AuraSeq-Fusions Kit-DATA SHEET

07/30/2021

Test Description(Cont.)

The recent technological advances in next-generation sequencing (NGS) and its applications in the field of oncology have allowed the identification of actionable somatic variants that have become targets of cancer therapeutics, which could benefit individuals with tumors harboring such genomic alterations. The increasing utilization of targeted therapies, such as TKIs in clinical practice is adding new dimensions to molecular testing for cancer patients ⁽³⁾. Sequentially testing for oncogenic drivers that can become targets of TKIs lessens the efficiency of the process, mostly when biopsies often comprise scarce tissue samples. Thus, highly multiplexed assays, such as the ones on NGS platforms, allow the identification of drug targets in different genes simultaneously, assisting physicians to select personalized therapies ⁽⁴⁾.

Methodology

Next Generation Sequencing

Test Description

The AuraSeq-Fusions panel utilizes Next Generation Sequencing (NGS) and
is used to detect cancer-related genomic alterations such as single nucleotide variants (SNVs) and small insertions and deletions (Indels), copy number variants (CNVs) and fusions. This test is intended to detect genomic alterations in several metastatic or advanced cancers, including:

Lung adenocarcinoma (NSCLC) (e.g.: ROS1, BRAF, EGFR, ALK, ERBB2, KRAS, MET (METex14 and METamp), and RET). These genes are recommended by national guidelines ⁽¹⁾.
Colorectal cancer (CRC) (e.g.: KRAS, NRAS, BRAF, NTRK1-fusions, and NTRK3-fusions). The first 3 genes are recommended by national guidelines ⁽²⁾.
Spitzoid melanoma (e.g.: NTRK1-fusions)
Glioblastoma multiforme (GBM) (e.g.: IDH1, IDH2, EGFRamp, EGFRvIII

isoform, NTRK1-fusions, FGFR1-fusions, and FGFR3-fusions)
Pilocytic astrocytoma (e.g.: BRAF-fusions, NTRK2-fusions) bladder cancer (FGFR3-fusions)
Breast cancer (NTRK3-fusions, FGFR1-fusions, FGFR2-fusions, and FGFR3-fusions)
Prostate cancer (e.g.: ERG-fusions, ETV1-fusions, ETV4-fusions, and FGFR1-fusions)
Thyroid carcinomas, including: papillary (e.g.: NTRK1-fusions, and NTRK3-fusions) and follicular (e.g.: PPARG-fusions)
Soft tissue sarcomas (e.g.: NTRK1-fusions and NTRK3 fusions)
Any other advanced carcinoma who has failed to respond to conventional chemotherapy or is about to start a tyrosine kinase inhibitors (TKIs) regime.

Method Performance Specifications

This assay performs with 100% (95%CI 92.6%-100.0%) sensitivity and 93.8% (95%CI 69.8%-99.8%) specificity. The limit of detection (LoD) is 5-6% of mutant DNA in total DNA, at a mean coverage of 1000X and a minimum coverage of 500X. Small Indels are detected when present at a minimum frequency of 10% of total DNA, at a mean coverage of 2000X and a minimum coverage of 500X. CNVs can be detected at a minimum gain of 4x on samples with a minimum of 20% neoplastic nuclei.

Specimen Requirements

All samples must be treated as potentially infectious material. Specimen material is human DNA extracted from formalin-fixed, paraffin-embedded blocks, slides or Diff-Quick smears.
When cutting multiple blocks, please use DNA AWAY between each block to avoid cross contamination.
Please use Non-positively-charged slides and 10% NBF fixative. • Please cut fresh unstained slides when testing is requested.

FFPE BLOCKS
Please, DO NOT send decalcified bone biopsies and samples fixed using Bouin’s, B-5, or any fixative containing heavy metals (i.e., zinc) and acids as they are INCOMPATIBLE with sensitive DNA-based methodologies.
Diff-Quick smears
Slides - (4) 10 μm sections, unbaked and unstained plus 1 H&E; H&E should be the last slide cut. Air dry.
Do not oven dry

Specimen Requirements

Use cold pack for transporting blocks, making sure cold pack is not in direct contact with specimen. Slides can be packed at room temperature.

Please Ship To:

Bernhardt Laboratories
Attn: Molecular Department
3728 Philips Highway, Suite 64
Jacksonville, FL 32207

Turnaround Time (Tat)

7-10 Days

SSTI PANEL