What type of samples can be analyzed?
All biologics can be tested. This includes cell lines (any cell banks), cell supernatant, virus stocks (seeds of vaccine strains, viral vectors for gene therapy), raw materials from animal origin, bacteriophages, bacterial strains, serums & trypsins from animal origin, and production intermediates.
How does PathoQuest construct its database?
PathoQuest’s database of is based on GenBank, an NIH developed genetic sequence database which contains an annotated collection of all publicly available DNA sequences. PathoQuest filters out sequences with poor assignation data, cleans some redundancies, and classify viruses according the Baltimore classification. PathoQuest’s databank is regularly updated and all modifications are registered via our quality system.
What kind of quality controls are used?
In addition to Illumina instrumentation QC (including PhiX phage addition) and verification of the extraction and library quality using an Agilent Bioanalyzer and Qubit Fluorometric Quantitation, PathoQuest incorporates negative and positive controls that are processed via the same procedure as with the samples tested and sequenced on the same flow cell.
What is the added value of transcriptomic approach for adventitious agent detection?
Utilizing a transcriptomic approach as a part of the process reduces the number of false positives associated with “dead DNA” which are frequently found in reagents and ingredients used in the testing process.
Do you use enrichment procedure upfront for NGS testing?
An upfront enrichment procedure for detection of adventitious viruses increases the sensitivity of PathoQuest’s testing process. For targeted sequencing, PCR enrichment of the region to be sequenced or capture on beads can be applied.
What are the key benefits of using NGS for insertion site detection and characterization?
Since the accuracy of NGS sequencing is very high, very high quality sequences are generated. NGS is less sensitive for GC rich regions compared to Sanger sequencing.
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