Omni 2

Manufactured by Thermo Fisher Scientific

The Omni 2.5 is a high-performance benchtop homogenizer designed for efficient sample preparation. It features a powerful motor and a range of interchangeable probes to accommodate a variety of sample volumes and viscosities.

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Lab products found in correlation

Snp array 6, by Thermo Fisher Scientific (2 mentions) Expression beadchip, by Illumina (1 mentions) Snp 6, by Thermo Fisher Scientific (1 mentions) Cytoscan hd, by Thermo Fisher Scientific (1 mentions) Omni express, by Thermo Fisher Scientific (1 mentions)

3 protocols using omni 2

Genotype Imputation and Transcriptional Profiling of Prostate Samples

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IMPUTE2 (v. 2.3.2)⁶⁴ was used to perform the genotype imputation of rs2853669 from three cohorts, TCGA, Stockholm, and Cambridge, composed of 389, 94, and 119 prostate samples, respectively. QCtool (v.2.0.7) (20 (link)) was used to assess and perform quality control by setting parameters “-threshold 0.9, -snp-stats”. SNPs that failed to pass the quality checking were excluded from imputation. 1000 Genomes Phase 3 data were selected as reference panel (18 (link)). Parameters were set as default “–Ne = 2000 and –k hap = 500”. A SNP-centered 2-MB region was set for the imputation on chromosome 5. Genotypes in the Gen format were converted to dosage format for downstream analysis. The transcriptional profiling was assessed by Illumina Expression Bead Chip in Swedish and Cambridge human prostate tissue samples, while RNA-seq was used in TCGA samples. The Stockholm and TCGA cohorts were genotyped on Illumina Omni 2.5 and Affymetrix SNP array 6, respectively.

Dong X., Zhang Q., Hao J., Xie Q., Xu B., Zhang P., Lu H., Huang Q., Yang T., Wei G.H., Na R, & Gao P. (2021). Large Multicohort Study Reveals a Prostate Cancer Susceptibility Allele at 5p15 Regulating TERT via Androgen Signaling-Orchestrated Chromatin Binding of E2F1 and MYC. Frontiers in Oncology, 11, 754206.

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Prostate Cancer eQTL Analysis

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We tested for eQTL associations between genotypes of rs11672691 and gene expression levels of CEACAM21 and PCAT19 using data from TCGA (Cancer Genome Atlas Research Network, 2015 (link); Cerami et al., 2012 (link)), Swedish and Wisconsin cohorts, which comprised of 389, 94, and 462 prostate samples, respectively. Association between genotype and gene expression was analyzed using the Matrix Expression Quantitative Trait Loci (Matrix eQTL) R package, parameters “useModel = modelLINEAR”, “errorCovariance = numeric ()” were used. We applied the principal-component analysis covariates for the TCGA cohort. R was used to perform the statistical tests and plot figures for the association between SNP genotypes and gene expression levels. The transcriptional profilings were assessed by Illumina Expression BeadChip in Swedish human prostate tissue samples, while RNA-seq in TCGA samples. The Stockholm and TCGA cohorts were genotyped on Illumina Omni 2.5 and Affymetrix SNP array 6, respectively.

Gao P., Xia J.H., Sipeky C., Dong X.M., Zhang Q., Yang Y., Zhang P., Cruz S.P., Zhang K., Zhu J., Lee H.M., Suleman S., Giannareas N., Liu S., Tammela T.L., Auvinen A., Wang X., Huang Q., Wang L., Manninen A., Vaarala M.H., Wang L., Schleutker J, & Wei G.H. (2018). Biology and clinical implications of the 19q13 aggressive prostate cancer susceptibility locus. Cell, 174(3), 576-589.e18.

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Evaluating CNVR Probe Coverage

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In order to evaluate the coverage by array probes for all CNVR sets, we used bedtools (v2.29.2) [67 (link)] intersect to determine all markers falling within a respective CNVR and then counted the number of markers, reporting zero for no intersection. For this we used array probe maps from several chip designs from [4 (link)]: Illumina’s OmniExpress, CytoSNP850, Omni25, Omni5 as well as Affymetrix SNP 6.0 and CytoScan HD

Lavrichenko K., Johansson S, & Jonassen I. (2021). Comprehensive characterization of copy number variation (CNV) called from array, long- and short-read data. BMC Genomics, 22, 826.

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