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Profiling of copy-number variation in tumors from heterozygous and homozygous Tp53C273X knockout rats

ABSTRACT: We used Nimblegen HD aCGH to detect copy-number variants between tumor and ear control-DNA samples from heterozygous and homozygous Tp53C273X knockout rats

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE55895 | GEO | 2015/04/09

SECONDARY ACCESSION(S): PRJNA241262

REPOSITORIES: GEO

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Profiling of copy-number variation in tumors from heterozygous and homozygous Tp53C273X knockout rats

Project description:We used Nimblegen HD aCGH to detect copy-number variants between tumor and ear control-DNA samples from heterozygous and homozygous Tp53C273X knockout rats Comparison of tumor DNA with ear control-DNA from the same animal

2015-04-09 | E-GEOD-55895 | biostudies-arrayexpress

Profiling of copy-number variation between BN and M520 rats

Project description:We used Nimblegen HD aCGH to detect copy-number variants between genomes of BN and M520 rats

2012-12-31 | GSE27368 | GEO

Profiling of copy-number variation between BN and SHR rats

Project description:We used Nimblegen HD aCGH to detect copy-number variants between genomes of BN and SHR rats

2010-01-30 | GSE20102 | GEO

Profiling of copy-number variation between DNA isolation from different tissues of BN and ACI rats

Project description:We used Nimblegen HD aCGH to detect DNA recovery from different tissue samples

2013-03-21 | GSE45308 | GEO

Profiling of copy-number variation between BN and SHR rats

Project description:We used Nimblegen HD aCGH to detect copy-number variants between genomes of BN and SHR rats Comparison of single BN against single SHR individual in a dye-swap experiment

2010-05-15 | E-GEOD-20102 | biostudies-arrayexpress

Profiling of copy-number variation between BN and M520 rats

Project description:We used Nimblegen HD aCGH to detect copy-number variants between genomes of BN and M520 rats Comparison of single BN against single M520 individual in a dye-swap experiment

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Profiling of copy-number variation between DNA isolation from different tissues of BN and ACI rats

Project description:We used Nimblegen HD aCGH to detect DNA recovery from different tissue samples Comparison of DNA isolated from different tissues of BN and ACI rats in dye-swap setup

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Copy number variation in inbred and wild mice

Project description:Copy number variants were determined in 3-5 males from 13 inbred laboratory mouse strains and 21 Mus musculus individuals caught in various geographic locations, using Nimblegen 385k arrays. CopyMap was used to predict CNVs.

2010-12-31 | GSE24424 | GEO

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.

2012-01-17 | GSE30121 | GEO

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

2012-01-17 | GSE30120 | GEO

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