Solid Biopsy (OncoDEEP®)

Q: Which types of cancer is the OncoDEEP® Kit recommended for?

The OncoDEEP ® Kit is recommended for a wide range of cancer types. Its comprehensive gene panel and ability to detect various genomic alterations make it applicable to solid tumors across different cancer types. It can help in identifying relevant variants and genetic signatures in cancers such as lung cancer, breast cancer, colorectal cancer, ovarian cancer, melanoma, and many others.

Q: How long does it take to get my reports available in OncoKDM®?

The turnaround time for OncoDEEP ® Kit is determined from the receipt of sequencing data to their validation by OncoDNA ® , and subsequently, the release of reports on both platforms. The typical TAT is within 48 hours or two business days.

Q: How many genes are covered by OncoDEEP® Kit panel?

The OncoDEEP ® Kit panel covers 638 genes. These genes have been carefully selected based on their biological and therapeutic relevance in various solid tumor types. The comprehensive coverage of these genes allows for the detection of genomic alterations and complex genetic signatures associated with cancer.

Initiated for patients by oncology experts

Initiated for patient testing, the OncoDEEP^® Kit is built on the OncoDEEP^® molecular diagnostic test, which is the result of more than a decade of strong collaboration with oncology experts.

10 years of knowledge that matters

Since 2013, OncoDNA has performed more than 100,000 tests, enabling us to build a comprehensive database (OncoKDO^®) comprising 4,6 million variants across 22,000 genes, along with information on 1,600 drugs and 10,000 clinical trials. This vast repository of information allows OncoDNA to provide our clients with the most accurate and up-to-date molecular profiling for personalized cancer treatment.

An all-in-one solution with the largest panel in the market

OncoDEEP^® Kit DNA & RNA panel is the largest and the most complete of the market. This panel is composed of probes targeting 638 genes for a final content of 1.8 Mb. It supports identification of all relevant variants involved in various solid tumor types with genes carefully selected based on their biological and therapeutical relevance.

In addition, specific sequences have been added to cover key regions associated with phenotypes of interest such as 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 promoter of TERT.

A unique capture method for high quality data with less sequencing

OncoDEEP^® Kit uses a unique Twist Biosciences’ capture method allowing high coverage and uniformity with less DNA/RNA input and less sequencing needed.

An easy process automatization

Thanks to the compatibility with Illumina’s technology, the easy automation process simplifies tasks by continuing using the current tools without disturbing the automate routine activities and losing time in extra training and manipulations.

Flexible and high-performance sequencing technology

The OncoDEEP^® Kit has been meticulously designed to seamlessly integrate with a wide range of advanced sequencing platforms, including those from Illumina, while also being compatible with other technologies available in the market. This broad compatibility allows researchers to focus entirely on their scientific goals without the concern of technical obstacles. By optimizing the OncoDEEP^® Kit for use with multiple platforms, we achieve the perfect balance between cost efficiency and consistent precision, ensuring reliable results without compromising accuracy.

Provider	Sequencer	FC type	Max number of samples
Illumina	NextSeq 500/550	Mid Output	8
	NextSeq 500/550	High Output	16-24
	NextSeq 2000	P2	24-32
	NextSeq 2000	P3	72-96
	NovaSeq 6000	SP	48-56
	NovaSeq 6000	S1	112
	NovaSeq X	1.5B	112
MGI	DNBSEQ-G400	FCS	16-24
	DNBSEQ-G400	FCL	96-104
	DNBSEQ-T7	DNBSEQ-T7RS HT V3.0	368-376
Elements Bioscience	AVITII
		Low Output	8-12
		Medium Output	24-32
		High Output	48-64

With this technological flexibility, high-performance sequencing is now more accessible than ever. Laboratories can process multiple samples per flow cell, as outlined in the table above, regardless of the sequencing system chosen. This streamlined process enables faster and more efficient sequencing, leading to more accurate data and better outcomes.

From sample preparation to clinical insights in just 5 days

OncoDEEP^® Kit revolutionizes the diagnostic process by significantly reducing the timeline from DNA extraction to clinical and biological interpretation to just 5 days. This accelerated timeframe enables healthcare professionals to make faster decisions, resulting in enhanced patient care and improved outcomes.

Day 1: Extraction

Extracted DNA and/or RNA from FFPE tumor tissue or unstained slides

Day 2: Library preparation

DNA fragmentation, end repair & dA tailing
Ligation Twist universal adapters and purification
PCR amplification using Twist UDI Primers, purification and QC

Day 3: Target Enrichment

Libraries preparation for hybridization
Binding hybridized targets to streptavidin beads
Post-capture PCR amplification, purification and QC

Day 4: Sequencing

DNA concentration adjustment according to sequencer specifications
Flow-cell loading

Extended QC data visualization for samples - OncoDNA.

Day 5: Analyse and interpretation

Upload FASTQ files
Secondary and tertiary analysis via OncoDEEP pipeline
Clinical and biological interpretation through OncoKDM
QC visualization

Day 1

Day 2

Day 3

Day 4

Day 5

Clinically-relevant oncology targets and biomarkers

Designed by oncology experts, the OncoDEEP^® panel contains the most relevant and complete cancer gene panel. Over the time this panel was optimized to include all clinically-relevant oncology targets. The panel is composed of 638 genes, reporting genomic alterations (SNV, insertion, deletion, CNV) and complex genetic signature (HRD, MSI and TMB).

Genes alterations

Insertion / Deletion / CNV / SNV

Introns

ALK / ROS1 / RET / translocation / MET-Exon 14

Genes fusions

ALK / ROS1 / RET / FGFR1 / FGFR2 / FGFR3 / NTRK1 / NTRK2 / NTRK3 / BRAF / NRG1

Unusual splicing

BRCA1 / BRCA2 / PTEN / AR / EGFR / ERBB2 / MET / PALB2 / RB1

TMB

Tumor Mutational Burden (TMB) is a biomarker that can predict how responsive solid tumors may be to immunotherapy. The higher the TMB score, the greater the likelihood of a positive response to immunotherapy.

MSI

Microsatellite instability (MSI) is a hypermutable phenotype caused by the loss of DNA mismatch repair (MMR) activity, which is associated with inactivation, loss or epigenetic silencing of MMR genes (MSH2, MLH1, MSH6 and PMS2).

HRD

The determination of HRD status can provide crucial information, which can be used to personalize the treatment of patients with ovarian, breast, pancreatic and prostate cancer.

Clear data insight and clinical interpretation

Easy sequencing files upload

After the sequencing, output files (FASTQ + Medata files) are uploaded

Easy sequencing files upload

After the sequencing, output files (Fastq + medata files) are uploaded on a secured storage to automatically launch a batch of samples.

Variants identification & annotation

Our BioIT pipeline performs the secondary analysis of genomic data

Variants identification & annotation

Our BioIT pipeline performs the secondary analysis of genomic data by aligning the data, identifying, annotating and classifying the variants, and cleaning the bias.

Data cross-referencing with our proprietary knowledge base

We use our proprietary knowledge base to perform tertiary analysis

Data cross-referencing with our proprietary knowledge base

We use our proprietary knowledge base OncoKDO to perform tertiary analysis by cross-referencing molecular data, resulting in the clinical interpretation of the data.

Clinical validation by scientific team

Our team of oncology experts reviews each report

Clinical validation by scientific team

Our team of oncology experts reviews each report before making it available on OncoKDM

OncoKDM^® ’s comprehensive interpretation reports provide labs with eight essential assets to enhance the understanding of NGS data, including detailed annotations, a list of actionable variants, a list of therapies recommendation and a summary of relevant clinical trials.

Extensive QC data visualization

Besides providing labs with QC data on sample quality such as read length and read quality, OncoKDM also offers genomic information at both the sample and gene levels.

We considered multiple in-house comprehensive genomic profiling NGS options, but during the validation phase, our results demonstrated that OncoDNA’s OncoDEEP single multiplex assay provides a consistent, time-efficient, and simple sample-to-clinical report solution for accurate comprehensive genomic profiling in FFPE samples.

Marcel Trautmann

Head of the molecular diagnostics and translational cancer research lab

Frequently Asked Questions

Which types of cancer is the OncoDEEP® Kit recommended for?

The OncoDEEP^® Kit is recommended for a wide range of cancer types. Its comprehensive gene panel and ability to detect various genomic alterations make it applicable to solid tumors across different cancer types. It can help in identifying relevant variants and genetic signatures in cancers such as lung cancer, breast cancer, colorectal cancer, ovarian cancer, melanoma, and many others.

How long does it take to get my reports available in OncoKDM®?

The turnaround time for OncoDEEP^® Kit is determined from the receipt of sequencing data to their validation by OncoDNA^®, and subsequently, the release of reports on both platforms. The typical TAT is within 48 hours or two business days.

How often do we update our annotation database / information?

We regularly update our annotation database and information to ensure that it reflects the most relevant and accurate information for clinical interpretation and decision-making. The frequency of updates may vary, but it is done on a regular basis to incorporate new scientific discoveries, clinical findings, and emerging genomic data.

Can I edit the analysis report after it has been published in OncoKDM®?

Depending on your workspace configuration, you can edit almost every part of the report until you validate it. Every change is recorded and can be reviewed in the report’s history of changes.

How many genes are covered by OncoDEEP® Kit panel?

The OncoDEEP^® Kit panel covers 638 genes. These genes have been carefully selected based on their biological and therapeutic relevance in various solid tumor types. The comprehensive coverage of these genes allows for the detection of genomic alterations and complex genetic signatures associated with cancer.