A Novel Method of Amplification of FFPET-Derived RNA Enables Accurate Disease Classification with Microarrays

Williams, P. Mickey; Li, Rui; Johnson, Nathalie A.; Wright, George W.; Heath, Joe-Don; Gascoyne, Randy D.

doi:10.2353/jmoldx.2010.090164

Cited by 53 publications

(55 citation statements)

References 26 publications

(23 reference statements)

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“…36 The Linton model performed consistently well in reclassifying 233 DLBCL FF samples (Lenz data set) under 10-fold cross validation, with a mean AUC of 0.969. The signature was validated in an external data set 35 samples (that passed QC on all platforms) measured on U133 Plus 2.0 array (gold standard) compared with real-time quantitative PCR (red) or QGP (blue). The t-test P value represents a statistically significant difference between real-time quantitative PCR and QGP.…”

Section: Discussionmentioning

confidence: 99%

QuantiGene Plex Represents a Promising Diagnostic Tool for Cell-of-Origin Subtyping of Diffuse Large B-Cell Lymphoma

Hall

Usher

Byers

et al. 2015

The Journal of Molecular Diagnostics

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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.

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Section: Discussionmentioning

confidence: 99%

QuantiGene Plex Represents a Promising Diagnostic Tool for Cell-of-Origin Subtyping of Diffuse Large B-Cell Lymphoma

Hall

Usher

Byers

et al. 2015

The Journal of Molecular Diagnostics

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“…Formalin-fixed, paraffin-embedded (FFPE) samples are routinely archived within clinical trials. Although obtaining reliable GEPs from FFPE samples using commercially available chip (i.e., Affymetrix and Illumina) has been considered challenging for a long time, we and others have recently shown that it is feasible (16)(17)(18), in particular, by improving and optimizing the processing approach (19). However, predictors developed using frozen samples would underperform on FFPE-derived GEPs due to the unpredictable lower performances of some probesets.…”

Section: Her2mentioning

confidence: 99%

Subtype-Specific Metagene-Based Prediction of Outcome after Neoadjuvant and Adjuvant Treatment in Breast Cancer

Callari

Cappelletti

D'Aiuto

et al. 2016

Clinical Cancer Research

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Purpose: In spite of improvements of average benefit from adjuvant/neoadjuvant treatments, there are still individual patients with early breast cancer at high risk of relapse. We explored the association with outcome of robust gene clusterbased metagenes linked to proliferation, ER-related genes, and immune response to identify those high-risk patients.Experimental Design: A total of 3,847 publicly available geneexpression profiles were analyzed (untreated, N ¼ 826; tamoxifen-treated, N ¼ 685; chemotherapy-treated, N ¼ 1,150). Genes poorly performing in formalin-fixed samples were removed. Outcomes of interest were pathologic-complete response (pCR) and distant metastasis-free survival (DMFS). In ER the association with risk of relapse was not significant. Conclusions: We developed metagene-based predictors able to define low and high risk of relapse after adjuvant/neoadjuvant therapy. High-risk patients so defined should be preferably considered for trials with investigational agents.

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“…However, recent improvements in protocols that use nucleic acid extracted from FFPE routinely processed tissues for microarrays increases the likelihood that these technologies can be used in routine practice. 5,78 The information generated up to now has been based on the use of frozen samples. Validation studies using these new protocols for routine samples will be necessary to confirm the applicability of the results.…”

Section: Detection Of Oncogenic Pathways With Implications For Targetmentioning

confidence: 99%

Whole genome profiling and other high throughput technologies in lymphoid neoplasms—current contributions and future hopes

Campo

2013

Modern Pathology

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The development of high throughput technologies based on the knowledge of the human genome has opened the possibility to search for global genomic alterations in tumors responsible for their development and progression that may have important clinical implications. One of the major applications of this genomic knowledge has been the design of different types of microarray platforms for the analysis of DNA alterations and gene expression profiling (GEP). The main contributions of the DNA studies in lymphoid neoplasms include the definition of relatively characteristic genomic profiles for specific disease entities, the demonstration of common chromosomal alterations across entities, the identification of genes and pathways targeted by the altered chromosomal regions, and the identification of chromosomal alterations with prognostic implications. RNA GEP studies in these tumors have enhanced the molecular characterization of known entities and facilitated the recognition of new subtypes and categories of lymphoid neoplasms, the identification of new biomarkers and prognostic models, and the detection of oncogenic pathways with potential implications for targeted therapies. The recent development of the next generation sequencing (NGS) technologies and its application in lymphoid neoplasms already have provided an initial view of the complex landscape of somatic mutations in these tumors and some findings with important functional and clinical implications. This review addresses the major contributions and limitations of the microarray technologies in the understanding of lymphoid neoplasms and discusses how this knowledge may be transferred into the clinics. The initial results of the NGS studies are also presented.

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A Novel Method of Amplification of FFPET-Derived RNA Enables Accurate Disease Classification with Microarrays

Cited by 53 publications

References 26 publications

QuantiGene Plex Represents a Promising Diagnostic Tool for Cell-of-Origin Subtyping of Diffuse Large B-Cell Lymphoma

QuantiGene Plex Represents a Promising Diagnostic Tool for Cell-of-Origin Subtyping of Diffuse Large B-Cell Lymphoma

Subtype-Specific Metagene-Based Prediction of Outcome after Neoadjuvant and Adjuvant Treatment in Breast Cancer

Whole genome profiling and other high throughput technologies in lymphoid neoplasms—current contributions and future hopes

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