Caprion-HistoGeneX:
A Combined Offering

Building on its unrivaled histopathology platforms, HistoGeneX offers a suite of well-established and emerging molecular platforms, leveraging a unique combination of expertise, quality, and efficiency.  Importantly, our scientists and board-certified pathologists can integrate numerical molecular data with visual morphological information to maximize the information extracted from clinical trial samples.

Our laboratories can support the handling and analysis of various specimen types, and our analytical validation process is thorough and supported by partnerships with various reagent manufacturers. Keeping your downstream applications in mind, our team also provides guidance on specimen collection and management.

DNA/RNA extraction

Methods used for DNA and RNA extraction can greatly affect downstream analysis. At HistoGeneX, 90% of our extractions are performed manually, preventing yield losses and reductions in purity often observed with (semi-)automated techniques. We have a broad experience with the extraction of nucleic acids from various tissue sources: whole blood, plasma, cell lines, FFPE, frozen, and fresh tissues, and ensure quality for all of them. We also offer dual extraction possibilities where we simultaneously extract DNA and RNA from the same FFPE material.

In addition to employing commercial molecular extraction products, we developed proprietary methods of optimal fixation and tissue processing to obtain high molecular weight RNA and DNA from paraffin embedded tissue samples and cells.

Enrichment of specific tissue components or tumor cells by accurate microdissection prior to extraction is made possible through a close collaboration between our scientists and in-house pathologists.

Find out more about our DNA/RNA extraction services

Mutation Analysis

At HistoGeneX, DNA mutation detections are performed using well-established single target mutation assays on different platforms as well as next generation sequencing analysis protocols, allowing us to detect both single and multiple target mutations while following regulatory requirements. Using the latest technology, our team uses validated panels or generates customized ones, and reports identified variants together with their clinical relevance in a time frame aligned with clinical trials.

In addition to readily available targeted sequencing panels used to detect single nucleotide variants (SNV), small insertions ,deletions, copy number variations (CNVs), and tumor mutational burden in specific genes frequently mutated in solid tumors, we also offer the SuperARMS® Pan Lung Cancer PCR Panel by AmoyDx which can detect 167 mutations and fusion events in 11 target genes specific to lung cancer.

Find out more about our Mutation Analysis services

Fusion Detection

Targeted Next Generation Sequencing (NGS), RNASeq, ARMS PCR, and NanoStringTM are all assays we harness for RNA fusion detection. Validated panels are used to detect cancer specific fusions and point mutations. Some offer the possibility to investigate these fusions without requiring knowledge of their specific break points.

Ready-to-use panels include:

  • RNASeq (NGS): 21,415 target genes
  • Archer® FusionPlex Comprehensive Thyroid and Lung (CTL) (NGS):
    36 hotspot gene targets in thyroid and lung cancers
  • SuperARMS® (real-time PCR): 11 target genes for lung samples
  • NanoStringTM – Lung RNA Fusion Panel: 63 probes

Customization to your needs:
Panels can be customized to investigate specific fusions and point mutations.

Find out more about our Fusion Detection services

Expression Analysis

Expression analysis can be performed on a limited set of gene targets using RT-qPCR. Alternatively, with the NanostringTM system, up to 800 RNA targets of choice can be accurately quantified, with the possibility to add custom targets.

With RNASeq using the TruSeq RNA Exome/Enrichment assay on an Illumina sequencing platform, expression profiling can be performed for over 21,000 RNA targets. All assays come with data analysis solutions. For downstream data analysis of RNASeq results, HistoGeneX offers a fully validated Bio-IT pipeline, which includes HLA typing, fusion, and differential gene expression. Upon request our Bio-IT team is happy to assist you in finding or developing the optimal data analysis solution to fit your needs.

Find out more about our RNA expression analysis

DNA Methylation

DNA methylation is an epigenetic modification that can have diverse consequences on gene expression. In the field of oncology, it often serves as a biomarker given the abnormal patterns of methylation frequently observed in cancer samples.

Using our real-time methylation-specific polymerase chain reaction (MSP) assay, we can determine the relative copy number of methylated O6-Methylguanine-DNA Methyltransferase (MGMT), a DNA repair enzyme that is frequently deactivated by hypermethylation in human cancer, including glioblastoma.

Our team can also customize assays for other specific methylation targets and provide adequate validation services.

Find out more about our DNA methylation services

Microsatellite instability (MSI)

Microsatellite instabilities (MSI) result from the systematic accumulation of deletions/insertions in short repetitive DNA sequences in tumor cells due to a deficient mismatch repair (MMR) system. MSI occur in approximately 15% of all colorectal cancers and are clinically useful to identify patients with hereditary nonpolyposis colorectal cancer (HNPCC, Lynch Syndrome) caused by germline mutations of MMR genes. The MSI status may also predict a patient’s response to certain chemotherapies. More recently, it has been used as a biomarker for immunotherapeutic response, making the MSI status an increasingly relevant tool in genetic and immuno-oncology research.

At HistoGeneX, we use panels consisting of quasimonomorphic mononucleotide repeats to determine MSI status. These are very sensitive and do not require matching normal tissue or blood. The PromegaTM MSI assay v1.2 provides a high throughput solution for multiplex amplification of five repeat markers (BAT-25, BAT-26, NR-21, NR-24 and MONO-27) in the DNA to determine MSI status. The IdyllaTM MSI Assay (IVD label) covers seven repeats biomarkers in different genes (ACVR2A, BTBD7, DIDO1, MRE11, RYR3, SEC31A, and SULF2), establishing the MSI status directly from formalin-fixed paraffin embedded (FFPE) tissue in a sample-specific cartridge.  MSI status is also determined using the TSO500 from Illumina.

Find out more about our microsatellite instability services

DNA Fragment Analysis

DNA fragment analysis is achieved using capillary electrophoresis (CE) to separate and detect fluorescently labeled DNA fragments after amplification by PCR. Analysis can provide information on the size, relative quantity, and genotype of the fragment.

Current applications of fragment analysis at HistoGeneX include MSI testing, our gender specificity assay for reliable gender determination, and the MHC class I Loss of Heterozygosity (LOH) assay for the analysis of 9 SNPs around chromosome 6.

Contact us for more information on our expertise in DNA Fragment Analysis

Circulating Tumor Cells by RareCyte®

Circulating tumor cells (CTCs) provide a dynamic view of cancer progression and can be detected in peripheral blood. Our well-established blood processing workflow in combination with the RareCyte® platform allow us to easily identify and quantify these cells by fluorescent staining and perform genomic analysis at the single cell level. By performing low pass whole genome sequencing on retrieved CTCs, we can detect Copy Number Variations (CNVs).

Find out more about our CTC services