title: QuantiGene Plex Represents a Promising Diagnostic Tool for Cell-of-Origin Subtyping of Diffuse Large B-Cell Lymphoma.
abstract: Emerging therapies targeting the molecularly distinct GCB and non-GCB/ABC subtypes of diffuse large B-cell lymphoma (DLBCL) have created the need to develop an accurate subtyping assay for routine use. We investigated the potential of QuantiGene Plex (QGP)-branched DNA signal amplification assay-for DLBCL subtyping. We performed in silico analysis of public DLBCL datasets to develop and validate a naïve Bayes classifier, and migrated the resulting 21-gene classifier to QGP and real-time quantitative PCR (qPCR) assays. Forty DLBCL formalin-fixed, paraffin-embedded tumors of known subtype (20 per subtype by gene expression profiling of paired fresh-frozen tissues) were reclassified, and results for QGP (on 38/40 for 21/21 targets) and qPCR (on 40/40 samples for 19/21 targets) compared for recapitulation of microarray data and classification accuracy. The 21-gene bayesian classifier achieved mean area under the curve values >0.9 on independent validation. QGP showed a higher correlation with microarray data (mean R(2) = 0.66 ± 0.05 versus 0.34 ± 0.07; P < 0.0001) and classification accuracy (92.1% versus 78.9%). The proportion of validated targets was also higher for QGP (85.7% versus 47.4%). The QGP protocol was rapid and simple to perform, at a cost similar to qPCR. These promising preliminary results strongly support ongoing work to develop a QGP companion diagnostic assay for DLBCL subtyping.
authors.affiliation: Lymphoma Translational Research Group, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom.
authors.forename: John S
authors.initials: JS
authors.lastname: Hall
authors.affiliation: Lymphoma Translational Research Group, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom.
authors.forename: Suzanne
authors.initials: S
authors.lastname: Usher
authors.affiliation: Lymphoma Translational Research Group, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom.
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Byers
authors.affiliation: Lymphoma Translational Research Group, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom.
authors.forename: Rebekah C
authors.initials: RC
authors.lastname: Higgins
authors.affiliation: Applied Computational Biology and Bioinformatics Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom.
authors.forename: Danish
authors.initials: D
authors.lastname: Memon
authors.affiliation: Lymphoma Translational Research Group, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom; The Department of Medical Oncology, Christie National Health Service Foundation Trust, Manchester, United Kingdom.
authors.forename: John A
authors.initials: JA
authors.lastname: Radford
authors.affiliation: Lymphoma Translational Research Group, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom; The Department of Medical Oncology, Christie National Health Service Foundation Trust, Manchester, United Kingdom. Electronic address: kim.linton@manchester.ac.uk.
authors.forename: Kim M
authors.initials: KM
authors.lastname: Linton
mesh_terms: D001499:Bayes Theorem; D015331:Cohort Studies; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D016403:Lymphoma, Large B-Cell, Diffuse / Q000145:classification* / Q000235:genetics / Q000473:pathology*; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis; D009928:Organ Specificity / Q000235:genetics*; D016612:Paraffin Embedding; D011379:Prognosis; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods