All Genomic Services

CellCarta offers a suite of well-established and emerging molecular platforms such as

• Next-Generation Sequencing (NGS)
• Digital and quantitative PCR
• Single-cell sequencing

Our laboratories can support the handling and analysis of various sample types, and our analytical validation process is thorough and supported by partnerships with various reagent manufacturers.

All our workflows, including

1. DNA/RNA extraction
2. gene expression
3. mutation analysis
4. and data analysis

are performed under extensive quality control while keeping your downstream applications in mind.

Using proprietary tools, our team can design custom design qPCR/dPCR assays to further support your experiment.

CellCarta accompanies you all the way to data analysis by offering a comprehensive Bio-IT pipeline and adapted molecular analysis software to deliver data analysis solutions that fit your needs.

Choose from our extensive list of genomics assays, fit for all phases of drug development from discovery and non-clinical through clinical trials.

Methods used for DNA and RNA extraction can greatly affect downstream analysis.

We have a broad experience with the extraction of various types of nucleic acids (genomic DNA, mRNA, cfDNA, cfRNA, miRNA and more) from many relevant clinical sample types:

• whole blood, PBMCs, plasma, buffy coat
• cell lines
• FFPE
• FFT
• Fine-needle aspirate (FNA)
• and fresh tissues

We ensure quality for all of them with manual and automated methods. We also offer dual extraction possibilities where we simultaneously extract DNA and RNA  separately from the same FFPE material.

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

Our team specializes in developing exploratory extraction methods.  Whether you are looking to test novel conditions, explore uncommon tissue types, or address complex multi-omics inquires, you’ll benefit from our preanalytical experience. Our expertise goes beyond extraction, encompassing upstream kitting and logistics as well as downstream assay development, ensuring that we navigate your extraction method with all factors in mind. 

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

Gene expression analysis is performed with sensitivity and specificity using PCR-based methods aligned with your study needs.

Our team can support any qPCR or dPCR clinical applications using off-the-shelf assays or custom assays, and the latest technologies such as the QuantStudio system, the Rotorgene, system, the cobas systems, QIAcuity, and Bio-Rad QX200. 

We support exploratory assays on the QuantStudio or Lightcycler systems, QIAcuity or Bio–Rad QX200.   

Learn more about our digital PCR capabilities

Learn more about our quantitative PCR capabilities

CellCarta provides RNA profiling information using next-generation sequencing (NGS) with the appropriate platforms to tackle any sequencing project size (NovaSeq X Plus, NovaSeq 6000, NextSeq 550Dx).

For a more targeted analysis of specific genes, RT-qPCR and the Nanostring^TM nCounter^® system are offered to accurately quantify panels of targets of interest.

As a 10x Genomics certified service provider of the Chromium X platform, CellCarta can also offer valuable single-cell RNA sequencing services.

Learn more about our RNA sequencing services

At CellCarta, DNA mutation detections are performed using well-established single target mutation assays on different PCR platforms (qPCR, dPCR) as well as NGS analysis protocols.

It allows us to detect both single and multiple target mutations while following regulatory requirements. Custom design of sensitive mutation detection assays is also performed.

Harnessing the latest technology (NovaSeq X Plus, NovaSeq6000, NextSeq 500Dx, MiSeq), our team uses validated panels or develops customized ones, and reports identified variants together with their clinical relevance in a time frame aligned with clinical trials needs.

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:

• Pan Lung Cancer qPCR Panel by AmoyDx: Detection of 167 mutations and fusion events in 11 target genes specific to lung cancer. This panel can be run on FFPE samples.
• Aspyre-Lung by Biofidelity: 11 genes (NCCN) including 114 variants (77 DNA mutations and 36 RNA fusions, and 1 exon skipping event). This panel can be run on DNA and RNA extracted from FFPE and on cell free DNA (cfDNA) and RNA (cfRNA) from blood samples. 
• 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 X Plus, NovaSeq 6000 and NextSeq 550Dx. This panel can be run on both DNA/cfDNA FFPE and plasma samples.
• TSO Comprehensive assay by Illumina: This assay is an in vitro diagnostics test that uses targeted NGS to detect variants in 517 genes. Detection of SNVs, multinucleotide variants, insertions, deletions and gene amplifications from DNA, and gene fusions and splice variants from RNA in FFPE tumor tissues is performed with the NextSeq 550Dx. TMB score and MSI status can also be reported. This assay is validated and can be used for patient management in both EU and US.
• TruSight Oncology 500 ctDNA V2 by Illumina: Pan cancer panel targets 523 genes to assess all main variant classes (SNV, MNV, indels, CNV, gene rearrangement) in ctDNA. This panel is run on blood plasma. 
• OncoReveal CDx by Pillar (NGS) Pan-Cancer solid tumor – NSCLC, CRC, Breast, Ovarian 22 gene – 103 amplicons DNA Panel for FFPE 

Contact us for more information about our Mutation Analysis services!

Targeted Next Generation Sequencing (NGS), RNASeq, qPCR, and digital PCR 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:

• Pan Lung Cancer qPCR Panel by AmoyDx (real-time PCR): 11 target genes for lung samples
• TSO500 Panel by Illumina (NGS): 523 DNA and 55 RNA targets

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!

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 occurs in approximately 15% of all colorectal cancers and is clinically useful in identifying 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.

• The Promega^TM 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 TSO500 Panel by Illumina can also be used to determine the MSI status.

Our RNA IO data analysis workflow is performed on bulk RNAseq data from FFPE tumor samples and can be used to investigate both MSI and TMB status, as well as predict immune checkpoint inhibition response.

Contact us for more information about our microsatellite instability services!

Using the Chromium system from 10XGenomics, CellCarta can provide single-cell RNASeq profiling.

The heterogeneity of samples normally masked in bulk RNA sequencing analysis can be captured through this method by profiling thousands of individual cells.

The assay is customizable to detect the whole transcriptome, the expression of targeted genes, specific surface proteins, and even single guide RNA (sgRNA) from CRISPR screen.

With the Visium system from 10X Genomics and GeoMx DSP from Nanostring-our team can provide a spatial map of the whole transcriptome within the morphological context of the tissue.

Spatial gene expression data is key in identifying spatiotemporal gene expression patterns and can offer great insight on the tumor and its immune microenvironment.

Contact us for more information about our single-cell and spatial gene expression services