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Genomic copy number alterations as predictive markers in breast cancer

ABSTRACT: Genomic copy number alterations as predictive markers in breast cancer

PROVIDER: PRJNA108393 | ENA |

REPOSITORIES: ENA

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Genomic copy number alterations as predictive markers in breast cancer

Project description:This SuperSeries is composed of the following subset Series: GSE10128: Genomic copy number alterations as predictive markers of systemic recurrence in breast cancer GSE10129: Genomic copy number alterations as predictive markers of neoadjuvant chemotherapy response in breast cancer Refer to individual Series

2010-05-27 | E-GEOD-10181 | biostudies-arrayexpress

Genomic copy number alterations as predictive markers of systemic recurrence in breast cancer

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Genomic copy number alterations as predictive markers of systemic recurrence in breast cancer

Project description:Array CGH containing 4,044 human bacterial artificial chromosome clones was used to assess copy number changes in 31 pairs of clinicopathologically well matched recurred / nonrecurred breast cancer tissues. Array CGH containing 4,044 human bacterial artificial chromosome clones was used to assess copy number changes in 31 pairs of clinicopathologically well matched recurred / nonrecurred breast cancer tissues.

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Genomic copy number alterations as predictive markers of neoadjuvant chemotherapy response in breast cancer

Project description:Array CGH containing 4,044 human bacterial artificial chromosome clones was used to assess different copy number changes between chemotherapy responsive and non-resposive breast cancer tissues. Array CGH containing 4,044 human bacterial artificial chromosome clones was used to assess different copy number changes between chemotherapy responsive and non-resposive breast cancer tissues.

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Recurrent copy number alterations are associated with poor prognosis and HPV infection in penile carcinomas

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DNA copy number alterations in radiation-induced rat mammary carcinomas

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Acquired Copy Number Alterations in Adult Acute Myeloid Leukemia Genomes

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DNA copy number alterations in radiation-induced rat renal carcinomas

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High-resolution mapping of copy-number alterations with massively parallel sequencing

Project description:In order to benchmark the reproducibility of Affymetrix Genome-Wide Human SNP Array 6.0 for detecting copy-number alterations, we performed replicate hybridizations of 3 tumor cell lines and 2 paired normal cell lines obtained from the American Type Culture Collection (ATCC). We calculated copy numbers at each SNP probeset by a custom copy-number pipeline (PMID: 18772890). For each cell line, copy number data from replicate arrays are supplied in the accompanying matrix files. For each SNP probeset, we calculated the median copy number across replicate arrays. We compared the copy-number alterations detected by Circular Binary Segmentation segmentation of these arrays with statistical analyses of short sequence reads obtained from the Illumina/Solexa 1G GenomeAnalyzer. Shotgun sequencing results can be found in the NCBI Short Read Archive, accession number SRP000246 Keywords: disease state analysis

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