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| Status |
Public on May 03, 2019 |
| Title |
Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: Comparison of gene expression profiling approaches [QiaSeq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Background: High-throughput transcriptomics has matured into a very well established and widely utilised research tool over the last two decades since the first mRNA profiling microarrays. Clinical datasets generated on a range of different platforms continue to be deposited in public repositories provide an ever-growing, valuable resource for reanalysis. Cost and tissue availability normally preclude processing samples across multiple technologies, making it difficult to directly evaluate performance, reliability and to what extent gene expression data from different platforms can be compared or integrated.
Purpose: In this study, we describe our experiences using nine new and established mRNA profiling techniques including Lexogen QuantSeq, Qiagen QiaSeq, BioSpyder TempO-Seq, Ion AmpliSeq, Nanostring, Affymetrix Clariom S or U133A, Illumina BeadChip and Ion Total RNA-seq of formalin-fixed paraffin embedded (FFPE) and fresh frozen (FF) sequential patient-matched breast tumour samples.
Results: The number of genes represented and reliability were found to vary between the platforms, but overall all methods provided data which were largely comparable. Crucially we found that it is possible to integrate data for combined analyses across FFPE/FF and platforms using established batch correction methods as required to increase cohort sizes. However, some platforms appear to be better suited to FFPE samples, particularly archival material. Overall, we illustrate that technology selection is a balance between required resolution, sample quality, availability and cost.
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| Overall design |
Sequencing of patient-matched sets of human breast cancer biopsy samples using 9 different mRNA profiling platforms. We assess the feasibility of integrating data from FFPE or FF tissue sequenced using different platforms and compare these different technoolgies.
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| Contributor(s) |
Turnbull AK, Selli C, Martinez-Perez C, Sims AH |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
May 02, 2019 |
| Last update date |
May 03, 2019 |
| Contact name |
Carlos Martinez-Perez |
| E-mail(s) |
carlos.martinez-perez@igmm.ed.ac.uk
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| Organization name |
The University of Edinburgh
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| Department |
Institute of Genetics and Molecular Medicine
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| Street address |
Western General Hospital, Crewe Road South
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| City |
Edinburgh |
| ZIP/Postal code |
EH4 2XU |
| Country |
United Kingdom |
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| Platforms (1) |
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| Samples (25)
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| This SubSeries is part of SuperSeries: |
| GSE130645 |
Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: Comparison of gene expression profiling approaches |
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| Relations |
| BioProject |
PRJNA540861 |
| SRA |
SRP194624 |
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