); Liu et al., 2013 (link); Tidball et al., 2016 (link)). Episomally reprogrammed lines tested negative for episomal reprogramming vector integration. Each line was assessed for chromosomal abnormalities by G-band karyotyping (Cell Line Genetics, Madison, Wisconsin, USA), single nucleotide polymorphism (SNP) chip microarray analysis (Infinium Core Exome-24 BeadChip, Illumina, San Diego, California, USA), or both. Both iPSC lines from the PMSE subjects had a normal karyotype. The SNP chip microarray revealed that the iPSC line from PMSE subject 1 contained a 3.9 Mb gain of genomic material at 3q25.32-q26.1, and the iPSC line from PMSE subject 2 contained a 12 Mb gain of genomic material at 12p13.33-p13.2.
Dang L.T., Vaid S., Lin G., Swaminathan P., Safran J., Loughman A., Lee M., Glenn T., Majolo F., Crino P.B, & Parent J.M. (2021). STRADA-mutant human cortical organoids model megalencephaly and exhibit delayed neuronal differentiation. Developmental neurobiology, 81(5), 696-709.
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3

Genotyping Methods Across Asthma Studies

Cited 3 times
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In BREATH and PAGES, genotypes were determined by using Taqman-based allelic discrimination assays on an ABI 7,700 sequence detection system (Applied Biosystems, Foster City, Calif)4 (link),27 (link) In followMAGICS, samples were genotyped using Illumina Sentrix HumanHap300 BeadChip array (Illumina, Inc.)15 (link) In both GALA II and SAGE, samples were genotyped using the Axiom® LAT1 array (Affymetrix Inc.), and quality control (QC) procedures were performed as described previously.28 (link),29 (link) In PACMAN and ESTATe, samples were genotyped using the Illumina Infinium CoreExome-24 BeadChip (Illumina, Inc.).30 In PASS, genotyping was performed using the Illumina Omni Express 8v1 array (Illumina, Inc.). QC procedures and imputation are described elsewhere.22 (link) In SCSGES, genotyping was conducted using Kompetitive Allele Specific PCR (KASP) genotyping platform (LGC, Inc). QC was performed based on the quality of clustering.23 (link) In the SLOVENIA study, genotyping of 336 samples was performed with the Illumina Global Screening Array-24 v1.0 BeadChip (Illumina). QC procedures and imputation described elsewhere.30
Karimi L., Vijverberg S.J., Engelkes M., Hernandez-Pacheco N., Farzan N., Soares P., Pino-Yanes M., Jorgensen A.L., Eng C., Mukhopadhyay S., Schieck M., Kabesch M., Burchard E.G., Chew F.T., Sio Y.Y., Potočnik U., Gorenjak M., Hawcutt D.B., Palmer C.N., Turner S., Janssens H.M., Maitland-van der Zee A.H, & Verhamme K.M. (2021). ADRB2 Haplotypes and Asthma Exacerbations in Children and Young Adults: An Individual Participant Data Meta-Analysis. Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology, 51(9), 1157-1171.
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4

Genome-wide Genotyping of Human Leucocytes

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DNA was extracted from human blood leucocyte nuclei and were genotyped by Infinium CoreExome-24 BeadChip (Illumina, San Diego, CA). Genotypes were called from Genome studio using the human genome assembly GRCh37 as calling reference. 117 study participants were genotyped for 547,644 single nucleotide polymorphisms (SNPs) after updating genome to build 37. Quality control and genome-wide association study (GWAS) was performed using PLINK1.950 (link) for sample and SNP call-rates (98%), sex check, excess heterozygosity and homozygosity, inbreeding, pedigree (relatedness), removal of non-European ancestry, Hardy-Weinberg Equilibrium (HWE, 0.005) and minor allele frequency (MAF, 1%) resulting in 105 samples and 272,588 SNPs.
Nielsen R.L., Helenius M., Garcia S.L., Roager H.M., Aytan-Aktug D., Hansen L.B., Lind M.V., Vogt J.K., Dalgaard M.D., Bahl M.I., Jensen C.B., Muktupavela R., Warinner C., Aaskov V., Gøbel R., Kristensen M., Frøkiær H., Sparholt M.H., Christensen A.F., Vestergaard H., Hansen T., Kristiansen K., Brix S., Petersen T.N., Lauritzen L., Licht T.R., Pedersen O, & Gupta R. (2020). Data integration for prediction of weight loss in randomized controlled dietary trials. Scientific Reports, 10, 20103.
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5

Genotyping of FMS-related SNPs

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Genotyping was performed at the iGE3 genomic platform of the University of Geneva (UniGE) using an Infinium CoreExome-24 BeadChip from Illumina containing 555,356 markers including 4000 custom markers (Mouterde et al., under review1), among which 906 SNPs selected on the basis of their potential association to FMS and/or central pain sensitization through literature-mining (list of FMS related SNPs in Supplementary Data 1).
Genotype intensities were called using Illumina GenomeStudio™. All sample call rates (CRs) from the genotyping experiment exceeded 99%. The mean genotyping CR for the 302 samples was 99.73%. All SNPs were evaluated by the Illumina cluster quality score and SNPs with GenTrain score < 0.7 were discarded.
In the final data set, SNPs with a genotyping CR below 98%, a significant deviation from Hardy–Weinberg equilibrium (HWE) or a minor allele frequency (MAF) below 5% (CR < 98%, HWE p < 10–5, MAF < 0.05) were discarded. All genetic coordinates refer to the Ensembl GRCh37 reference assembly.
Gloor Y., Matthey A., Sobo K., Mouterde M., Kosek E., Pickering G., Poloni E.S., Cedraschi C., Ehret G, & Desmeules J.A. (2022). Uncovering a Genetic Polymorphism Located in Huntingtin Associated Protein 1 in Modulation of Central Pain Sensitization Signaling Pathways. Frontiers in Neuroscience, 16, 807773.
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6

Genetic Variants in Lean and Obese

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The presence of SNPs in genomic DNA from Lean and Obese individuals was analyzed by the Infinium CoreExome-24 BeadChip (Illumina) using DNA extracted from blood cells with DNeasy Blood and Tissue Kit (QIAGEN) as according to the manufacturer's recommendations.
Donkin I., Versteyhe S., Ingerslev L.R., Qian K., Mechta M., Nordkap L., Mortensen B., Appel E.V., Jørgensen N., Kristiansen V.B., Hansen T., Workman C.T., Zierath J.R, & Barrès R. (2016). Obesity and Bariatric Surgery Drive Epigenetic Variation of Spermatozoa in Humans. Cell metabolism, 23(2).
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