Custom 244k whole genome microarray

Manufactured by Illumina

The Custom 244K whole genome microarray is a high-density array designed for genome-wide analysis. It provides comprehensive coverage of the human genome, with probes targeting over 244,000 genetic markers. The array enables researchers to perform a variety of genomic studies, including association studies, copy number variation analysis, and genotyping.

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Lab products found in correlation

Genomic analyzer, by Illumina (1 mentions)

3 protocols using custom 244k whole genome microarray

Comprehensive Breast Cancer Transcriptomics Analysis

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The TCGA data portal was used to download the breast cancer data [27 (link)]. A total of 396 cases of breast cancer were analyzed according to the PAM50 predictor. We downloaded level 3 gene expression data derived from an Agilent custom 244K whole genome microarray and somatic mutation data using exome sequencing from Illumina Genomic Analyzer. Gene expression level was median centered by genes.
Gene expression of 59 breast cancer cell lines using GeneChip Human Genome U133 Plus 2.0 Array included in CCLE was analyzed using GENE-E software, version 3.0.230 [28 (link)].
The five analysis sets are shown in Supplementary Table S4 where we have indicated the specific evaluations that were performed for each set of data.

Lee H.J., Song I.H., Park I.A., Heo S.H., Kim Y.A., Ahn J.H, & Gong G. (2016). Differential expression of major histocompatibility complex class I in subtypes of breast cancer is associated with estrogen receptor and interferon signaling. Oncotarget, 7(21), 30119-30132.

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Basal-like Breast Cancer Genomic Analysis

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The Cancer Genome Atlas (TCGA) data portal was used to download breast cancer data [14 (link)]. A total of 84 cases of basal-like breast cancer were analyzed. We downloaded level-3 gene expression data derived from an Agilent custom 244K whole genome microarray and somatic mutation data from an Illumina Genomic Analyzer (San Diego, CA). The gene expression level was median-centered by gene.

Lee M., Song I.H., Heo S.H., Kim Y.A., Park I.A., Bang W.S., Park H.S., Gong G, & Lee H.J. (2018). Expression of Immunoproteasome Subunit LMP7 in Breast Cancer and Its Association with Immune-Related Markers. Cancer Research and Treatment : Official Journal of Korean Cancer Association, 51(1), 80-89.

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Basal-like Breast Cancer Transcriptome Analysis

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TCGA data portal was used to download the breast cancer data. 18 In total, 84 cases of basal-like breast cancer were analysed according to the PAM50 predictor. We downloaded level-3 gene expression data derived from an Agilent custom 244K whole-genome microarray and somatic mutation data obtained using exome sequencing from Illumina Genomic Analyzer. Gene expression levels were median-centred by genes.
Gene Set Enrichment Analysis (GSEA) was performed using javaGSEA v2.2.4, with gene sets derived from the Kyoto Encyclopedia of Genes and Genomes pathway database. 19 Basal-like tumours were dichotomised based on the mean ADAR1 gene expression value.
ADAR mRNA expression of eight breast cancer cell lines using GeneChip Human Genome U133 Plus 2.0 Array included in cancer cell line encyclopedia (CCLE) was analysed (Supplementary Figure S1).

Song I.H., Kim Y.A., Heo S.H., Park I.A., Lee M., Bang W.S., Park H.S., Gong G, & Lee H.J. (2017). ADAR1 expression is associated with tumour-infiltrating lymphocytes in triple-negative breast cancer. Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine, 39(10).

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