Evaluating the restoration of DNA derived from archival formalin-fixed paraffin embedded tissues for genomic profiling by SNP-CGH analysis
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE43406 | GEO | 2013/07/01
SECONDARY ACCESSION(S): PRJNA185989
REPOSITORIES: GEO
Similar Datasets
Project description:Pathology archives contain vast resources of clinical material in the form of formalin-fixed paraffin embedded (FFPE) tissue samples. Due to the methods of tissue fixation and storage, the integrity of DNA and RNA available from FFPE tissue is compromised, meaning obtaining informative data regarding epigenetic, genomic and expression alterations can be challenging. Here we have investigated the utility of repairing damaged DNA derived from FFPE tumours prior to single nucleotide polymorphism (SNP) arrays for whole genome DNA copy number analysis. To investigate whether repairing the DNA might improve performance in SNP array assay, we used the DNA Restore protocol from Illumina as a pre-treatment step prior to applying the DNA to the Infinium assay using the Human CytoSNP FFPE-12v2.1 arrays. DNA was extracted from FFPE samples spanning five decades involving tumor material obtained from surgical specimens and post-mortems. Various aspects of the protocol were assessed, including the method of DNA extraction, the role of Quality Control quantitative PCR in predicting sample success and the effect of DNA restoration on assay performance, data quality and the prediction of copy number aberrations (CNAs). In total 8 cases were analysed in this experiment, involving 43 SNP arrays of tumour and matched normal DNA samples, replicates and other control arrays.
2013-07-01 | E-GEOD-43406 | 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:BACKGROUND: Array Comparative Genomic Hybridization (aCGH) is a rapidly evolving technology that still lacks complete standardization. Yet, it is of great importance to obtain robust and reproducible data to enable meaningful multiple hybridization comparisons. Special difficulties arise when aCGH is performed on archival formalin-fixed, paraffin-embedded (FFPE) tissue due to its variable DNA quality. Recently, we have developed an effective DNA quality test that predicts suitability of archival samples for BAC aCGH. METHODS: In this report, we first used DNA from a cancer cell-line (SKBR3) to optimize the aCGH protocol for automated hybridization, and subsequently optimized and validated the procedure for FFPE breast cancer samples. We aimed for highest throughput, accuracy, and reproducibility applicable to FFPE samples, which can also be important in future diagnostic use. RESULTS: Our protocol of automated array-CGH on archival FFPE ULS-labeled DNA showed very similar results compared with published data and our previous manual hybridization method. CONCLUSION: This report combines automated aCGH on unamplified archival FFPE DNA using non-enzymatic ULS labeling, and describes an optimized protocol for this combination resulting in improved quality and reproducibility.
2007-02-23 | GSE7122 | GEO
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 Colorectal tumor tissue and corresponding normal tissue from 4 patients was used. The samples included a rectal adenoma (T514), one right-sided Dukes B (T44) and two Dukes C carcinomas (T106, T108). Copy number and genotyping was compared between the following platforms: - Illumina Sentrix BeadArrays with linkage mapping panel version IV - Affymetrix GeneChip Mapping 10K Xba1 arrays - 3.7 K LUMC BAC array The first Illumina experiment (201 suffixes) showed low intensity values, and was repeated (260 suffixes) The Sentrix plates were filled up with other patient material to process a total of 24 samples with different types of normal and affected tissue. Normal samples have been used for normalization
2006-09-01 | E-GEOD-5347 | biostudies-arrayexpress
Project description:BACKGROUND: Array Comparative Genomic Hybridization (aCGH) is a rapidly evolving technology that still lacks complete standardization. Yet, it is of great importance to obtain robust and reproducible data to enable meaningful multiple hybridization comparisons. Special difficulties arise when aCGH is performed on archival formalin-fixed, paraffin-embedded (FFPE) tissue due to its variable DNA quality. Recently, we have developed an effective DNA quality test that predicts suitability of archival samples for BAC aCGH. METHODS: In this report, we first used DNA from a cancer cell-line (SKBR3) to optimize the aCGH protocol for automated hybridization, and subsequently optimized and validated the procedure for FFPE breast cancer samples. We aimed for highest throughput, accuracy, and reproducibility applicable to FFPE samples, which can also be important in future diagnostic use. RESULTS: Our protocol of automated array-CGH on archival FFPE ULS-labeled DNA showed very similar results compared with published data and our previous manual hybridization method. CONCLUSION: This report combines automated aCGH on unamplified archival FFPE DNA using non-enzymatic ULS labeling, and describes an optimized protocol for this combination resulting in improved quality and reproducibility. In this study, we optimized the BAC araay-CGH protocol for automated hybridization for FFPE breast cancer samples. We have tested hybridization temperature and duration, different hybridization buffer conditions, and post-hybridization washing.
2010-06-12 | E-GEOD-7122 | biostudies-arrayexpress
Project description:Formalin-fixed paraffin-embedded (FFPE) samples are a highly desirable resource for epigenetic studies, but there is no suitable platform to assay genome-wide methylation in these widely available resources. Recently, Thirwell et al. (2010) have reported a modified ligation-based DNA repair protocol to prepare FFPE DNA for the Infinium methylation assay. In this study, we have tested the accuracy of methylation data obtained with this modification by comparing paired fresh-frozen (FF) and FFPE colon tissue from colorectal cancer patients. We report locus-specific correlation and concordance of tumor-specific differentially-methylated loci (DML), both of which were not previously assessed. We used Illumina’s Infinium Methylation 27 K chip for 12 pairs of FF and 12 pairs of FFPE tissue from tumor and surrounding healthy tissue from the resected colon of the same individual after repairing the FFPE DNA using Thirwell’s modified protocol.
2014-10-23 | E-GEOD-33181 | biostudies-arrayexpress
Project description:The capability to spatially explore RNA biology in formalin-fixed paraffin-embedded (FFPE) tissues holds transformative potential for histopathology research. Here, we present pathology-compatible deterministic barcoding in tissue (Patho-DBiT) by combining in situ polyadenylation and computational innovation for spatial whole transcriptome sequencing, tailored to probe the diverse RNA species in clinically archived FFPE samples. It permits spatial co-profiling of gene expression and RNA processing, unveiling region-specific splicing isoforms, and high-sensitivity transcriptomic mapping of clinical tumor FFPE tissues stored for five years. Furthermore, genome-wide single nucleotide RNA variants can be captured to distinguish malignant subclones from non-malignant cells in human lymphomas. Patho-DBiT also maps microRNA regulatory networks and RNA splicing dynamics, decoding their roles in spatial tumorigenesis. Cellular-level Patho-DBiT dissects the spatiotemporal cellular dynamics driving tumor clonal architecture and progression. Patho-DBiT stands poised as a valuable platform to unravel rich RNA biology in FFPE tissues to aid in clinical pathology evaluation.
2024-08-12 | GSE274641 | GEO
Project description:A study to evaluate techniques for repairing DNA from formalin-fixed paraffin-embedded (FFPE) tissue samples by direct comparison of FFPE DNA repair methods prior to analysis on genome-wide methylation array to matched fresh frozen (FF) tissues.
2014-12-17 | GSE59038 | GEO
Project description:The proteomics of archival samples has advanced significantly during the last two decades, making possible the use of vast FFPE tissue archives in biomarker studies. However, due to the limited data regarding comparison of the performance of different protocols, there is currently no consensus on the most effective protocol for shotgun proteomic analysis of FFPE tissue. In-solution digestion method using Rapigest as detergent and FASP method, both reported to deliver superior results on FFPE tissues were compared using two label-free data-independent LC-MS/MS acquisition modes. Archival FFPE prostate tissues stored 7 years and mirroring fresh frozen samples were processed with both protocols in 3 technical replicates. Data were comparatively evaluated in terms of protein and peptide identifications in fresh frozen and FFPE samples, analysis of the fresh and FFPE tissues representative proteome (molecular weight distribution, distribution according to protein’s pI, cellular component analysis of proteins and quantitation accuracy) and technical reproducibility of the Rapigest and FASP protocols.
2021-01-15 | PXD021074 | Pride
Project description:Formalin-fixed paraffin-embedded (FFPE) samples are the only remaining biological archive for many toxicological and clinical studies, yet their use in genomics has been limited due to variability in RNA quality from formalin fixation. Older FFPE samples, which often have highly degraded RNA, pose a particularly difficult technical challenge. Recent developments in probe-based targeted sequencing technologies show promise in addressing this issue, while also being more cost effective than traditional RNA-sequencing (RNA-seq) methods. In the current study, we evaluated dose-dependent transcriptional changes from paired frozen and archival FFPE liver samples stored for over 20 years using targeted resequencing (TempO-Seq) and whole-genome RNA-seq methods. Samples were originally collected from male mice exposed to a reference chemical (dichloroacetic acid, DCA) at 0, 198, 313 and 427 mg/kg-day, (n=6/dose) by drinking water for 6 days. TempO-Seq showed high overlap in differentially expressed genes (DEGs) between matched FFPE and flash-frozen (FROZ) samples and concordance in fold-changes across the highest two dose levels of DCA vs. control (R2 ≥ 0.94). Similarly, high concordance in fold-changes was observed between TempO-Seq FFPE and RNA-seq FROZ results (R2 ≥ 0.92). Only 28 DEGs or fewer were identified in RNA-seq FFPE samples. Modeling of DCA-dependent changes in gene sets identified benchmark doses from TempO-Seq FROZ and FFPE samples that were within 1.4-fold of RNA-seq FROZ samples (93.9 mg/kg-d), whereas RNA-seq FFPE samples were 3.3-fold higher (310.3 mg/kg-d). This work demonstrates that targeted sequencing may provide a more robust method for quantifying gene expression profiles from aged archival FFPE samples.
2022-10-10 | GSE186113 | GEO