Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA96207 | ENA |
REPOSITORIES: ENA
Similar Datasets
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: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. Overall study comprises 6 samples analyzed across three platforms with an additional dilution range (5 concentrations) of a seventh sample on two platforms. This Series represents NimbleGen platform-derived data.
2012-01-17 | E-GEOD-30120 | biostudies-arrayexpress
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. Overall study comprises 6 samples analyzed across three platforms with an additional dilution range (5 concentrations) of a seventh sample on two platforms. This Series represents Agilent platform-derived data.
2012-01-17 | E-GEOD-30121 | biostudies-arrayexpress
Project description:High density SNP microarrays provide insight into the genomic events that occur in diseases like cancer by their capability to measure both LOH and genomic copy numbers. Where currently available methods are restricted to the use of fresh frozen tissue, we now describe the design and validation of copy number measurements using the Illumina BeadArray platform and its application to formalin fixed, paraffin embedded (FFPE) tissue. In fresh frozen tissue, using a set of colorectal tumors with numerous chromosomal aberrations, our method measures copy number patterns that are comparable to values from established platforms, like Affymetrix GeneChip and BAC array-CGH. Moreover, paired comparisons of fresh frozen and FFPE tissue showed nearly identical patterns of genomic changes. We conclude that this method enables the use of paraffin embedded material for research into both LOH and numerical chromosomal abnormalities. These findings make the large pathological archives available for genomic analysis, which could be especially relevant for hereditary disease where fresh material from affected relatives is rarely available. Keywords: platform comparison and method development
2006-09-01 | GSE5347 | GEO
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:DNA copy number changes with or without accompanying copy neutral changes such as unparental disomy (UPD) is a feature of the cancer genome that is linked to cancer development. However, technical problems with archived formalin-fixed, paraffin-embedded (FFPE) tissue samples have limited their general use in genomic profiling studies done using high-density single nucleotide polymorphism (SNP) microarray. To overcome the current problems with the use of this material in the detection of DNA copy number and copy neutral changes, we have devised two new protocols for extracting DNA from FFPE tissue. Genotyping efficiency and accuracy were improved using our novel protocols. After censoring the larger fragments, we obtained call rates for FFPE DNA equivalent to those for FF tissue DNA, with concordance rates between FFPE and FF tumor exceeding 99%. Identical DNA copy number changes were obtained for FFPE and FF; and between two new extraction protocols in tumor samples by using Affymetrix® high-density oligo-based SNP microarray platform. We observed UPD and recurrent gains and losses in tumor samples. Interestingly, we also identified UPD in the 5q and 13q regions in matching normal blood, FF adjacent breast tissue and tumor tissue in two samples. In conclusion, our new two DNA extraction protocols should substantially improve the ability to use archived material to help elucidate the complexity of early-stage breast cancer genomes. Keywords: SNP based array
2008-09-18 | GSE9154 | GEO
Project description:Renal epithelial neoplasms have characteristic chromosomal imbalances that can be used for classification. We have previously shown that virtual karyotypes (v-karyotype) derived from SNP microarrays can be performed on formalin-fixed paraffin embedded (FFPE) tissue samples but a direct comparison with karyotypes obtained by conventional cytogenetics has not been done. 20 archival FFPE tumor samples were analyzed with Affymetrix 10K 2.0 or 250K Nsp SNP microarrays.
2009-02-19 | GSE12808 | GEO
Project description:Renal epithelial neoplasms have characteristic chromosomal imbalances that can be used for classification. We have previously shown that virtual karyotypes (v-karyotype) derived from SNP microarrays can be performed on formalin-fixed paraffin embedded (FFPE) tissue samples but a direct comparison with karyotypes obtained by conventional cytogenetics has not been done. 20 archival FFPE tumor samples were analyzed with Affymetrix 10K 2.0 or 250K Nsp SNP microarrays. 19 archival FFPE tumor samples were analyzed with Affymetrix 10K 2.0 or 250K Nsp SNP microarrays and virtual-karyotype results compared to those obtained by Cytogenetics.
2009-02-19 | E-GEOD-12808 | biostudies-arrayexpress
Project description:Robust molecular subgrouping and copy-number profiling of medulloblastoma from small amounts of archival tumor material. Validation of patterns identified by whole-genome bisulphite sequencing in a larger cohort. DNA methylation profiles of 276 primary medulloblastoma and 8 normal cerebellum control samples were generated from fresh-frozen and formalin-fixed paraffin-embedded material using the Illumina 450k methylation array.
2014-02-28 | E-GEOD-54880 | biostudies-arrayexpress