Genomics

Dataset Information

0

A novel diagnostic approach for the classification of small B-cell lymphoid neoplasms based on the NanoString platform


ABSTRACT: Small B-cell lymphoid neoplasms (SBCLNs) are a heterogeneous group of diseases characterized by malignant clonal proliferation of mature B-cells. However, the classification of SBCLNs remains a challenge, especially in cases where histopathological analysis is unavailable or those with atypical laboratory findings or equivocal pathologic data. In this study, gene expression profiling of 1,039 samples from 27 GEO datasets was first investigated to select highly and differentially expressed genes among SBCLNs. Samples from 57 SBCLN cases and 102 nonmalignant control samples were used to train a classifier using the NanoString platform. The classifier was built by employing a cascade binary classification method based on the random forest algorithm with 35 refined gene signatures. Cases were successively classified as chronic lymphocytic leukemia/small lymphocytic lymphoma, conventional mantle cell lymphoma, follicular lymphoma, leukemic non-nodal mantle cell lymphoma, marginal zone lymphoma, lymphoplasmacytic lymphoma/Waldenström’s macroglobulinemia, and other undetermined. The classifier algorithm was then validated using an independent cohort of 197 patients with SBCLNs. Under the distribution of our validation cohort, the overall sensitivity and specificity of proposed algorithm model were >95% respectively for all the cases with tumor cell content greater than 0.72. Combined with additional genetic aberrations including IGH-BCL2 translocation, MYD88 L265P mutation, and BRAF V600E mutation, the optimal sensitivity and specificity were respectively found at 0.88 and 0.98. In conclusion, the established algorithm demonstrated to be an effective and valuable ancillary diagnostic approach for the sub-classification and pathologic investigation of SBCLN in daily practice. Overall design: Using the NanoString platform, we developed the assay which may help classify small B-cell lymphoid neoplasms.

INSTRUMENT(S): NanoString nCounter Human SBCLN gene expression custom v1

ORGANISM(S): Homo sapiens  

SUBMITTER: Wei Zhang  

PROVIDER: GSE183030 | GEO | 2021-11-18

REPOSITORIES: GEO

Dataset's files

Source:
Action DRS
GSE183030_RAW.tar Raw
filelist.txt Txt
Items per page:
1 - 2 of 2

Similar Datasets

2020-01-01 | S-EPMC7253736 | BioStudies
1000-01-01 | S-EPMC3179701 | BioStudies
2007-01-01 | S-EPMC1924473 | BioStudies
2011-01-01 | S-EPMC4657859 | BioStudies
2002-01-01 | S-EPMC1906992 | BioStudies
2018-01-01 | S-EPMC6265260 | BioStudies
2019-01-01 | S-EPMC6833098 | BioStudies
2015-01-01 | S-EPMC4422099 | BioStudies
1000-01-01 | S-EPMC3367895 | BioStudies
2021-09-02 | GSE171424 | GEO