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Agilent 244A aCGH array for comparison of lung tumor CNA to high-throughput sequencing data

ABSTRACT: 1 lung tumor was profiled for copy-number alterations with the high-resolution Agilent 244A aCGH Array.

ORGANISM(S): Homo sapiens

PROVIDER: GSE20574 | GEO | 2010/05/27

SECONDARY ACCESSION(S): PRJNA129849

REPOSITORIES: GEO

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Agilent 244A aCGH array for comparison of lung tumor CNA to high-throughput sequencing data

Project description:1 lung tumor was profiled for copy-number alterations with the high-resolution Agilent 244A aCGH Array. One lung tumor sample were assayed on the Agilent Human Genome CGH 244A Microarrays with the intent of comparing the genomic alterations reported by the array platform with those reported by high-thoughput sequencing. Human male genomic DNA (Promega P/N G1471) was used as reference. Individual log2 ratios of background subtracted signal intensities were obtained from the Agilent Feature Extraction software version 9.5. The log2 ratios were centered to a median of zero and the resulting log2 ratio values for each probe were segmented using GLAD. All probes within the genomic bounds of a given GLAD-derived segment were given the mean copy number value of probes within that segment.

2010-05-27 | E-GEOD-20574 | biostudies-arrayexpress

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Project description:373 tumors were profiled for copy-number alterations with the high-resolution Agilent 244A aCGH Array.

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Agilent 244A aCGH array for squamous cell carcinoma of the lung

Project description:24 SCC tumors were profiled for copy-number alterations with the high-resolution Agilent 244A aCGH Array

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Agilent 244A aCGH array for breast, lung, melanoma, ovary, and prostate

Project description:373 tumors were profiled for copy-number alterations with the high-resolution Agilent 244A aCGH Array. Tumor samples were assayed on Agilent Human Genome CGH 244A Microarrays with the intent of surveying the landscape of genomic alterations in 5 tumor types. Human male genomic DNA (Promega P/N G1471) was used as reference. Individual log2 ratios of background subtracted signal intensities were obtained from the Agilent Feature Extraction software version 9.5. The log2 ratios were centered to a median of zero and the resulting log2 ratio values for each probe were segmented using GLAD. All probes within the genomic bounds of a given GLAD-derived segment were given the mean copy number value of probes within that segment.

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Agilent 400K aCGH data for 30 human gastric cancers

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Project description:Copy number alteration (CNA) is a good signpost to identify cancer related genes. CNAs were analyzed using the Agilent 244K array comparative genomic hybridization (aCGH) in fresh-frozen tumor and matched normal tissues from 10 gastric cancer patients.

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1000 Genomes Phase 3 aCGH samples

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Project description:Copy number alteration (CNA) is a good signpost to identify cancer related genes. CNAs were analyzed using the Agilent 400K array comparative genomic hybridization (aCGH) in fresh-frozen tumor and matched normal tissues from 30 gastric cancer patients. Whole genomic CNAs in 30 human gastric cancers were analyzed using the Agilent aCGH-400K arrays. Matched normal tissues were used as the reference.

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Three commercial array platforms compared for DNA copy number detection with DNA isolated from FFPE tissue [Agilent]

Project description:Formalin-fixed, paraffin-embedded (FFPE) archival tissue is an important source of DNA material. The most commonly used technique to identify copy number aberrations from chromosomal DNA in tumorigenesis is array comparative genomic hybridization (aCGH). Although copy number analysis using DNA from FFPE archival tissue is challenging, several research groups have reported high quality and reproducible DNA copy number results using aCGH. Aim of the present study is to compare aCGH platforms suitable for copy number analysis using FFPE derived DNA. Two dual channel aCGH platforms (Agilent and NimbleGen) and a single channel SNP based platform (Affymetrix), were evaluated using seven FFPE colon cancer samples, median absolute deviation (MAD), deflection, signal-to-noise ratio (SNR) and DNA input requirements were used as quality criteria. Large differences were observed in MAD values and deflection between platforms; Agilent and NimbleGen showed better MAD values (0.13 for both) compared to Affymetrix (0.22). Contrary, Affymetrix showed a better deflection of 0.94, followed by 0.71 for Agilent and 0.51 for NimbleGen. Since the deflection compensates for the MAD the Signal to Noise Ratios (SNR) were comparable; Agilent ranks first, Affymetrix second and NimbleGen third with SNRs of 3.9, 3.6 and 3.3 respectively. DNA input amounts of 40ng are sufficient for high quality profiles with Affymetrix. For Agilent DNA input amounts of 50ng are sufficient for high quality profiles. For results of similar quality NimbleGen requires at least 100ng. Copy number analysis using DNA derived from FFPE archival material is feasible and shows reproducible results on high-resolution copy number platforms. Input amounts of DNA from FFPE material lower than recommended still yield high quality profiles without additional amplification steps.

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Paradigm Test Set aCGH Array

Project description:aCGH data was used in Paradigm analysis for exploration of networks affected by copy number and gene expression changes based on mutation spectra of recurrently mutated genes in breast cancer.

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