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 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, next generation sequencing (NGS), and data analysis, are performed under extensive quality control while keeping your downstream applications in mind. Using proprietary tools, our team can custom design PCR primers and probes 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.
Methods used for DNA and RNA extraction can greatly affect downstream analysis. We have a broad experience with the extraction of nucleic acids from many relevant clinical sample types: 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.
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 assays.
CellCarta provide RNA profiling information using next-generation sequencing (NGS) with the appropriate platforms to tackle any sequencing project size (NovaSeq 6000, NextSeq 550Dx, MiSeq). For specific gene targets, RT-qPCR and the NanostringTM nCounter® system are offered to accurately quantify custom targets.
Our team also developed a high throughout sequencing method for pre-clinical compound screening with a workflow that can process up to 384 cell lysates without the need for RNA extraction.
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, allowing 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 (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:
Targeted Next Generation Sequencing (NGS), RNASeq, ARMS PCR, digital 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.
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.
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.