A rapid, multiplex digital PCR assay for EGFR, KRAS, BRAF, ERBB2 variants and ALK, RET, ROS1, NTRK1 gene fusions in non-small cell lung cancer
Leatham, B.; McNall, K.; Subramanian, H. K.; Jacky, L.; Alvarado, J. G.; Yurk, D.; Wang, M.; Green, D. C.; Tsongalis, G. J.; Rajagopal, A.; Schwartz, J.
Show abstract
Digital PCR (dPCR) is emerging as an ideal platform for the detection and tracking of genomic variants in cancer due to its high sensitivity and simple workflow. The growing number of clinically-actionable cancer biomarkers creates a need for fast, accessible methods that allow for dense information content and high accuracy. Here, we describe a proof-of-concept amplitude modulation based multiplex dPCR assay capable of detecting 12 single nucleotide and indel variants in EGFR, KRAS, BRAF, and ERBB2, 14 gene fusions in ALK, RET, ROS1, NTRK1, and MET exon 14 skipping present in non-small cell lung cancer (NSCLC). We also demonstrate the use of multi-spectral target signal encoding to improve the specificity of variant detection by reducing background noise up to 11-fold. The assay reported an overall 100% PPA and 98.5% NPA compared to a sequencing-based assay in a cohort of 62 human FFPE samples. In addition, the dPCR assay rescued actionable information in 10 samples that failed to sequence, highlighting the utility of a multiplexed digital assay as a potential reflex solution for challenging NSCLC samples.
Matching journals
The top 12 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Development and Implementation of a scalable and versatile test for COVID-19 diagnostics in rural communities 94%
- NULISA: a novel proteomic liquid biopsy platform with attomolar sensitivity and high multiplexing 94%
- Comprehensive benchmarking of methods for mutation calling in circulating tumor DNA 93%
Similar papers in this journal
- Evaluating the Radiation Sensitivity Index and 12-chemokine gene expression signature for clinical use in a CLIA laboratory 92%
- Probabilistic mixture models improve calibration of panel-derived tumor mutational burden in the context of both tumor-normal and tumor-only sequencing 90%
- Drug-gene interaction screens coupled to tumour data analyses identify the most clinically-relevant cancer vulnerabilities driving sensitivity to PARP inhibition 89%
Similar papers in this journal
- Versatile and flexible microfluidic qPCR test for high-throughput SARS-CoV-2 and cellular response detection in nasopharyngeal swab samples 94%
- CaBagE: a Cas9-based Background Elimination strategy for targeted, long-read DNA sequencing 93%
- A low-cost fluorescence reader for in vitro transcription and nucleic acid detection with Cas13a 93%
Similar papers in this journal
- COV-ID: A LAMP sequencing approach for high-throughput co-detection of SARS-CoV-2 and influenza virus in human saliva 93%
- RAY: CRISPR diagnostic for rapid and accurate detection of SARS-CoV2 variants on a paper strip 93%
- HyDrop: droplet-based scATAC-seq and scRNA-seq using dissolvable hydrogel beads 91%
Similar papers in this journal
- Quantitative target engagement of RIPK1 in human whole blood via the cellular thermal shift assay for potential pre-clinical and clinical applications 91%
- Keeping it clean: the cell culture quality control experience at the National Center for Advancing Translational Sciences 90%
- MICRO-TAG enzyme complementation enables quantification of cellular drug-target engagement in temperature series 90%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.