Expanding epigenomics to archived FFPE tissues: An evaluation of DNA repair methodologies
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE59038 | GEO | 2014/12/17
SECONDARY ACCESSION(S): PRJNA254173
REPOSITORIES: GEO
Similar Datasets
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. Formalin-fixed paraffin-embedded tissue from three colon adenocarcinoma samples were subjected to different FFPE-oriented DNA repair approaches and sequences, then compared with corresponding fresh frozen tissues. All samples were hybridized to the Illumina Infinium 450k Human Methylation BeadChip.
2014-12-17 | E-GEOD-59038 | biostudies-arrayexpress
Project description:BackgroundEpigenome-wide association studies are emerging in the field of cancer epidemiology with the rapid development of large-scale methylation array platforms. Until recently, these methods were only valid for DNA from flash frozen (FF) tissues. Novel techniques for repairing DNA from formalin-fixed paraffin-embedded (FFPE) tissues have emerged; however, a direct comparison of FFPE DNA repair methods before analysis on genome-wide methylation array to matched FF tissues has not been conducted.MethodsWe conducted a systematic performance comparison of two DNA repair methods (REPLI-g Ligase vs. Infinium HD Restore Kit) on FFPE-DNA compared with matched FF tissues on the Infinium 450K array. A threshold of discordant methylation between FF-FFPE pairs was set at Δβ > 0.3. The correlations of β-values from FF-FFPE pairs were compared across methods and experimental conditions.ResultsThe Illumina Restore kit outperformed the REPLI-g ligation method with respect to reproducibility of replicates (R(2) > 0.970), highly correlated β-values between FF-FFPE (R(2) > 0.888), and fewest discordant loci between FF-FFPE (≤0.61%). The performance of the Restore kit was validated in an independent set of 121 FFPE tissues.ConclusionsThe Restore kit outperformed RELPI-g ligation in restoring FFPE-derived DNA before analysis on the Infinium 450K methylation array. Our findings provide critical guidance that may significantly enhance the breadth of diseases that can be studied by methylomic profiling.ImpactEpigenomic studies using FFPE tissues should now be considered among cancers that have not been fully characterized from an epigenomic standpoint. These findings promote novel epigenome-wide studies focused on cancer etiology, identification of novel biomarkers, and developing targeted therapies. See all the articles in this CEBP Focus section, "Biomarkers, Biospecimens, and New Technologies in Molecular Epidemiology."
| S-EPMC4256717 | biostudies-literature
Project description:Aim of the project was to evaluate several MS-comaptible detergents for processing fresh frozen (FF) and formalin fixed paraffin embedded (FFPE) microdissected human kidney tissue. Here we have evaluated sensitivity of the methods and their applicability on FF and FFPE tissues, as well as investigated for the appropriateness of the use of FFPE tissues.
2022-02-22 | PXD020793 | Pride
Project description:The study aimed to apply 95GC, originally developed using fresh‑frozen (FF) tissues, to formalin‑fixed paraffin‑embedded (FFPE) tissues, because FFPE tissues are routinely prepared and are readily available. Although we previously reported the applicability of 72GC to FFPE tissues (DOI: 10.1016/j.clbc.2013.11.006), the present study aimed to improve the accuracy of 95GC for FFPE tissues using the reference robust multiarray average (refRMA) method, optimized for FFPE tissues. Therefore, a 95GC RS (Recurrence Score) was first developed and then the accuracy of the newly developed 95GC algorithm for FFPE tissues was evaluated using the 95GC RS. These 14 pairs of FF and FFPE data are included in the concordance analysis of 95GC high/low results between FF and FFPE (Figure 3B). J05 was created in a form more suited to the actual clinical setting, such as leaving the postoperative samples for 4 hours before immersing them in formalin. A long time passed, and now it is unclear how these 14 cases were distributed among the analysis. *Note: This old data has been updated multiple times by the other members. Then, there are some differences from the original paper and unclear points still remain. Therefore, do not use it for formal analysis aimed at public insurance coverage etc. This is for research purposes only. Please cite this paper when writing a new paper. PMID: 31638234 DOI: 10.3892/or.2019.7358
2023-07-11 | GSE236723 | GEO
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 study aimed to develop the 72GC (the 72-gene classifier) for recurrence-risk prediction for patients with estrogen receptor positive and node-negative breast cancer. 72-GC could differentiate the high-risk from the low-risk patients with a high statistical significance, and is considered to be applicable to formalin-fixed, paraffin embedded (FFPE) tumor tissues because the results of 72-GC on FF (fresh-frozen) tissues and FFPE tissues showed a high concordance. J06 31 pairs of FF (fresh‑frozen) and FFPE data are included in the concordance analysis of 72GC high/low results between FF and FFPE (Table 3). A long time passed, and now it is unclear how these 31 cases were distributed among the analysis. *Note: This old data has been updated multiple times by the other members. Then, there are some differences from the original paper and unclear points still remain. Therefore, do not use it for formal analysis aimed at public insurance coverage etc. This is for research purposes only. Please cite this paper when writing a new paper. PMID: 24461457 DOI: 10.1016/j.clbc.2013.11.006
2023-07-11 | GSE236725 | GEO
Project description:Background: The main bottleneck for genomic studies of tumors is the limited availability of fresh frozen (FF) samples collected from patients, coupled with comprehensive long-term clinical follow-up. This shortage could be alleviated by using existing large archives of routinely obtained and stored Formalin-Fixed Paraffin-Embedded (FFPE) tissues. However, since these samples are partially degraded, their RNA sequencing is technically challenging. Results: In an effort to establish a reliable and practical procedure, we compared three protocols for RNA sequencing using pairs of FF and FFPE samples, both taken from the same breast tumor. In contrast to previous studies, we compared the expression profiles obtained from the two matched sample types, using the same protocol for both. Three protocols were tested on low initial amounts of RNA, as little as 100 ng, to represent the possibly limited availability of clinical samples. For two of the three protocols tested, poly(A) selection (mRNA-seq) and ribosomal-depletion, the total gene expression profiles of matched FF and FFPE pairs were highly correlated. For both protocols, differential gene expression between two FFPE samples was in agreement with their matched FF samples. Notably, although expression levels of FFPE samples by mRNA-seq were mainly represented by the 3'-end of the transcript, they yielded very similar results to those obtained by ribosomal-depletion protocol, which produces uniform coverage across the transcript. Further, focusing on clinically relevant genes, we showed that the high correlation between expression levels persists at higher resolutions. Conclusions: Using the poly(A) protocol for FFPE exhibited, unexpectedly, similar efficiency to the ribosomal-depletion protocol, with the latter requiring much higher (2-3 fold) sequencing depth to compensate for the relative low fraction of reads mapped to the transcriptome. The results indicate that standard poly(A)-based RNA sequencing of archived FFPE samples is a reliable and cost-effective alternative for measuring mRNA-seq on FF samples. Expression profiling of FFPE samples by mRNA-seq can facilitate much needed extensive retrospective clinical genomic studies.
2018-05-03 | GSE113976 | GEO
Project description:Analysis of 60 FFPE (formalin-fixed, paraffin-embedded) ovarian cancer tissue samples to evaluate preservation quality and viability of global and phosphoproteomic analysis
2018-10-19 | PXD008832 | Pride
Project description:Comparative analysis of reproducibility of Fresh Frozen (FF) derived DNA, FFPE derived DNA and FFPE derived DNA restored using the Infinium FFPE DNA Restoration solution (FFPEr) when used on the Infinium HumanMethylation450 BeadChip assay.
2015-03-25 | GSE66555 | GEO
Project description:Formalin-fixed paraffin-embedded (FFPE) ring trial
| PRJEB32144 | ENA