Biotech Companion Services

High-throughput transcriptome profiling using RNA-sequencing (RNA-Seq), a sensitive and precise method for gene expression analysis, has quickly become the preferred method to better understand the functional biology of disease. In cell line development and characterization of cell and gene- therapies, RNA profiling can deliver insight into cell-specific genes, variation in expression levels of genes under different growth conditions, or drug treatment. It can also uncover information on pathways involved in specific drug responses and aid in modeling the treatment or in the drug discovery process.

Single-cell and Spatial Transcriptomics: Transcriptome characterization of cell populations to identify clusters of cells with specific expression profiles and cluster-specific biomarkers (gene expression).

Ribosome profiling: A new frontier in RNA sequencing that allows for specific quantification of transcripts under active ribosome translation.

Long reads cDNA RNA-seq: the power of long-reads to obtain a complete characterization and quantification of isoforms, splice-variants, and long non-coding RNAs.

Bulk RNA-seq: our standard RNA sequencing, also available with a dedicated workflow to generate libraries for ultra-low amount of RNA (picograms).

The high depth of coverage provided by NGS can identify thousands of independent copies of the same integration cassette or vector within a given specimen. This allows for the detection of low frequency de novo mutations that might have occurred during cell line propagation or subcloning. We have established efficient protocols for the targeted sequencing of a region of interest (ROI) at very high depth. Specialized bioinformatics tools are then used to detect mutations occurring at very low frequency, avoiding false positives caused by sequencing errors or PCR artifacts.

Vector Cassette characterization (INTEGRITY): Fully sequence tens of kilobases of vector/cassette with high coverage to identify any mutation that can be causative of unwanted missense mutations.

Ultra-low mutation assay (Duplex-Seq): Targeted assay for detection of mutations as low as 0.1% in frequency in specific loci of interest. Sequencing of both DNA strands allows for in silico removal of any sequencing or PCR artifacts in variant calling.

The precise determination of a transgene integration site is required for several technological applications. Registration and protection of new biotechnology products, GMO application, and risk assessment in gene and cell therapy are some of the areas that require detailed integration information to assess the level of safety of the products and to rule out potential activation of proto-oncogenes.

Integration site analysis can also be used as a cell line development screening method to select the most promising clones. Our methods have been validated in serveral contexts and can provide a reliable method also to ensure the desidered monoclonality.

A complete cell line characterization is crucial for both early stages of cell line development and subsequent assessment of its stability. Long-read sequencing can now provide high-quality cell line genome assembly and annotation of gene models and regulatory elements, providing a solid base for cell line optimization, gene editing, metabolic engineering, and analytical development (including vector integrity, insertional profiling and clonality assessment).

Cell line high-quality genome assembly: Long-read based assembly coupled with chromosome reconstruction with Hi-C data. Can be substituted for FISH analysis to characterize large-scale genomic rearrangement and generate a new high-quality reference genome for a proprietary cell line.

Bacterial/yeast genome assembly: Fast-turnaround long-read based assembly to deliver chromosome and plasmid reconstruction and automated annotation.

Plasmid Sequencing: Ultra-rapid turnaround to deliver full length annotated plasmid sequence.