Colon lung v2 ampliseq panel

Manufactured by Thermo Fisher Scientific

Sourced in United States

The Colon Lung v2 AmpliSeq Panel is a targeted next-generation sequencing (NGS) assay designed for the analysis of genetic variants in colon and lung cancer samples. The panel targets specific regions of genes associated with these cancer types. The assay utilizes the AmpliSeq technology to generate amplicons for sequencing on Thermo Fisher Scientific's NGS platforms.

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Lab products found in correlation

Maxwell 16 research, by Promega (1 mentions)

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AmpliSeq panel (22 citations) Ion AmpliSeq Colon and Lung Cancer Panel v2 (6 citations) Ion Ampliseq Colon-Lung Cancer Research Panel V2 (2 citations)

2 protocols using colon lung v2 ampliseq panel

Targeted Colon and Lung Cancer Panel

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For this study, we used the Colon Lung v2 AmpliSeq Panel (Thermo Scientific, Waltham, USA) according to the manufacturer’s instructions.
The panel comprises 92 amplicons covering hotspot and targeted regions of 22 genes involved in colon and lung cancer tumorigenesis (KRAS, EGFR, BRAF, PIK3CA, AKT1, ERBB2, PTEN, NRAS, STK11, MAP2K1, ALK, DDR2, CTNNB1, MET, TP53, SMAD4, FBXW7, FGFR3, NOTCH1, ERBB4, FGFR1, FGFR2). We used 10ng DNA input for each NGS library generation following the AmpliSeq Library protocol Version E.0 (Thermo Scientific, Waltham, USA).

Wessolly M., Stephan-Falkenau S., Streubel A., Werner R., Borchert S., Griff S., Mairinger E., Walter R.F., Bauer T., Eberhardt W.E., Blum T.G., Schmid K.W., Kollmeier J., Mairinger T, & Mairinger F.D. (2020). A Novel Epitope Quality-Based Immune Escape Mechanism Reveals Patient’s Suitability for Immune Checkpoint Inhibition. Cancer Management and Research, 12, 7881-7890.

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Personalized Neoantigen Prediction from NSCLC Samples

Cited 1 time

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After DNA isolation on a Maxwell® 16 Research (Promega Corporation, Madison, USA) as recommended in the manufacturer’s protocol, all tumor samples were sequenced using a small panel of 22 genes and 92 amplicons covering hotspots characteristic for NSCLC (Colon Lung v2 AmpliSeq Panel by Thermo Scientific, Waltham, MA, USA).
Non-synonymous mutations with a coverage above 500 reads and an allelic frequency above 3.0% were included into the analysis. Variants with an allelic frequency below 3.0% were filtered out and regarded as artifacts due to formalin fixation. Considering the percentage of tumor cells, the mutations validated needed to be detectable in at least 10% of the tumor sample.
The influence of mutations on proteasomal cleavage was predicted by the machine learning tool NetChop 3.1 [43 (link), 44 (link)]. The binding of the resulting epitopes to MHC class I was subsequently simulated by NetMHC 4.0 [45 (link), 46 ], also based on convolutional neural networks. The whole procedure is described in detail in our previous works [34 (link)].

Wessolly M., Stephan-Falkenau S., Streubel A., Wiesweg M., Borchert S., Mairinger E., Kollmeier J., Reis H., Bauer T., Schmid K.W., Mairinger T., Schuler M, & Mairinger F.D. (2022). Digital gene expression analysis of NSCLC-patients reveals strong immune pressure, resulting in an immune escape under immunotherapy. BMC Cancer, 22, 46.

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