Oncology

HEREDITARY CANCER

Hereditary Breast Ovarian Cancer is a genetically based disease that can run in families and causes breast or ovarian cancer. The two most analyzed genes in the world form the basis of this disease: BRCA 1 and BRCA 2. Individuals with mutations in these two genes increase their lifetime risk of developing breast or ovarian cancer, and the disease often starts at an early age.

BRCA 1 and BRCA 2 genes are genes involved in DNA damage repair pathways and prevent cells from turning into cancer cells. 7% of breast cancers and 11-15% of ovarian cancers are caused by mutations in BRCA 1 or BRCA 2, which are inherited in an autosomal dominant manner.

When assessing cancer risk, the individual's family history reveals the need for genetic testing. According to the test result, the frequency of control can be increased and preventive interventions can be made.

Did you know that thanks to the bioinformatics algorithm we use, it is possible to perform deletion/duplication analysis on next generation sequencing data?

HEREDITARY CANCERS NEW GENERATION SEQUENCING SOLUTIONS

Consolidated solution to sequencing by analysis

SOPHIA offers targeted and comprehensive sequencing solutions from hereditary diseases to oncology. The SOPHIA DDM platform makes bioinformatics analysis easy for clinicians with its user-friendly interface.

Hereditary Cancer Solution by SOPHiA GENETICS contains the coding region and ± 25 bp intron/exon boundaries of 26 genes associated with hereditary cancer syndromes.

Sophia Genetics Hereditary Cancer Panel

SOLID TUMORS

New Generation Sequencing Panels

ArcherDx Technology

ArcherDX produces solutions for solid tumors and hematological oncology in order to provide advanced genomic analysis with accurate and sensitive methods in cancer samples. Anchored Multiplex PCR (AMP™) chemistry used in ArcherDX solutions, using bidirectional primers and molecular barcodes (MBC), can accurately detect simple and complex genetic mutations from low nucleic acid materials obtained from FFPE, fresh tissue and blood samples with Next Generation Sequencing (NGS) method. designed to detect. With its flexible structure, AMP chemistry allows DNA, RNA and ctDNA sequencing in different tumor types. DNA-based panels target SNV, Indel, and CNV variant strains, while RNA-based panels detect fusion (translocation) and expression. *

The obtained data is processed on the ArcherDX analysis platform designed by ArcherDX experts and presented to the clinician.

*In RNA-based panel content, point mutation can be determined for selected genes if specified in the document containing the kit details.

For more detail about ArcherDx Technology:

ArcherDx Technologyi

RNA BASED PANELS- DETERMINATION OF FUSION AND EXPRESSION

FusionPlex® Lung - 14 Gen – ArcherDx

FusionPlex® Oncology Research – 75 Gen – ArcherDx

FusionPlex® Solid Tumor – 53 Gen – ArcherDx

FusionPlex® Thyroid and Lung – 36 Gen – ArcherDx

DNA BASED PANELS- SNV, INDEL, CNV

SOPHiA GENETICS Technology

SOPHiA GENETICS provides services in the fields of radiology, genomics and clinical research by using its mathematical data processing expertise in life sciences and medical fields. He offers clinical-level solutions to experts in the field of genomics to accurately detect and interpret genomic variants in cancer and hereditary diseases. Next-Generation Sequencing (NGS) solutions include targeted panel designs from exome coverage to clinical exome and from there to hereditary disease and oncology solutions. SOPHiA offers the SOPHiA DDM platform to help clinicians diagnose, annotate and pre-classify genomic variants more effectively, and support clinicians at every step of comprehensive studies with capture-based working kits.

For more informations about SOPHiA GENETICS:

SOPHiA GENETICS Technology

RNA BASED PANELS- DETERMINATION OF FUSION AND EXPRESSION

Solid Tumor Plus Solution – 137 RNA Fusion – Sophia Genetics

DNA BASED PANELS- SNV, INDEL, CNV

* MSI analysis can be done with Solid Tumor Solution panel.

* DNA and RNA samples can be studied with Solid Tumor Plus panel.

Liquid Biopsy Solutions

Liquid biopsy is a non-invasive surgical biopsy alternative that enables tumor profiling by taking blood from the patient. Especially in metastatic cancers, molecular tests applied together with the isolation of tumor DNA that is free in the blood circulation of the patient can provide treatment-guiding information.

While getting a biopsy is getting more and more difficult for cancer patients whose treatment process is progressing, molecular tests have become mandatory for many new drugs used in second or third-line treatments. For this reason, especially for patients who cannot be biopsied, performing molecular tests only by taking blood provides an option for the patient to receive treatment.

56G Oncology Solution - 56 Gen - Accel-Amplicon

LiquidPlex - 28 Gen – ArcherDx

Comprehensive Tumor Profiling

Detection of cancer biomarkers is a fundamental step for an individual and disease-specific treatment approach, but it presents certain challenges. For example, in lung cancer, in addition to single gene analyzes such as EGFR, ALK, and ROS, comprehensive analyzes such as gene fusions, tumor mutation load and microsatellite instability have started to gain importance and take place in guidelines. Incremental testing of cancer biomarkers can lead to extra time and cost in certain situations.

Comprehensive genomic profiling of the tumor can be performed using blood and tissue samples with TruSight Oncology 500 panels. It is used to detect DNA and RNA variants in different tumor types and immunotherapy biomarkers microsatellite instability (MSI) and tumor mutation load (TMB). With these panels, which allow simultaneous screening of hundreds of different biomarkers, rapid and comprehensive results can be obtained, especially in cases where the sample amount is limited.

Save Cost and Time with TruSight Oncology 500

Pan-cancer content compatible with guidelines and clinical studies
Detection of DNA and RNA variants in 523 genes as well as microsatellite instability (MSI) and tumor mutation load (TMB) with a single sample

Highly Accurate Results

High analytical specificity and sensitivity thanks to the combined use of advanced bioinformatics analysis and probe hybridization method
Use of unique molecular index (UMI) for high sensitivity in variant detection
Illumina's proven sequencing (SBS) technology
Fast workflow from sample to report

TruSight Oncology 500

Detection of key cancer biomarkers from FFPE tumor tissue with TruSight Oncology 500.

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TruSight Oncology 500 High-Throughput

Possibility to work up to 192 samples at once

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TruSight Oncology 500 ctDNA

Analysis of free-circulating tumor DNA from plasma with TruSight Oncology 500 ctDNA

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Epic Array

DNA methylation plays an important and dynamic role in the regulation of gene expression. Abnormal methylation (hyper- or hypomethylation) in DNA plays a role in many disease processes, such as cancer and neurological disorders, as well as aging and development.

Infinium MethylationEPIC BeadChip Kit

Metiylation: When whole genome sequencing isn't enough!

More than 850,000 methylation sites across the genome can be analyzed at single nucleotide resolution with the Infinium MethylationEPIC BeadChip Kit. By analyzing different samples, including FFPE, in parallel, a high-throughput study can be carried out at low cost. Infinium HD array technology allows for content selection, unlike the limitations of other methylated DNA capture methods. Methylome analysis can be performed in all enhancer and coding regions for epigenome-wide association studies in different human tissues.

Comprehensive Methylation Analysis

CpG sites other than CpG islands
Non-CpG methylation sites (CHH sites) identified in human stem cells
Tumor and normal tissue comparative methylation analysis
FANTOM5 enhancer region
ENCODE open chromatin and enhancer region
DNase hypersensitive regions
miRNA promoter regions

Integrated Data Analysis

The Illumina GenomeStudio Methylation Module enables fast and practical analysis of methylation data. Can perform comparative methylation analysis in small-scale studies with GenomeStudio; Thanks to advanced visual tools, you can display many different data such as scatter and line charts, heat maps in a single graph. With the GenomeStudio Genome Browser, you can easily view important information such as chromosome coordinates, GC percentage, position on the CpG island and methylation β value.

Free access to many analysis tools for normalization and comparative analysis in large-scale studies.

Click for usage videos of analysis tools

Real Time PCR (RT-PCR) Solutions

Abandonment of Molecular Oncology: Quick Result!

With our AmoyDx solution partner, you can study metastatic solid tumor molecular markers such as EGFR, KRAS, NRAS, BRAF, EML4/ALK, ROS1 with real-time PCR method. Real-time PCR continues to be an indispensable method for solid or liquid tumors with its fast result time and sensitivity.

Discover AmoyDx's NCCN-compliant kits with the power of real-time PCR

Amoy Dx molecular oncology kits provide fast and reliable results in your studies from FFPE tissue with 1% sensitivity;

Blood, pleural effusion, frozen or fresh tissue, FFPE tissue samples are studied,
Compatible with BioRad, Roche, ABI, Rotorgene and Stratagene systems,
Includes positive and negative control and internal control,
Kits with drug equivalents are CE-IVD validated.
Workflow can be completed in <8 hours.
Various parameters can be studied together under the same PCR conditions.
Mutation detection can be done at the rate of 1%.

For more details about kit lists

Mutasyon Kits

EGFR 29 Mutations Detection Kit (CE-IVD)

EGFR tyrosine kinase inhibitors (TKIs) are a class of treatment targeting Non-Small Cell Lung Cancer with EGFR mutation. The response of CHD lung cancer patients with different EGFR mutations to TKI treatments may be different. Detection of mutations before treatment facilitates patient-specific treatment selection.

The National Comprehensive Cancer Network has recommended identification of EGFR mutations prior to EGFR-TKI therapy since 2009.

The AmoyDx EGFR Mutation Detection Kit is a Real Time PCR-based assay designed for high accuracy detection of 29 EGFR mutations in exons 18-21 in HRV Lung Cancer patients. Using ADx-ARMS technology with specific primers and probes, this kit can detect mutations with 1% sensitivity.

KRAS Mutation Detection Kit (CE-IVD)

NRAS Mutation Detection Kit (CE-IVD)

BRAF V600 Mutations Detection Kit (CE-IVD)

PIK3CA Five Mutations Detection Kit (CE-IVD)

EGFR/ALK/ROS1 Mutations Detection Kit (CE-IVD)

HER2 Mutation Detection Kit

Fusion Kits

EML4-ALK Fusion Gene Detection (CE-IVD)

Most of the ALK fusion variants seen in non-small cell lung cancer are EML4-ALK fusions, and this oncogene represents one of the newest molecular targets in non-small cell lung cancer.

The EML4-ALK Fusion Gene Detection Kit is an RT-PCR-based assay designed for the qualitative detection of 21 EML4-ALK fusions in human tissue samples. RNA purified from FFPE tissue is converted to cDNA with the RT enzyme supplied with the kit. EML4-ALK fusion cDNAs are specifically amplified with PCR primers and detected quantitatively with fluorescent probes.

ROS1 Gene Fusions Detection Kit (CE-IVD)

NTRK Gene Fusions Detection Kit (CE-IVD)

RET Gene Fusions Detection Kit (CE-IVD)

Droplet Digital PCR Solutions (ddPCR)

Droplet Digital PCR technology is a digital PCR method that uses a water-oil emulsion droplet system. With a special microfluidic system, 1 PCR reaction is divided into 20,000 droplets, and separate PCR reactions take place in each droplet.

With ddPCR technology, the absolute copy number of target DNA and RNA molecules is obtained without the use of standard curves and references. The use of ddPCR in clinical diagnosis, especially in the field of oncology, gains importance thanks to the results with high accuracy and sensitivity that cannot be obtained with the traditional PCR method. Mutations with a low variant fraction can be detected in hematological malignancies without the need to use a tumor-specific standard curve in the determination of minimal residual disease.

For more details about Technology and test options: