Humanomniexpressexome 8 v1.2 beadchip

Manufactured by Illumina

The HumanOmniExpressExome-8 v1.2 BeadChip is a high-throughput genotyping array designed to provide comprehensive genome-wide coverage for the human genome. It includes probes for over 950,000 genetic variants, including those found in the exome. The BeadChip is intended for use in large-scale genomic studies and can analyze multiple samples in parallel.

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Lab products found in correlation

Humanomniexpress 12 beadchip, by Illumina (2 mentions) Humanomni2.5 8 beadchip, by Illumina (2 mentions) Flexi gene dna kits, by Qiagen (1 mentions) Human omniexpressexome 8 v1.0 bead chip, by Illumina (1 mentions) Genomestudio v2011, by Illumina (1 mentions)

6 protocols using humanomniexpressexome 8 v1.2 beadchip

Genetic Modifiers of Nutritional Status

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Genomewide scan has been conducted on the cohort using the Illumina HumanOmniExpressExome-8 V1.2 BeadChip, including genetic variants of importance for n-3 LCPUFA and vitamin D levels and metabolism, which will be included in the analyses of the intervention. This data will allow us to analyse to which extent the effect of early exposures are modified by host genetics.

Mohammadzadeh P., Rosenberg J.B., Vinding R., Møllegaard Jepsen J.R., Lindberg U., Følsgaard N., Erlang Sørensen M., Sulaiman D., Bilenberg N., Mitta Raghava J., Fagerlund B., Vestergaard M., Pantelis C., Stokholm J., Chawes B., Larsson H., Glenthøj B.Y., Bønnelykke K., Ebdrup B.H, & Bisgaard H. (2022). Effects of prenatal nutrient supplementation and early life exposures on neurodevelopment at age 10: a randomised controlled trial - the COPSYCH study protocol. BMJ Open, 12(2), e047706.

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GWAS Genotyping of ALDH2 Variant

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DNA samples of the subjects were analyzed using the HumanOmniExpressExome‐8 v1.2 BeadChip, HumanOmniExpress‐12 BeadChip, or HumanOmni2.5‐8 BeadChip arrays (Illumina Inc). Genotyping was conducted at the Genetics Division or Department of Clinical Genomics, Fundamental Innovative Oncology Core (FIOC), National Cancer Center Research Institute or at the RIKEN Center for Integrative Medical Sciences. In the present study, we extracted genotyping information on rs671 (ALDH2 Glu504Lys) from the above data.

Iwasaki M., Budhathoki S., Yamaji T., Tanaka‐Mizuno S., Kuchiba A., Sawada N., Goto A., Shimazu T., Inoue M, & Tsugane S. (2020). Inclusion of a gene‐environment interaction between alcohol consumption and the aldehyde dehydrogenase 2 genotype in a risk prediction model for upper aerodigestive tract cancer in Japanese men. Cancer Science, 111(10), 3835-3844.

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DNA Extraction and Genotyping Protocol

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DNA samples from participants were extracted from the buffy coat of the peripheral white blood cells using FlexiGene DNA kits (QIAGEN) and genotyped using the HumanOmniExpressExome‐8 v1.2 BeadChip, HumanOmniExpress‐12 BeadChip or HumanOmni2.5‐8 BeadChip arrays (Illumina Inc.). Detailed information is described in Methods S1.

Nakano S., Yamaji T., Katagiri R., Sawada N., Inoue M., Tsugane S, & Iwasaki M. (2022). p53 Arg72Pro polymorphism, adiposity status, and cancer risk: Two case‐cohorts within a Japanese prospective study. Cancer Science, 113(12), 4385-4393.

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Genome-Wide Variant Genotyping and QC

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We genotyped 160 individuals across 964,193 variants genome-wide with the Illumina HumanOmniExpressExome- 8v1.2 beadchip. We removed SNPs if they deviated from Hardy-Weinberg Equilibrium (HWE) (p < 1 × 10^− 7), had a minor allele frequency < 5%, missingness > 2%, or a heterozygosity rate greater than 3 standard deviations from the mean (PLINK [55 (link), 56 ]). For mapping eQTLs, we removed SNPs on the Y chromosome. Following QC, we used 608,017 variants for further analysis. We removed one sample with high missingness and outlying heterozygosity rate from further analysis.

Davenport E.E., Amariuta T., Gutierrez-Arcelus M., Slowikowski K., Westra H.J., Luo Y., Shen C., Rao D.A., Zhang Y., Pearson S., von Schack D., Beebe J.S., Bing N., John S., Vincent M.S., Zhang B, & Raychaudhuri S. (2018). Discovering in vivo cytokine-eQTL interactions from a lupus clinical trial. Genome Biology, 19, 168.

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Genetic and Epigenetic Effects on Traits

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Genetic effects at 560,797 SNPs (minor allele frequency > 1%; scaled to mean 0, variance 1) from the Illumina HumanOmniExpressExome-8 v1.0 Bead Chip or Illumina HumanOmniExpressExome-8 v1.2 Bead Chip were examined [37 (link)], setting prior mixture variances to 0.00001, 0.0001 and 0.001. For the genetic analysis, phenotypes were pre-corrected for age, sex and 20 genetic PCs. To estimate the additive and independent effects of DNAm and genetic data on complex traits, a combined analysis was run—using the phenotype corrections specified for the EWAS model—setting prior mixture variances as above.

McCartney D.L., Hillary R.F., Conole E.L., Banos D.T., Gadd D.A., Walker R.M., Nangle C., Flaig R., Campbell A., Murray A.D., Maniega S.M., Valdés-Hernández M.D., Harris M.A., Bastin M.E., Wardlaw J.M., Harris S.E., Porteous D.J., Tucker-Drob E.M., McIntosh A.M., Evans K.L., Deary I.J., Cox S.R., Robinson M.R, & Marioni R.E. (2022). Blood-based epigenome-wide analyses of cognitive abilities. Genome Biology, 23, 26.

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Karyotyping Using SNP Array Genotyping

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Karyotyping was performed by SNP array‐based genotyping using the Human OmniExpressExome‐8‐v1.2 BeadChip (Illumina, Inc) at the Institute for Human Genetics (Life & Brain Center, University of Bonn, Germany). Processing was performed on gDNA following the manufacturer’s procedures. Log R ratio and B‐allele frequency plots were generated in GenomeStudio V2011.1 (Illumina, Inc) using the provided manifest and cluster files, version 1.2‐B. Copy number regions were detected using the cnvPartition version 3.1.6. A visual inspection was performed for mosaicism states.

Mehrjardi N.Z., Molcanyi M., Hatay F.F., Timmer M., Shahbazi E., Ackermann J.P., Herms S., Heilmann‐Heimbach S., Wunderlich T.F., Prochnow N., Haghikia A., Lampert A., Hescheler J., Neugebauer E.A., Baharvand H, & Šarić T. (2020). Acquisition of chromosome 1q duplication in parental and genome‐edited human‐induced pluripotent stem cell‐derived neural stem cells results in their higher proliferation rate in vitro and in vivo. Cell Proliferation, 53(10), e12892.

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