Molecular Profiling Capabilities

CellCarta 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 obtained from our histopathology platforms 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 CellCarta, 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, FFT, 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.

Enrichment of specific tissue components or tumor cells by accurate macrodissection prior to extraction is made possible through the combination of our digital pathology platform and our in-house, board-certified pathologists.

Contact us for more information about our DNA/RNA extraction services

Mutation Analysis

At CellCarta, 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 (NovaSeq 6000, NextSeq 500Dx, MiSeqDx), 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 comprehensive panels:

  • SuperARMS® Pan Lung Cancer PCR Panel by AmoyDx: Detection of 167 mutations and fusion events in 11 target genes specific to lung cancer.
  • TruSight Oncology 500 (TSO500) Panel by Illumina: Detection of >500 biomarkers covering multiple solid tumor types and relevant to immuno-oncology, including microsatellite instability (MSI) and tumor mutational burden (TMB) with NovaSeq 6000 and NextSeq 550Dx.

Contact us for more information about our Mutation Analysis services

Fusion Detection

Targeted Next Generation Sequencing (NGS), RNASeq, ARMS PCR, and NanoStringTM nCounter® 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
  • Archer® ImmunoverseTM panel – targeting VDJ rearrangements of T cell receptors (TCR)
  • SuperARMS® Pan Lung Cancer PCR Panel by AmoyDx (real-time PCR): 11 target genes for lung samples
  • TSO500 Panel by Illumina (NGS): 523 DNA and 55 RNA targets relevant to immuno-oncology, including MSI and TMB.
  • NanoStringTM nCounter® – Lung RNA Fusion Panel: 63 probes

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

Contact us for  more information 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 nCounter® 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, covering 98.3% of the RefSeq exome. The sequencers used include: NovaSeq 6000 and NextSeq 550Dx.

All assays come with data analysis solutions. For downstream data analysis of RNASeq results, CellCarta 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.

Contact us for more information about our RNA expression analysis

Microsatellite instabilities (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 CellCarta, 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.
  • The TSO500 Panel by Illumina is also used to determine the MSI status.

Contact us for more information  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 CellCarta 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 about 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).

Contact us for more information about our CTC services

Single-Cell Sequencing (10XGenomics)

Using the ChromiumTM System from 10XGenomics, CellCarta can provide multiomic single-cell profiling. The heterogeneity of samples normally masked in bulkRNA sequencing analysis, can be captured through this method by profiling tens of thousand of individual cells. The assay is customizable to detect the whole transcriptome, the expression of targeted genes, specific surface protein and even single guide RNA (sgRNA) from CRISPR screen.

Contact us for more information about our single-cell sequencing services