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Action OncoKitDx (Automatic)

Protocol automated using Magnis NGS Prep System

Description

Analysis of the main clinically useful genomic biomarkers associated with the most common solid tumors, using a fully automated protocol and NGS sequencing

Format

24 rxn

Technology

NGS sequencing

Reference

IMG-365

Compatible equipment

NextSeq 500/550Dx System

Protocol automated using Magnis NGS Prep System
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  • Dynamic kit that updates the target genes included in the panel according to the latest scientific evidence.
  • Detection of SNVs and INDELs.
  • Analysis of gene fusions and rearrangements (SVs) associated with targeted therapies.
  • Detection of microsatellite instability (MSI).
  • Detection of CNVs in selected genes, as well as genomic losses and gains across the genome.
  • Pharmacogenetic analysis associated with response to chemotherapeutic treatments.
  • UMI-based molecular tagging, increasing the sensitivity of bioinformatic analysis.
  • Included analysis software: Data genomics.
  • STID: Integrated sample identification system for sample traceability.
  • Coverage: 99.3% of bases covered at a depth of 100.
  • Uniformity: 98.9% of bases covered at >20% of the median coverage.
  • Sensitivity and specificity: > 99.9%.
  • Limit of detection (LOD) for SVs, SNVs, and INDELs: 5%.
  • CNV limit of detection, relative to the total copy number of a sample, established at 30% for losses and 15% for single-copy gains.
  • For in vitro diagnostic use only.

Action OncoKitDx uses a technology for library preparation by mechanical fragmentation and enrichment of regions of interest by hybridization with capture probes. This technology is fully automated. Subsequently, massive sequencing is carried out on Illumina platforms.

Compatible sequencing platforms NextSeq 500/550Dx System
Number of reactions 24
Number of samples per run Mid Output v2.5 kit (150 cycles): 12
High Output v2.5 kit (150 cycles): 32
Sequencing Paired-end (2 x 75 cycles)
Amount of input DNA 50-200 ng
Recommended DNA quality DIN >3
Genomic region analyzed 500 Kb
Target genes SNVs and INDELs: AKT1*, ALK, ARID1A, ATM, ATRX, BAP1, BRAF, BRCA1, BRCA2, CDH1, CHEK2, CTNNB1, EGFR, ERBB2, ESR1, FGFR1, FGFR4, GNA11, GNAQ, H3F3A, HIST1H3B, HIST1H3H, HRAS, IDH1, IDH2, KIT, KRAS, MAP2K1, MET, MLH1, MSH2, MSH6, MTOR, MYC, NRAS, NTRK1, NTRK2, NTRK3, PALB2, PBRM1, PDGFRA, PIK3CA, PMS2 + 5’UTR, PTEN, POLD1, POLE, RET, ROS1, SDHA, SDHB, SDHD, TERT + 5’UTR, TSC1*, TSC2*, TP53 and VHL.

* Hotspot sequencing

SVs: ALK (intron 19), ATP1B1 (introns 3 and 4), BRAF (introns 7, 8, 9 and 10), EGFR (introns 7, 23, 24 and 25), ETV6 (introns 4 and 5), FGFR2 (intron 17 and region 3’UTR), FGFR3 (intron 17 and region 3’UTR), NTRK1 (introns 8, 9, 10, 11 and 12), NTRK2 (introns 12 and 15), RET (introns 9, 10 and 11) y ROS1 (introns 31, 32, 33, 34 and 35).
Sample type DNA from fresh, frozen, and paraffin-embedded tissue
Action OncoKitDx (Automatic): MSDS (english)
Action OncoKitDx (Automatic): Application note HRD (english)
Action OncoKitDx (Automatic): Instructions for use
Analysis certificate

Action OncoKitDx (Automatic)

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