A rapid, multiplex digital <scp>PCR</scp> assay to detect gene variants and fusions in non‐small cell lung cancer

Leatham, Bryan; McNall, Katie; Subramanian, Hari K. K.; Jacky, Lucien; Alvarado, John; Yurk, Dominic; Wang, Mimi; Green, Donald C.; Tsongalis, Gregory J.; Rajagopal, Aditya; Schwartz, Jerrod J.

doi:10.1002/1878-0261.13523

Cited by 3 publications

(2 citation statements)

References 37 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…High Definition (HDPCR) NSCLC panel utilizes dPCR, where endpoint fluorescent intensities are modulated so that each unique target produces a unique endpoint intensity [17,25,26]. The HDPCR NSCLC Panel (ChromaCode, Carlsbad, CA, USA) comprises three wells: two wells to detect DNA targets, and one to detect RNA fusions.…”

Section: Hdpcr Nsclcmentioning

confidence: 99%

Analytical Performance and Concordance with Next-Generation Sequencing of a Rapid, Multiplexed dPCR Panel for the Detection of DNA and RNA Biomarkers in Non-Small-Cell Lung Cancer

Cabrera,

Gole,

Leatham

et al. 2023

Diagnostics

View full text Add to dashboard Cite

FDA approval of targeted therapies for lung cancer has significantly improved patient survival rates. Despite these improvements, barriers to timely access to biomarker information, such as nucleic acid input, still exist. Here, we report the analytical performance and concordance with next-generation sequencing (NGS) of a highly multiplexed research-use-only (RUO) panel using digital PCR (dPCR). The panel’s analytical sensitivity and reactivity were determined using contrived DNA and RNA mixes. The limit of blank was established by testing FFPE curls classified as negative by pathology. Concordance was established on 77 FFPE samples previously characterized using the Oncomine Precision Assay®, and any discordant results were resolved with Archer Fusionplex® and Variantplex® panels. The analytical sensitivity, reported as the estimated mutant allele fraction (MAF), for DNA targets ranged from 0.1 to 0.9%. For RNA targets (ALK, RET, ROS, NTRK 1/2/3 Fusions, and MET Exon 14 skipping alteration), the analytical sensitivity ranged from 23 to 101 detected counts with 5 ng of total RNA input. The population prevalence-based coverage ranged from 89.2% to 100.0% across targets and exceeded 99.0% in aggregate. The assay demonstrated >97% concordance with respect to the comparator method.

show abstract

Section: Hdpcr Nsclcmentioning

confidence: 99%

Analytical Performance and Concordance with Next-Generation Sequencing of a Rapid, Multiplexed dPCR Panel for the Detection of DNA and RNA Biomarkers in Non-Small-Cell Lung Cancer

Cabrera,

Gole,

Leatham

et al. 2023

Diagnostics

View full text Add to dashboard Cite

show abstract

“…On the other hand, the detection of some biomarkers requires the use of high-throughput sequencing or chip technologies, which are costly and require specialized equipment and personnel, limiting their use in resource-limited areas. Therefore, it is necessary to develop more convenient and economical detection methods, such as using multiplex PCR or multiplex IHC to detect specific genes or proteins ( 57 , 144 ).…”

Section: The Application Of Tissue-resident Immune Cells In Non-small...mentioning

confidence: 99%

Roles of tissue-resident immune cells in immunotherapy of non-small cell lung cancer

Tang,

Wang,

Tang

2023

Front. Immunol.

View full text Add to dashboard Cite

Non-small cell lung cancer (NSCLC) is the most common and lethal type of lung cancer, with limited treatment options and poor prognosis. Immunotherapy offers hope for improving the survival and quality of life of NSCLC patients, but its efficacy depends on the tumor immune microenvironment (TME). Tissue-resident immune cells are a subset of immune cells that reside in various tissues and organs, and play an important role in fighting tumors. In NSCLC, tissue-resident immune cells are heterogeneous in their distribution, phenotype, and function, and can either promote or inhibit tumor progression and response to immunotherapy. In this review, we summarize the current understanding on the characteristics, interactions, and roles of tissue-resident immune cells in NSCLC. We also discuss the potential applications of tissue-resident immune cells in NSCLC immunotherapy, including immune checkpoint inhibitors (ICIs), other immunomodulatory agents, and personalized cell-based therapies. We highlight the challenges and opportunities for developing targeted therapies for tissue-resident immune cells and optimizing existing immunotherapeutic approaches for NSCLC patients. We propose that tissue-resident immune cells are a key determinant of NSCLC outcome and immunotherapy response, and warrant further investigation in future research.

show abstract

MSI-H Detection by ddPCR in Endoscopic Ultrasound Fine Needle Biopsy (EUS-FNB) from Pancreatic Ductal Adenocarcinoma

Piano,

Boldrin,

Moserle

et al. 2024

IJMS

View full text Add to dashboard Cite

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive disease with limited survival. Curative opportunities are only available for patients with resectable cancer. Palliative chemotherapy is the current standard of care for unresectable tumors. Numerous efforts have been made to investigate new therapeutic strategies for PDAC. Immunotherapy has been found to be effective in treating tumors with high microsatellite instability (MSI-H), including PDAC. The ability of the Endoscopic Ultrasound Fine Needle Biopsy (EUS-FNB) to reliably collect tissue could enhance new personalized treatment by permitting genomic alterations analysis. The aim of this study was to investigate the feasibility of obtaining adequate DNA for molecular analysis from EUS-FNB formalin-fixed-paraffin-embedded (FFPE) specimens. For this purpose, FFPE-DNA obtained from 43 PDAC archival samples was evaluated to verify adequacy in terms of quantity and quality and was tested to evaluate MSI-H status by droplet digital PCR (ddPCR). All samples were suitable for ddPCR analysis. Unlike the 1–2% MSI-H frequency found with traditional techniques, ddPCR detected this phenotype in 16.28% of cases. This study suggests the ddPCR ability to identify MSI-H phenotype, with the possibility of improving the selection of patients who may benefit from immunotherapy and who would be excluded by performing traditional diagnostic methods.

show abstract

A rapid, multiplex digital PCR assay to detect gene variants and fusions in non‐small cell lung cancer

Cited by 3 publications

References 37 publications

Analytical Performance and Concordance with Next-Generation Sequencing of a Rapid, Multiplexed dPCR Panel for the Detection of DNA and RNA Biomarkers in Non-Small-Cell Lung Cancer

Analytical Performance and Concordance with Next-Generation Sequencing of a Rapid, Multiplexed dPCR Panel for the Detection of DNA and RNA Biomarkers in Non-Small-Cell Lung Cancer

Roles of tissue-resident immune cells in immunotherapy of non-small cell lung cancer

MSI-H Detection by ddPCR in Endoscopic Ultrasound Fine Needle Biopsy (EUS-FNB) from Pancreatic Ductal Adenocarcinoma

Contact Info

Product

Resources

About