All laboratory work was performed according to the respective manufacturer’s protocol available online. The preparation of formalin-fixed, paraffin-embedded (FFPE) tissue samples was performed identically for all three workflows. The purification of DNA from the FFPE tissue samples was performed using the Maxwell® RSC Instrument (Promega Corporation) with the Maxwell® RSC FFPE Plus DNA Kit (Promega Corporation). Therefore, the tumor containing area of a tissue section or respectively the total area of a normal tissue section was scraped off the slide, placed into a 1.5 ml tube and centrifuged at maximum speed for 15 sec. 20 μl of 20 mg/ml Proteinase K and 180 μl Incubation Buffer was added. Overnight samples were heated at 70°C. After incubation the samples were mixed with 400 μl Lysis Buffer and transferred to the Maxwell® RSC Cartridge. Further preparation and the instrument run were performed according to manufacturer’s protocol. The concentration of DNA was measured with the Qubit 4 Fluorometer (Invitrogen). For the library preparation, panel-specific amounts of DNA were used as input: 40 ng for the GeneRead™ QIAact BRCA UMI Panel (QIAGEN), 20 ng for the Oncomine™ Comprehensive Assay v3 (Thermo Fisher) and 20 ng for the AmpliSeq™ BRCA Panel (Illumina®).
Ampliseq brca panel
Manufactured by Illumina
Sourced in United States
The AmpliSeq™ BRCA Panel is a targeted next-generation sequencing (NGS) panel designed to analyze the coding regions and splice sites of the BRCA1 and BRCA2 genes. The panel utilizes AmpliSeq technology to generate a targeted library for sequencing on Illumina sequencing platforms.
Automatically generated - may contain errors
Lab products found in correlation
Oncomine comprehensive assay v3, by Thermo Fisher Scientific (1 mentions)
Maxwell rsc ffpe plus dna kit, by Promega (1 mentions)
Qubit 4 fluorometer, by Thermo Fisher Scientific (1 mentions)
Maxwell rsc instrument, by Promega (1 mentions)
Cobas egfr mutation test v2, by Roche (1 mentions)
Sophia ddm software, by Sophia Genetics (1 mentions)
Qiaamp dna ffpe tissue isolation kit, by Qiagen (1 mentions)
2 protocols using ampliseq brca panel
1
FFPE DNA Extraction and Library Prep
2
Comprehensive Genomic Profiling of Solid Cancers
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EGFR, KRAS/NRAS and BRAF mutation testing of non-small cell lung cancer, metastatic colorectal cancer and metastatic melanoma were performed from formalin-fixed and paraffinembedded (FFPE) tumor samples obtained by biopsy/resection by qPCR [4, 18] while somatic BRCA1/2 mutation testing for high-grade platinum-sensitive ovarian cancer was performed by Next-generation sequencing (NGS). Genomic DNA was isolated from one to six 10 μm sections FFPE tissue blocks using the QIAamp® DNA FFPE Tissue isolation kit (Qiagen, UK) for colorectal and ovarian cancers, while Cobas® DNA Sample Preparation Kit was used for DNA extraction from lung cancer and melanoma tissue. KRAS and NRAS mutation testing was performed using the AmoyDx ® KRAS/NRAS Mutations Detection Kit on Applied Biosystems 7500 Fast Real Time PCR system (Applied Biosystems™). EGFR and BRAF mutation testing were performed using the Cobas ® EGFR Mutation Test v2 and Cobas ® 4800 BRAF V600 Mutation Test on Cobas ® 4800 (Roche Diagnostics). The presence of BRCA1/2 somatic mutations was detected using multiplex PCR-based AmpliSeq BRCA Panel and MiSeq next-generation sequencing system (Illumina, San Diego, USA). Variant analysis and interpretation were performed by Sophia DDM software (SophiaGenetics).
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