Unknown,Transcriptomics,Genomics,Proteomics

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Expression data from normal and Malignant hematopoietic cells

ABSTRACT: This data was used to determine levels of BRCA1 and BRCA2 in primary human leukemia samples. Samples were determined to be high BRCA1 and/or BRCA2 or low BRCA1 and/or BRAC2. This data was used to determine levels of BRCA1 and BRCA2 in primary human leukemia samples. Samples were determined to be high BRCA1 and/or BRCA2 or low BRCA1 and/or BRAC2. AML cell lines and patient samples, B ALL cell lines and Patient samplest, T ALL cell lines and patient samples, norma B cells, normal granulocytes, normal monocytes, normal T cells and normal CD34+ cells were used for RNA extraction and hybridization on Affymetrix microarrays. All the AML, B ALL, T ALL cell lines were cultured in vitro under appropriate culture conditons and harvested in their log phase growth for RNA extraction. AML, B ALL, and T ALL patient samples were collected...(I assume these are the PBMCs from eitehr peripheral blood or bone marrow from patients, please confirm). Normal B cells, granulocytes, monocytes, and T cells were purified from human peripheral blood of normal healthy donors.

ORGANISM(S): Homo sapiens

SUBMITTER: Yezhou Sun

PROVIDER: E-GEOD-48558 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Use of DNA damaging agents and RNA pooling to assess expression profiles associated with BRCA1 and BRCA2 mutation status in familial breast cancer patients Background: A large number of rare sequence variants of unknown clinical significance have been identified in the breast cancer susceptibility genes, BRCA1 and BRCA2. Determining the functional effect of these variants as well as their role in breast cancer susceptibility can be challenging using current classification methods. Methodology/Principal Findings: To identify predictors of pathogenic mutation status in familial breast cancer patients, we explored the use of gene expression arrays to assess the effect of two DNA damaging agents (irradiation and mitomycin C) on cellular response in relation to BRCA1 and BRCA2 mutation status. A range of regimes were used to treat 27 lymphoblastoid cell-lines (LCLs) derived from affected women in high-risk breast cancer families (nine BRCA1, nine BRCA2, and nine non-BRCA1/2 or BRCAX individuals) and nine LCLs from healthy individuals. Using an RNA pooling strategy, we found that treating LCLs with 1.2 μM mitomycin C and measuring the gene expression profiles 1 hour post-treatment had the greatest potential to discriminate BRCA1, BRCA2 and BRCAX mutation status. A classifier was built using the expression profile of nine QRT-PCR validated genes that were associated with BRCA1, BRCA2 and BRCAX status in RNA pools. These nine genes could distinguish BRCA1 from BRCA2 carriers with 83% accuracy in individual samples, but three-way analysis for BRCA1, BRCA2 and BRCAX had a maximum of 59% prediction accuracy. Conclusions/Significance: Our results suggest that, compared to BRCA1 and BRCA2 mutation carriers, non-BRCA1/2 (BRCAX) individuals are genetically heterogeneous. This study also demonstrates the effectiveness of RNA pools to compare the expression profiles of cell-lines from BRCA1, BRCA2 and BRCAX cases after treatment with irradiation and mitomycin C as a method to prioritize treatment regimes for detailed downstream expression analysis.

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Expression data from normal and Malignant hematopoietic cells

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