Comparability of scalable, automated hMSC culture using manual and automated process steps

Automation will likely to play a key role in the development of scalable manufacturing processes for cell-based therapies. In this study, we have compared the effects of manual centrifugation and automated non-centrifugation cell culture process steps, performed using TAP biosystems’ CompacT SelecT automated cell culture platform, upon hMSC morphology, number, viability, surface marker expression, Short tandem repeat (STR) profile, and paracrine function. Furthermore, the comparability between flow cytometry analyses of hMSCs, performed at multiple sites, was investigated. No significant difference in hMSC growth and characteristics was observed between cells cultured using either the manual centrifugation process step or the automated non-centrifugation process step, in which residual dissociation agent is carried over. However, some variability in paracrine activity was observed between hMSCs cultured using alternative process steps. It is also apparent that differences in analytical methods can influence the inter-laboratory reproducibility of hMSC flow cytometry analysis, although differences in culture may also contribute to the variability observed in the expression of 2 of the 8 surface markers examined. This novel investigation into the effects of these two key process steps will help to improve the understanding of the influence of automated cell culture upon various cell culture parameters, as well as upon process comparability

Development of a highly sensitive liquid biopsy platform to detect clinically-relevant cancer mutations at low allele fractions in cell-free DNA

<div><p>Introduction</p><p>Detection and monitoring of circulating tumor DNA (ctDNA) is rapidly becoming a diagnostic, prognostic and predictive tool in cancer patient care. A growing number of gene targets have been identified as diagnostic or actionable, requiring the development of reliable technology that provides analysis of multiple genes in parallel. We have developed the InVision™ liquid biopsy platform which utilizes enhanced TAm-Seq™ (eTAm-Seq™) technology, an amplicon-based next generation sequencing method for the identification of clinically-relevant somatic alterations at low frequency in ctDNA across a panel of 35 cancer-related genes.</p><p>Materials and methods</p><p>We present analytical validation of the eTAm-Seq technology across two laboratories to determine the reproducibility of mutation identification. We assess the quantitative performance of eTAm-Seq technology for analysis of single nucleotide variants in clinically-relevant genes as compared to digital PCR (dPCR), using both established DNA standards and novel full-process control material.</p><p>Results</p><p>The assay detected mutant alleles down to 0.02% AF, with high per-base specificity of 99.9997%. Across two laboratories, analysis of samples with optimal amount of DNA detected 94% mutations at 0.25%-0.33% allele fraction (AF), with 90% of mutations detected for samples with lower amounts of input DNA.</p><p>Conclusions</p><p>These studies demonstrate that eTAm-Seq technology is a robust and reproducible technology for the identification and quantification of somatic mutations in circulating tumor DNA, and support its use in clinical applications for precision medicine.</p></div

Plot showing sensitivity and inter-operator variability of eTAm-Seq technology using low, medium and high input DNA.

<p>Experiments were performed in two laboratories (Laboratory 1 –upper; Laboratory 2 –lower) by different operators, performed on separate days and different NGS runs.</p

Sensitivity of the eTAm-Seq technology with 8000 amplifiable copies of DNA input per sample.

<p>Sensitivity of the eTAm-Seq technology with 8000 amplifiable copies of DNA input per sample.</p

Additional file 2: of The use of digital PCR to improve the application of quantitative molecular diagnostic methods for tuberculosis

Protocol for gDNA extraction and dPCR quantification of materials. (PDF 394 kb

Quantitative agreement of 5% AF and 1% AF reference standard spiked into plasma, and measured by eTAm-Seq technology and dPCR.

<p>Mean mutant AF (%) ± SD are displayed for each technology (n = 5* (5% AF standard); n = 6 (1% AF standard)). By spiking into plasma containing background wild-type DNA, the resulting mix was confirmed to contain lower AFs than the original reference standards (original mutant AF values 5% standard: 5% (<i>EGFR</i>); 6.3% (<i>KRAS</i>, <i>NRAS</i>, <i>PIK3CA</i>); 1% standard: 1% (<i>EGFR</i>), 1.3% (<i>KRAS</i>, <i>NRAS</i>, <i>PIK3CA</i>). (*1 data point omitted due to anomalous extraction efficiency).</p

InVision liquid biopsy tumor profiling panel.

<p>The coverage per gene is indicated, including hotspots, comprehensive or full coverage of coding regions (70%–100% tiling coverage) and CNVs. SNVs = Single Nucleotide Variants; Indels = short insertions or deletions; CNVs = Copy Number Variants.</p