INSTRUCTIONS FOR USE - ONCODEEP – GENERAL INFORMATION | VERSION 01
1 CONTENT
1 Content ............................................................................................................................................ 1
2 Definitions / Abbreviations.............................................................................................................. 2
3 Manufacturer Information ............................................................................................................... 2
4 device Name ................................................................................................................................... 2
5 information for device identification............................................................................................... 3
6 Device Description.......................................................................................................................... 4
7 Legal................................................................................................................................................. 7
8 Precautions of use .......................................................................................................................... 8
9 Intended Use ................................................................................................................................... 9
10 Intended User .............................................................................................................................. 9
11 Environment................................................................................................................................. 9
12 Contra-Indications ...................................................................................................................... 9
13 Description of the reagents ........................................................................................................ 9
14 List of material to be supplied by users .................................................................................... 9
15 Information about devices to be used in combination ........................................................... 10
16 Storage Conditions ................................................................................................................... 10
17 In-use stability............................................................................................................................ 10
18 Sterilisation ................................................................................................................................ 10
19 OncoDEEP Protocol for DNA Analysis ................................................................................... 10
20 OncoDEEP Protocol for RNA Analysis .................................................................................... 10
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INSTRUCTIONS FOR USE - ONCODEEP – GENERAL INFORMATION | VERSION 01
2 DEFINITIONS / ABBREVIATIONS
IVD: In Vitro Diagnostics.
NGS: Next Generation Sequencing.
IHC: ImmunoHistoChemistry
MSI: Microsatellite Instability
TMB: Tumor Mutational Burden
FDA: Food and Drug Administration
EMA: European Medicines Agency
QC: Quality Control
HRD: Homologous Recombination Deficiency
TMB: Tumor Mutational Burden
MSI: MicroSatellite Instability
FFPE: Formalin Fixed Paraffin Embedded
DNA: Deoxyribonucleic Acid
RNA: Ribonucleic Acid
SNV: Single Nucleotide Variant
CNV: Copy Number Variation
LOH: Loss of Heterozygosity
3 MANUFACTURER INFORMATION
OncoDNA SA +32(0)71 18 35 00 www.oncodna.com
1 rue Breguet scientificsupport@oncodna.com
6041 Gosselies
BELGIUM
4 DEVICE NAME
OncoDEEP
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INSTRUCTIONS FOR USE - ONCODEEP – GENERAL INFORMATION | VERSION 01
5 INFORMATION FOR DEVICE IDENTIFICATION
Each boxes and tubes are labelled with labels conform to the IVD Directive (98/79/EC). The labels
display pictograms to provide useful information to the end-user. An example of label is shown in
figure 1. The signification of each pictogram is given in figure 2.
Figure 1: OncoDEEP library prep Module 1 Label
Figure 2: Information displayed on the collection kit and labels
In vitro diagnostic medical device Manufacturer
Catalog Number Lot Number
Storage temperature limits Consult Instructions for use
CE Marking conformity
Use by (YEAR-MONTH-DAY)
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INSTRUCTIONS FOR USE - ONCODEEP – GENERAL INFORMATION | VERSION 01
6 DEVICE DESCRIPTION
OncoDEEP Kit is a next-generation sequencing (NGS) assay that enables in-house
comprehensive genomic profiling of tumor samples. It supports identification of all relevant DNA
variants implicated in various solid tumor types with genes carefully selected based on their
biological and therapeutical relevance.
OncoDEEP DNA panel is composed of probes targeting 638 genes for a final content of 1.8 Mb.
The OncoDEEP comprehensive gene panel is as shown below (Figure 1).
Figure 1:List of genes covered by the OncoDEEP panel
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INSTRUCTIONS FOR USE - ONCODEEP – GENERAL INFORMATION | VERSION 01
In addition, specific sequences have been added to cover key regions associated with phenotypes
of interest like tumor mutational burden (TMB), microsatellite instability (MSI), loss of
heterozygosity (LOH) in tumor suppressor genes (TSGs), introns tilling for genes ALK/ROS1/RET
and MET-ex14, sub-telomeric single-nucleotide polymorphisms (SNPs) for homologous
recombination deficiency (HRD) calculation and promotor of TERT.
Translational and clinical research require rapid approaches that are compatible with small input
amounts of nucleic acids derived from challenging research samples such as formalin-fixed,
paraffin embedded (FFPE) tissues. OncoDEEP Kit has been validated with FFPE samples and has
shown to achieve highly confident results with high sensitivity and specificity, thanks to Twist
hybrid-capture chemistry using enzymatic fragmentation and unique dual indexes (UDIs), Illumina
sequencing by synthesis (SBS) sequencing technology, and our sophisticated bioinformatics.
With our complete portfolio of secure online platforms, sequencing data can quickly and easily be
analysed, matching them with the latest therapies in oncology, and help build personalized
reports. Sample to report workflow can be achieved in 3-4 days with OncoDEEP DNA Kit as
illustrated in Figure 2.
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INSTRUCTIONS FOR USE - ONCODEEP – GENERAL INFORMATION | VERSION 01
Figure 2: OncoDEEP DNA Kit Sample-to-Result workflow
FFPE Tumor
Sample
~1
• DNA Extraction and Perform QC Hours
Sample
Preparation
• Step 1 : Perform DNA Fragmentation, End Repair, and dA-tailing
~3
• Step 2 : Ligate Twist Universal Adapters and Purify Hours
Library • Step 3 : PCR Amplify Using Twist UDI Primers, Purify, and Perform QC
Preparation
• Step 1 : Prepare Libraries for Hybridization
• Step 2 : Hybridize Capture Probes with Pools ~ 20
Target • Step 3 : Bind Hybridized Targets to Streptavidin Beads Hours
Enrichment • Step 4 : Post-Capture PCR Amplify, Purify, and Perform QC
• Denatured Library Preparation ~ 20
• Sequencing on Illumina NextSeq 500/550 or NextSeq2000 platforms Hours
Sequencing
Up to
• OncoKDM or Mercury 24
Hours
Analysis
Report
OncoDEEP Sample-to-Result workflow. The complete NGS workflow takes you from sample
preparation to NGS sequencing and data analysis. Sample to results can be achieved in 3-4 days.
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INSTRUCTIONS FOR USE - ONCODEEP – GENERAL INFORMATION | VERSION 01
7 LEGAL
This document and its annexes may contain references to other third-party resources such as
sources of information, hardware or software, products, or services and/or web sites owned or
licensed by third parties. OncoDNA does not control or take responsibility for any third-party
resources, including, without limitation, the accuracy, reliability, copyright compliance,
compatibility, performance, legality, or any other aspect of third-party resources. The inclusion of
such resources in this document does not imply endorsement by OncoDNA of any third-party
resources.
Certain processes described in this document and its annexes may be subject to patent rights or
licenses in local jurisdictions, including those owned or licensed by parties other than OncoDNA.
Purchase of this product does not include a license to perform any such processes. Users of this
product may, therefore, be required to obtain a patent license depending upon the particular
application and country in which the product is used before performing such processes.
OncoDNA and the various OncoDNA logos used herein are trademarks of OncoDNA Corporation.
All other trademarks are the property of their respective owners.
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INSTRUCTIONS FOR USE - ONCODEEP – GENERAL INFORMATION | VERSION 01
8 PRECAUTIONS OF USE
▪ Warnings, precautions and/or measures to be taken in the event of malfunction of the device or
its degradation as suggested by changes in its appearance that may affect performance: not
applicable.
▪ Warnings, precautions and/or measures to be taken in regard to the exposure to reasonably
foreseeable external influences or environmental conditions, such as magnetic fields, external
electrical and electromagnetic effects, electrostatic discharge, radiation associated with
diagnostic or therapeutic procedures, pressure, humidity, or temperature: the reagents of the kit
must be stored at appropriate temperature and protected from light/humidity as stated in chapter
14 storage conditions.
▪ Warnings, precautions and/or measures to be taken in regard to the risks of interference posed
by the reasonably foreseeable presence of the device during specific diagnostic investigations,
evaluations, therapeutic treatment or other procedures (e.g. electromagnetic interference emitted
by the device affecting other equipment): not applicable.
▪ Precautions related to materials incorporated into the device that are carcinogenic, mutagenic or
toxic, or that have endocrine disrupting properties or that could result in sensitization or allergic
reaction of the patient or user: not applicable.
▪ OncoDEEP is a device is intended for single use.
▪ Any warnings and/or precautions related to potentially infectious material that is included in the
device: not applicable.
▪ Wear appropriate protective equipment (lab coat, gloves, and protective glasses or goggles) at
all times when performing this protocol.
▪ For best results, read this document before performing the protocol, and follow the instructions
provided. OncoDNA cannot guarantee the performance of the OncoDEEP Library Preparation Kit
using Enzymatic/Mechanical Fragmentation and the Twist Universal Adapter System if
modifications are made to the protocol.
▪ This library preparation method may yield more material than needed for target enrichment.
Excess product can be stored at - 20°C for later use.
▪ Test the compatibility of your thermal cycler and PCR tubes by incubating at 95°C for up to 5
minutes to ensure the PCR tubes do not crack under heat and pressure. Adjust the tightness of
the thermal cycler lid and/or use a spacer specific to the thermal cycler model.
▪ To minimize contamination, two sample handling areas should be designated: Pre- and Post- PCR.
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INSTRUCTIONS FOR USE - ONCODEEP – GENERAL INFORMATION | VERSION 01
9 INTENDED USE
The intended purpose statement for the device described in this technical file is:
The OncoDEEP Kit is an integrated solution that combines a pan-cancer NGS assay for the in-
house comprehensive biomarker testing of solid tumor tissues. The solution contains a panel of
638 genes carefully selected for their clinical relevance in advanced solid tumor types. The
OncoDEEP Kit screens for cancer gene mutations in the DNA and RNA (SNVs, Indels, CNV, fusion
genes and unusual splicing events) as well as measures complex genomic signatures such as
homologous recombination deficiency (HRD), tumor mutational burden (TMB) and microsatellite
instability (MSI) from FFPE tumor tissue specimens.
The OncoDEEP Kit contains all the necessary reagents to prepare the NGS libraries and comes
together with an integrated bioinformatics pipeline for data analysis and interpretation.
10 INTENDED USER
The OncoDEEP kit is intended to be used by laboratory professionals with a background in
molecular biology and Next Generation Sequencing (lab technicians, biologists).
Patients have no contact with the device.
11 ENVIRONMENT
The device must be used in a laboratory environment with appropriate measures to prevent any
contamination of the sample or its byproduct during the analysis process.
12 CONTRA-INDICATIONS
OncoDEEP kit is only meant to be used for every solid tumor in adults or for glioblastoma in
children.
13 DESCRIPTION OF THE REAGENTS
Please refer to the specific protocols for DNA and RNA analysis in annex of this document for
detailed information about the reagents to be used by the end-user at each step of the protocol.
14 LIST OF MATERIAL TO BE SUPPLIED BY USERS
Please refer to the specific protocols for DNA and RNA analysis in annex of this document for
detailed information about the list of material to be supplied by the end-user.
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INSTRUCTIONS FOR USE - ONCODEEP – GENERAL INFORMATION | VERSION 01
15 INFORMATION ABOUT DEVICES TO BE USED IN COMBINATION
Compatible Sequencers Name
Illumina NextSeq series
16 STORAGE CONDITIONS
Depending on the reagent type, storage conditions may vary. Please check the information
displayed by the following symbol on each box to know the appropriate
storage conditions. The ideal storage conditions are mentioned next to the symbol by giving the
range of acceptable temperature for long term storage.
Appropriate storage conditions must be executed upon reception to prevent performance
degradation.
17 IN-USE STABILITY
Reagent stability is ensured until the date mentioned on the specific label affixed to the reagent
container. The appropriate date to take into account is the “use by date” displayed next to the
hourglass.
18 STERILISATION
Not applicable.
19 ONCODEEP PROTOCOL FOR DNA ANALYSIS
Please check the following annex: OD002-B-04- OncoDEEP DNA protocol
20 ONCODEEP PROTOCOL FOR RNA ANALYSIS
Please check the following annex: OD003-B-04- OncoDEEP RNA protocol
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