Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA193525 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We investigated a cohort of 34 archival cutaneous melanoma samples by Agilent 40 kb-resolution CGH array. We found a non-random distribution of precise CNAs predictive for clinical outcome. Although most of the alterations defined in this study have been already reported, we mapped novel melanoma-specific CNAs at highest accuracy. Moreover, our data revealed distinct amplifications hotspots, some of which were validated by quantitative real-time PCR, enabling the identification of novel melanoma oncogenic candidates. Keywords: Cutaneous melanoma, Copy number alterations, Biomarkers, FFPE We examined 34 primary melanoma formalin-fixed and paraffin-embedded (FFPE) samples by using array comparative genomic hybridization (aCGH) for DNA copy number alterations (CNAs). Genomic DNA was extracted, referred to a sex-matched diploid commercial control DNA (Promega Corporation, Madison, WI, cat. G1417 and G1521), and hybridized on the Agilent SurePrint G3 Human CGH Microarray 8x60k, cat. G4827A.
2013-07-01 | E-GEOD-45354 | biostudies-arrayexpress
Project description:We investigated a cohort of 34 archival cutaneous melanoma samples by Agilent 40 kb-resolution CGH array. We found a non-random distribution of precise CNAs predictive for clinical outcome. Although most of the alterations defined in this study have been already reported, we mapped novel melanoma-specific CNAs at highest accuracy. Moreover, our data revealed distinct amplifications hotspots, some of which were validated by quantitative real-time PCR, enabling the identification of novel melanoma oncogenic candidates. Keywords: Cutaneous melanoma, Copy number alterations, Biomarkers, FFPE
2013-07-01 | GSE45354 | GEO
Project description:In this experiment, FFPE samples of 41 primary cutaneous melanoma, 2 metastatic melanoma and 6 normal skin were used for DNA extraction and genotyping by Affymetrix OncoScan FFPE Assay, in order to define chromosomal alterations in copy number and loss of heterozygosity. Genomic damage was then correlated with clinical features of melanoma.
2015-11-01 | E-MTAB-3481 | biostudies-arrayexpress
Project description:The aim of this work was to identify the Copy Number Aberrations (CNAs) by high-resolution array Comparative Genomic Hybridization (aCGH) on 19 formalin-fixed, paraffin-embedded (FFPE) samples of treatment-naïve COM.
2020-01-13 | GSE131923 | GEO
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
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 | GSE30120 | GEO
Project description:To evaluate genetic profile in neuroblastoma stage 3 fresh frozen or paraffin embedded (FFPE) tumor samples were dedicated to array comparative genomic hybridization (aCGH) for analyzing copy number variations. It was used 200 ng of tumor DNA for aCGH analyses. The Agilent SurePrint G3 CGH ISCA v2 Microarray Kit 8x60K array platform was used for genome evaluation without enzymatic digestion. The resolution for aCGH evaluation was established on 0.15Mb for frozen samples and 1Mb for FFPE.
2023-02-24 | E-MTAB-12670 | biostudies-arrayexpress
Project description:373 tumors were profiled for copy-number alterations with the high-resolution Agilent 244A aCGH Array.
2010-07-29 | GSE20393 | GEO
Project description:1 lung tumor was profiled for copy-number alterations with the high-resolution Agilent 244A aCGH Array.
2010-05-27 | GSE20574 | GEO
Project description:24 SCC tumors were profiled for copy-number alterations with the high-resolution Agilent 244A aCGH Array
2015-03-11 | GSE40048 | GEO