Technical differences between sequencing and microarray platforms impact transcriptomic subtyping of colorectal cancer

Gene expression profiling has increasing relevance in the molecular screening of patients with colorectal cancer (CRC). We investigated potential platform-specific effects on transcriptomic subtyping according to established frameworks by comparisons of expression profiles from RNA sequencing and ex...

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Bibliographic Details
Published in:Cancer letters 2020-01, Vol.469, p.246-255
Main Authors: Eilertsen, Ina A., Moosavi, Seyed H., Strømme, Jonas M., Nesbakken, Arild, Johannessen, Bjarne, Lothe, Ragnhild A., Sveen, Anita
Format: Article
Language:English
Subjects:
Annotations
Arrays
Cancer
Classification
Classification concordance
Colorectal cancer
Colorectal carcinoma
Consensus molecular subtypes
Correspondence
CRC intrinsic subtypes
Cytotoxicity
DNA microarrays
Gene expression
Genes
Genomes
Lymphocytes
Medical prognosis
Microarray
Microsatellites
Nucleotides
Patients
Ribonucleic acid
RNA
RNA sequencing
Standardization
Tumors
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Summary:Gene expression profiling has increasing relevance in the molecular screening of patients with colorectal cancer (CRC). We investigated potential platform-specific effects on transcriptomic subtyping according to established frameworks by comparisons of expression profiles from RNA sequencing and exon-resolution microarrays in 126 primary microsatellite stable CRCs. There was a strong platform correspondence in global gene expression levels, albeit with systematic technical bias likely attributed to few sequencing reads covering short (
ISSN:0304-3835
1872-7980
DOI:10.1016/j.canlet.2019.10.040