Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Genome-wide Expression Assay Comparison Across Frozen and Fixed Postmortem Brain Tissue Samples

ABSTRACT: Comparison between in vitro transcription- and cDNA-mediated annealing, selection and ligation (DASL)-based assays on brain-specific reference RNA, and postmortem frozen and formalin fixed brain tissue from autistic and control cases. Investigation of data preprocessing techniques for DASL-assayed RNA samples from frozen brain tissue. IVT- and DASL-based expression assays were performed on 10 reference RNA samples (brain and pooled artificially degraded at 0, 10, 30, and 60 min), 4 formalin-fixed tissue-extracted RNA samples with replicates, and 57 frozen tissue-extracted RNA samples with replicates. A subset of the 57 (N=33 samples) from frozen brain tissue assayed using the DASL-based platform were then used to test different dataset preprocessing strategies implemented in the lumi package in R/Bioconductor. The data from frozen-tissue extracted DASL-processed RNA samples passing exclusion criteria were log2 transformed and normalized using quantile normalisation with lumi in R (quantile-normalized data available as a supplementary file linked to the Series record).

ORGANISM(S): Homo sapiens

SUBMITTER: Maggie Chow

PROVIDER: E-GEOD-28475 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Preprocessing and Quality Control Strategies for Illumina DASL Assay-Based Brain Gene Expression Studies with Semi-Degraded Samples.

Chow Maggie L ML Winn Mary E ME Li Hai-Ri HR April Craig C Wynshaw-Boris Anthony A Fan Jian-Bing JB Fu Xiang-Dong XD Courchesne Eric E Schork Nicholas J NJ

Frontiers in genetics 20120224

Available statistical preprocessing or quality control analysis tools for gene expression microarray datasets are known to greatly affect downstream data analysis, especially when degraded samples, unique tissue samples, or novel expression assays are used. It is therefore important to assess the validity and impact of the assumptions built in to preprocessing schemes for a dataset. We developed and assessed a data preprocessing strategy for use with the Illumina DASL-based gene expression assay ...[more]

PMID: 22375143

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Project description:For the effectiveness of targeted immunotherapy, which is currently one of the most promising treatments for brain tumors, it is necessary to know specific tumor-associated antigens (TAA). This project aimed to validate the suitability of formalin-fixed and paraffin-embedded (FFPE) material instead of fresh-frozen material for RNA sequencing and downstream TAA identification. Purpose: Detect potential oligodendroglioma-associated antigens using both fresh-frozen and FFPE brain tissues; assess the suitability of the FFPE material for TAA identification. Results: A comparative analysis based on the RNA-seq of canine oligodendroglioma showed that formalin fixation of the samples had a significant effect on the RNA-seq library in terms of quality. Read distribution analysis showed that the FFPE samples contained fewer reads mapping to exonic regions and were enriched with reads mapped to introns and intergenic regions, while the fresh-frozen samples were mostly enriched in reads mapping to exons. Mismatch profile and SNVs calling analyses revealed some substitution artefacts present in the FFPE samples and absent in the corresponding fresh-frozen samples. However, according to the Principal Component Analysis, 36% of the variance between the samples could be explained by the types of conservation, while 43% of the variance could still be attributed to different expression profiles between oligodendroglioma and control conditions. A differential expression analysis of fresh-frozen oligodendroglioma versus fresh-frozen control samples identified 62 potential TAA strongly up-regulated in tumor tissue. The same analysis using the FFPE samples showed 80% of these genes (49/62) also to be differentially expressed. Comparative analysis showed good agreement between FFPE and fresh-frozen RNA-seq libraries in terms of the accuracy of gene expression measurements indicating that archived FFPE tissue can be used for identification of TAA candidates by RNA-seq providing a wealthy source of clinical samples for research. The following 10 genes encoding cell surface proteins have been identified by both approaches as potential TAA candidates based on their strong overexpression in oligodendrogliomas: PDGFRA, NOTCH1, DLL1, GPER1, TNR, IQGAP3, CD44, ERBB3, BCAS1 and ROR2. Future projects still need to investigate their suitability as TAA for targeted immunotherapy. Conclusion: Formalin fixation of the samples had a significant impact on the RNA-seq quality in terms of the accuracy of gene expression measurements, as well as the quality of the nucleotide sequences. Nevertheless, the comparative analysis showed good agreement between FFPE and fresh-frozen RNA-seq libraries.

Project description:Comparison of gene expression profiles between a primary melanoma and an early metastatic specimen from the same patient will provide essential biological insight into early metastatic processes. The DASL (cDNA mediated annealing, selection, extension and ligation) assay has been used to generate gene expression data for 502 cancer-related genes from very small formalin-fixed sentinel node biopsy (SNB) melanoma samples, this data has been further compared with gene expression of the matched formalin-fixed primary melanoma. Tissue was sampled from twenty-five SNB deposits using laser capture microdissection. The mean number of genes detected using DASL with SNB samples was lower than when using a core of primary melanoma tumor (242 versus 434 genes). A large proportion of SNB samples failed (<240 genes detected) the assay (57.7%). Area of tissue microdissected, RNA concentration and qRT-PCR quality control did not predict performance of samples on the array but age of sampled tissue negatively correlated with number of genes detected (p=0.01). For samples that performed successfully, matched primary samples were available for 10 samples. Gene expression profiles correlated between all matched tumor pairs (Spearman’s rho 0.15-0.80, p<0.01), although a number of genes were differentially expressed between nodal and primary tumors in all tumor pairs. This study demonstrates that the DASL assay can be used to generate gene expression data from small formalin-fixed samples, but not consistently. Differentially expressed genes were identified across 10 matched primary and nodal tumor pairs suggesting that the DASL assay could be used to derive essential biological information about early metastasis. Formalin-fixed paraffin-embedded SNB samples and primary tumors were identified from two study sets. In Study 1, population ascertained melanoma patients were recruited to a cohort in the period from 2000 till the present day. Eight positive SNB samples were identified, from patients whose primary tumors had already been sampled for DASL studies. In Study 2, seventeen positive SNB samples were identified in a study designed to identify predictors of sentinel node positivity and relapse (SNB study). One nodal RNA sample, microdissected from a diagnostic H&E slide, was not sent for DASL analysis because of low RNA concentration (0.37 ng/μl), therefore a total of 26 nodal samples (including 2 replicate samples) were supplied to the Illumina DASL service provider. Of the 11 samples successfully yielding gene expression data, 10 had matched primary samples (e.g., Node_1 and Primary_1) for which gene expression data were available and is presented in this data set.

Dataset Information

Genome-wide Expression Assay Comparison Across Frozen and Fixed Postmortem Brain Tissue Samples

Publications

Preprocessing and Quality Control Strategies for Illumina DASL Assay-Based Brain Gene Expression Studies with Semi-Degraded Samples.

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