Incorporation of digital gene expression profiling for cell-of-origin determination (Lymph2Cx testing) into the routine work-up of diffuse large B cell lymphoma

Abstract

Diffuse large B cell lymphomas (DLBCL) represent a clinically heterogeneous group of lymphomas that are classified together based on similarities in morphology and immunophenotype. Gene expression profiling further classifies DLBCL into distinct molecular subgroups based on cell-of-origin (COO), including germinal center B cell type, activated B cell type, and unclassified type. COO assignment of DLBCL has important biological and prognostic significance, as well as emerging therapeutic implications. Herein, we describe the first clinical validation of a digital gene expression-profiling assay (Lymph2Cx) to perform COO assignment in the routine work-up of DLBCL using formalin-fixed paraffin-embedded (FFPE) tissue sections and describe the results of 90 consecutive DLBCL cases analyzed prospectively by a College of American Pathologists/Clinical Laboratory Improvement Amendments (CAP/CLIA)-certified clinical molecular diagnostics laboratory.

Transcriptional profiles define drug refractory disease in myeloma

“…NanoString nCounter technology, a direct multiplexed measurement of gene expression based on digital color‐barcoding technology [ 22 ], is a flexible, reproducible, and robust method when used for molecular subtyping of diffuse large B‐cell lymphoma [ 23 , 24 , 25 ]. In this study, we employed this technology to investigate the transcriptional expression of 121 genes potentially associated with IMiD or PI response, in both human myeloma cell lines (HMCLs) and primary MM patient samples collected at different times of the disease.…”

Molecular subtyping of CD5+ diffuse large B-cell lymphoma based on DNA-targeted sequencing and Lymph2Cx

“…The NanoString platform not only facilitates the routine gene expression-based COO classification of DLBCL but also allows this analysis to be conducted on FFPE tissues ( 59 ). In this study, we performed a Lymph2Cx assay to detect the mRNA expression of 15 lymphoma-related genes on the NanoString platform for COO analysis.…”

“…These two genes acted as the regulators of NF-κB and were considered to be markers for ABC DLBCL ( 63 – 65 ). The other four differentially expressed genes, SERPINA9 , MAML3 , ITPKB , and S1PR2 , all of which were suggested to be overexpressed in GBC DLBCL ( 59 ), were downregulated in CD5+ DLBCL. We also performed a survival analysis on the mRNA level of these 15 genes, in which the median mRNA level of all cases was treated as the cutoff value, and the cases were divided into high- and low-expression groups.…”

Clinical laboratory validation of the MCL35 assay for molecular risk stratification of mantle cell lymphoma

“…In the former, pre-labeled probes are purchased from NanoString, while in the latter, unlabeled probes are hybridized to both the target RNA of interest and "tags" pre-labeled with a standardized set of NanoString's fluorescent barcodes. As in our previous work with the Lymph2Cx assay, the Elements chemistry was evaluated due to the ability of the local laboratory to standardize the fluorescent barcodes between each run [12]. For this comparison, RNA from 12 specimens previously assayed with Standard chemistry in our prior MCL35 publication, representing the range of possible MCL35 risk scores, were assessed with Elements chemistry to examine for bias.…”

“…Here we report on the evaluation of the MCL35 assay as a clinical biomarker in the CAP-accredited/CLIA-certified Molecular Diagnostics-Arizona Laboratory (MDAZL), a lab with extensive experience in the development (Lymph2Cx, Lymph3Cx) and FDA validation (LymphMark™) of similar nCounter®-based molecular profiling assays [12]. Performance specifications for accuracy, precision, sensitivity, specificity, and clinical utility were assessed in this study.…”