Services
CellCarta offers a suite of well-established and emerging molecular platforms such as 10X Genomics Chromium and Visium, digital droplet PCR and much more.
Our scientists and board-certified pathologists can further 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. All our workflows, including DNA/RNA extraction, gene expression, NGS, and data analysis, are performed under extensive quality control while keeping your downstream applications in mind. CellCarta accompanies you all the way to data analysis by offering a comprehensive Bio-IT pipeline to deliver data analysis solutions that fit your needs.
Methods used for DNA and RNA extraction can greatly affect downstream analysis. 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 manual microdissection 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
Gene expression analysis is performed with sensitivity and specificity using PCR-based methods aligned with your study needs. Our team can support any quantitative PCR-based (qPCR) or digital PCR (dPCR) clinical applications using off-the-shelf assays or validated custom primers.
RNA sequencing (RNASeq) enables the analysis of information encoded in the transcriptome, such as splice variants, gene fusions, mutations and RNA editing events, many of which are of paramount relevance for biomarker-based diagnostics.
CellCarta can provide expression analysis for 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. Leveraging the power of next-generation sequencing (NGS), our platforms (NovaSeq 6000, NextSeq 550Dx, MiSeq) can be used to tackle any sequencing project size. Available RNASeq panels include:
For high-throughput molecular phenotyping, we offer two services both performed on crude cell lysates: HTPathwaySeq, optimal for MOA investigations, and HTTargetSeq, for the characterization of siRNAs and antisense oligonucleotides (ASO).
Learn more about our complete ASO drug development services
Contact us for more information on our RNA sequencing services
At CellCarta, DNA mutation detections are performed using well-established single target mutation assays on different qPCR platforms as well as NGS analysis protocols, allowing us to detect both single and multiple target mutations while following regulatory requirements. Using the latest technology (NovaSeq6000, NextSeq 500Dx, MiSeq), 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:
Contact us for more information about our Mutation Analysis services
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:
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 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.
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 bulkRNA sequencing analysis can be captured through this method by profiling 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.
With the Visium system from 10X Genomics, 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.
Contact us for more information about our single-cell and spatial gene expression services