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Profiling DNA copy number alterations of 44 lung cancer cell lines

ABSTRACT: Profiling DNA copy number alterations of 44 lung cancer cell lines

PROVIDER: PRJNA559466 | ENA |

REPOSITORIES: ENA

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Profiling DNA copy number alterations of 44 lung cancer cell lines

Project description:We established and characterized 24 lung cancer cell lines from Taiwan lung cancer specimens or pleural effusions. Three EGFR-mutant TKI-sensitive parental cell lines were cultured in gefitinib following well-established TKI dose-escalation protocols. 20 Caucasian lung cancer cell lines are purchased from the American Type Culture Collection and National Cancer Institute. We conducted 44 lung cancer cell lines with copy number variation, EGFR status and invasion ability.

2022-07-31 | GSE135617 | GEO

Copy number alterations in 8 lung cancer in Xuanwei samples

Project description:In order to screen potential novel 'driver genes' in lung cancer in Xuanwei (LCXW), genome-wide DNA copy number alterations (CNAs) were detected on 8 paired LCXW and non-cancerous lung (NCL) tissues by array-based comparative genomic hybridization microarrays. The log2 copy-number ratio calculation and CNA calls were determined using segMNT algorithm in NimbleScan. Log2 ratio test/control thresholds of 0.25 and -0.25 were defined as copy number gains and losses, respectively. Deviant signal intensity ratios involving 5 or more neighboring probes were considered as genomic aberrations. A large number of CNAs and DEGs were detected, respectively. Many recurrent CNAs were screened out, including gains at 5p15.33-p15.32, 5p15.1-p14.3 and 5p14.3-p14.2, and losses at 11q24.3, 21q21.1, 21q22.12-q22.13 and 21q22.2.

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Genomic DNA copy number alterations of radiation-induced lung adenocarcinomas in mice

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Acquired Copy Number Alterations in Adult Acute Myeloid Leukemia Genomes

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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

2008-11-14 | GSE13372 | GEO

Mapping of copy-number alterations with massively parallel sequencing

Project description:This SuperSeries is composed of the following subset Series: GSE12019: Fine-scale mapping of copy-number alterations with massively parallel sequencing GSE13372: High-resolution mapping of copy-number alterations with massively parallel sequencing Refer to individual Series

2008-11-13 | E-GEOD-13373 | biostudies-arrayexpress

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