ultraseek lung cancer panel  (agena bioscience)

Journal: Communications medicine

Article Title: Detection of actionable mutations in circulating tumor DNA for non-small cell lung cancer patients.

doi: 10.1038/s43856-025-00921-8

Figure Lengend Snippet: Fig. 1 | Pathogenic variants identified in study cohort. a Distribution of variants detected during routine tumor tissue next-generation sequencing (NGS) and that were listed in the pathology report for 132 patients. b Distribution of variants identified using the UltraSEEK Lung Panel on plasma-derived circulating cell-free DNA (ccfDNA) of the same patient cohort. c Distribution of all variants when combining tumor tissue and plasma analysis.

Article Snippet: UltraSEEK Lung Panel analysis Molecular profiling of ccfDNAwas performed using the UltraSEEK® Lung Panel v2 (Agena Bioscience, San Diego, CA, USA) according to the manufacturer’s recommendations, which comprises analysis of 78 SNVs and indels inBRAF,EGFR,ERBB2,KRAS, andPIK3CA (SupplementaryData 1).

Techniques: Next-Generation Sequencing, Clinical Proteomics, Derivative Assay

Journal: Communications medicine

Article Title: Detection of actionable mutations in circulating tumor DNA for non-small cell lung cancer patients.

doi: 10.1038/s43856-025-00921-8

Figure Lengend Snippet: Fig. 5 | Eligibility for targeted treatment strategies based on the molecular tumor profile. Distribution of all patients (n = 180) eligible for targeted therapy based on a tumor tissue NGS analysis only, b UltraSEEK plasma analysis only, and c the com- bined analysis of tumor tissue and plasma.

Article Snippet: UltraSEEK Lung Panel analysis Molecular profiling of ccfDNAwas performed using the UltraSEEK® Lung Panel v2 (Agena Bioscience, San Diego, CA, USA) according to the manufacturer’s recommendations, which comprises analysis of 78 SNVs and indels inBRAF,EGFR,ERBB2,KRAS, andPIK3CA (SupplementaryData 1).

Techniques: Clinical Proteomics

Journal: EMBO Molecular Medicine

Article Title: Mutation analysis in individual circulating tumor cells depicts intratumor heterogeneity in melanoma

doi: 10.1038/s44321-024-00082-6

Figure Lengend Snippet: ( A ) The UltraSEEK ® Melanoma Panel was tested on 5 mutations (certain mutations are detected by 2 different assays in the same panel) with our modified protocol on individual cells from melanoma tumor cell lines not chemically preserved. The number of cells with successful mutation detection over the number of efficiently lysed cells is mentioned. Created with BioRender.com. ( B ) Normalized intensity and signal to noise ratio (SNR) values obtained for each PCR assay for gDNA tested at 6.6 pg input in duplicate, not chemically preserved single cells and ‘Parsortix’ processed single cells. The horizontal line represents the threshold value of SNR (set to 10) and of the normalized intensity calculated on leukocytes. For MAP2K1 P124S_f2, only non-fixed single cells data are displayed due to the positive signal observed on one leukocyte that led to excluding this assay from further analysis.

Article Snippet: The UltraSEEK® Melanoma and Lung Panels (Agena Bioscience, San Diego, CA, USA) are designed to detect multiple hotspot mutations of melanoma or lung cancer entities from ctDNA, respectively (Dataset EV and EV for the complete list of mutations).

Techniques: Modification, Mutagenesis

Journal: EMBO Molecular Medicine

Article Title: Mutation analysis in individual circulating tumor cells depicts intratumor heterogeneity in melanoma

doi: 10.1038/s44321-024-00082-6

Figure Lengend Snippet: ( A ) Left: Schematic figure of the Parsortix ® enrichment workflow with melanoma tumor cell lines. Left panel: melanoma tumor cells were spiked into ‘Transfix’ blood, captured in the Parsortix ® cassette and harvested on a slide for staining to be picked by manual micromanipulation. Created using BioRender.com. Right panel: Recovery rate obtained for each assay on single cell with Parsortix ® enrichment. Detection rate is displayed above the bar and the number of cells with successful mutation detection over the number of efficiently lysed cells is mentioned within bars. Note that recovery data are presented for each PCR assay in case multiple PCR assays for the same mutation are present in the panel. ( B ) Number of mutations in ctDNA or CTCs in samples with both sufficient amount of cfDNA and at least one CTC efficiently lysed, as defined by internal process controls. Of note, the assays with positive signals observed in the leukocytes validation set have been removed. P -value was calculated using the Wilcoxon signed-rank test for paired data. ( C ) Landscape of the mutations detected in the different melanoma samples (tissue, cfDNA, CTC). On the top of the panel, patient ID is indicated with the type of sample analyzed. We distinguished samples obtained before initiation of treatment from those obtained during treatment. For patient 26, we grouped the 3 samples obtained during treatment. ‘Tissue UltraSEEK’ stands for the analysis of gDNA from a tumor tissue sample with UltraSEEK ® Melanoma Panel. The assays with positive values on leukocytes validation set are marked with an asterisk. SDHD.Mut3 stands for SDHD mutation Chr11:111, 957,544 C > T. .

Article Snippet: The UltraSEEK® Melanoma and Lung Panels (Agena Bioscience, San Diego, CA, USA) are designed to detect multiple hotspot mutations of melanoma or lung cancer entities from ctDNA, respectively (Dataset EV and EV for the complete list of mutations).

Techniques: Staining, Micromanipulation, Mutagenesis, Biomarker Discovery

Journal: EMBO Molecular Medicine

Article Title: Mutation analysis in individual circulating tumor cells depicts intratumor heterogeneity in melanoma

doi: 10.1038/s44321-024-00082-6

Figure Lengend Snippet: ( A ) The UltraSEEK ® Lung Panel was tested on 2 EGFR mutations and 2 PI3KCA mutations with our modified protocol on individual cells from lung (H1975) or breast tumor cell lines (MCF7 and T47D) not chemically preserved. The number of cells with successful mutation detection over the number of efficiently lysed cells is mentioned. ( B ) The UltraSEEK ® Lung Panel was tested on the 2 EGFR mutations with our modified protocol on individual cells from lung tumor cell lines processed with Parsortix ® enrichment method. The number of cells with successful mutation detection over the number of efficiently lysed cells is mentioned. ( C ) Normalized intensity and signal-to-noise ratio (SNR) values obtained for each PCR assay for gDNA tested at 6.6 pg input in duplicate, not chemically preserved single cells and ‘Parsortix’ processed single cells.

Article Snippet: The UltraSEEK® Melanoma and Lung Panels (Agena Bioscience, San Diego, CA, USA) are designed to detect multiple hotspot mutations of melanoma or lung cancer entities from ctDNA, respectively (Dataset EV and EV for the complete list of mutations).

Techniques: Modification, Mutagenesis

Journal: EMBO Molecular Medicine

Article Title: Mutation analysis in individual circulating tumor cells depicts intratumor heterogeneity in melanoma

doi: 10.1038/s44321-024-00082-6

Figure Lengend Snippet: ( A ) Left: Schematic figure of the CellSearch®/DEPArray™ enrichment workflow with melanoma and breast tumor cell lines. Left panel: melanoma or breast tumor cells were spiked into ‘CellSave’ blood, captured on the CellSearch ® platform and isolated as single cells with the DEPArray™ system. Created using BioRender.com. Right panel: Recovery rate obtained for each assay on single cell with CellSearch ® /DEPArray™ enrichment. The detection rate is displayed above the bar and the number of cells with successful mutation detection over the number of efficiently lysed cells is mentioned within bars. Note that recovery data are presented for each PCR assay in case multiple PCR assays for the same mutation are present in the panel. ( B , C ) Illustrative picture of melanoma CTCs and of the mutation calls in 2 melanoma patients (B. patient MEL21; C. Patient MEL31). Scale bar represents ca . 10 µm. ( D ) Illustrative picture of breast cancer CTCs and its subsequent analysis with UltraSEEK ® protocol (for 8 CTCs) or sequencing after WGA (for 6 CTCs). Successful cell lysis and gDNA amplification was obtained in 4/8 CTCs with UltraSEEK ® protocol and from 2/6 CTCs after WGA quality control. PI3KCA E545K mutation was detected in 4/4 CTC and 1/2 CTC, respectively. Scale bar represents ca . 10 µm. .

Article Snippet: The UltraSEEK® Melanoma and Lung Panels (Agena Bioscience, San Diego, CA, USA) are designed to detect multiple hotspot mutations of melanoma or lung cancer entities from ctDNA, respectively (Dataset EV and EV for the complete list of mutations).

Techniques: Isolation, Mutagenesis, Sequencing, Lysis, Amplification, Control

Journal: EMBO Molecular Medicine

Article Title: Mutation analysis in individual circulating tumor cells depicts intratumor heterogeneity in melanoma

doi: 10.1038/s44321-024-00082-6

Figure Lengend Snippet: *Duration of the protocol for WGA is dependent on WGA technologies. We included cell lysis that is also necessary into WGA protocol global time. We chose to compare the UltraSEEK ® -adapted protocol to WGA and next-generation sequencing (NGS) as it appears for us that NGS was the most adequate technology to analyze in parallel multiple hotspot mutations. Created using BioRender.com.

Article Snippet: The UltraSEEK® Melanoma and Lung Panels (Agena Bioscience, San Diego, CA, USA) are designed to detect multiple hotspot mutations of melanoma or lung cancer entities from ctDNA, respectively (Dataset EV and EV for the complete list of mutations).

Techniques: Lysis, Next-Generation Sequencing

Journal: International journal of molecular sciences

Article Title: Detection and Monitoring of Tumor-Derived Mutations in Circulating Tumor DNA Using the UltraSEEK Lung Panel on the MassARRAY System in Metastatic Non-Small Cell Lung Cancer Patients.

doi: 10.3390/ijms241713390

Figure Lengend Snippet: Figure 1. Detection of hotspot mutations common in NSCLC using UltraSEEK® Lung Panel. (A) Detection rate and (B) quantification of Seraseq® ctDNA Complete™Mutation Mix reference material at variant allele frequencies (VAFs) of 2.5%, 1.0%, 0.5%, and 0.1% were analyzed using 20 ng (black), 10 ng (dark grey), and 5 ng (light grey) ccfDNA input. Error bars represent the confidence intervals calculated from the detection rates per mutation; detailed results of ten hotspot mutations in EGFR, KRAS, BRAF, ERBB2, and PIK3CA are presented in Supplemental Table S1. Kruskal–Wallis test was performed, followed by Dunn’s multiple comparison test; all comparisons were not significant.

Article Snippet: Molecular profiling was performed at t0, t1, and tp using the UltraSEEK® Lung Panel on the MassARRAY® System [24,29,31,47,48] (Agena Bioscience, San Diego, CA, USA) and ddPCR [7,17] (Bio-Rad Laboratories, Pleasanton, CA, USA) according to the manufacturer’s recommendations (for details, see Supplemental Materials and Methods; Supplemental Table S9).

Techniques: Mutagenesis, Variant Assay, Comparison

Journal: International journal of molecular sciences

Article Title: Detection and Monitoring of Tumor-Derived Mutations in Circulating Tumor DNA Using the UltraSEEK Lung Panel on the MassARRAY System in Metastatic Non-Small Cell Lung Cancer Patients.

doi: 10.3390/ijms241713390

Figure Lengend Snippet: Figure 2. Concordance between mutations detected in tumor tissue and plasma-derived ccfDNA in EGFR, KRAS, BRAF, ERBB2, and PIK3CA. (A) Pie chart representing the patients in whom mutation detection using tissue NGS and plasma UltraSEEK® Lung Panel analyses was considered concordant (green) and discordant (grey) for all mutations covered by the UltraSEEK® Lung Panel. (B) Bar chart representing the distribution of all mutations detected using tumor tissue NGS reported in the pathology archives and plasma UltraSEEK® Lung Panel analysis. (C) Stacked bar chart displaying the distribution of individual mutations detected both with tissue NGS and plasma UltraSEEK®

Article Snippet: Molecular profiling was performed at t0, t1, and tp using the UltraSEEK® Lung Panel on the MassARRAY® System [24,29,31,47,48] (Agena Bioscience, San Diego, CA, USA) and ddPCR [7,17] (Bio-Rad Laboratories, Pleasanton, CA, USA) according to the manufacturer’s recommendations (for details, see Supplemental Materials and Methods; Supplemental Table S9).

Techniques: Clinical Proteomics, Derivative Assay, Mutagenesis

Journal: International journal of molecular sciences

Article Title: Detection and Monitoring of Tumor-Derived Mutations in Circulating Tumor DNA Using the UltraSEEK Lung Panel on the MassARRAY System in Metastatic Non-Small Cell Lung Cancer Patients.

doi: 10.3390/ijms241713390

Figure Lengend Snippet: Figure 3. Survival analysis according to ctDNA dynamics using the UltraSEEK® Lung Panel. Kaplan– Meier plot displaying the (A) progression-free survival (PFS) and (B) overall survival (OS) of patients with decreasing (blue), negative (black), stable (green), or increasing (red) ctDNA levels. (C) PFS and (D) OS of patients with decreasing ctDNA levels (blue) or no decrease in ctDNA (red). No decrease in ctDNA encompasses all patients without a >15% decrease in ctDNA. Horizontal dashed lines indicate the median survival; vertical lines indicate the moment at which the median survival was reached. HR, hazard ratio; CI, confidence interval. Log-rank test, p-value < 0.05, was considered significant.

Article Snippet: Molecular profiling was performed at t0, t1, and tp using the UltraSEEK® Lung Panel on the MassARRAY® System [24,29,31,47,48] (Agena Bioscience, San Diego, CA, USA) and ddPCR [7,17] (Bio-Rad Laboratories, Pleasanton, CA, USA) according to the manufacturer’s recommendations (for details, see Supplemental Materials and Methods; Supplemental Table S9).

Techniques: