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Scientific Applications

Assay validation

In Silico validation of Real-Time PCR assays

Use of in house Real-Time PCR assays for clinical microbiology diagnostics requires an intensive validation procedure before implementation. The validation procedure includes assay testing against clinical samples containing the microorganism of interest as well as testing for cross-reactivity of related microorganisms.

In addition, the validation procedure should include testing the assay against available sequences at ex. Genbank at NCBI or internal sequence data. This can be done by downloading the sequences of interest from e.g. Genbank and assessing binding sites manually one sequence at the time to check for matches and mismatches. However, this is a very time consuming procedure, and it is not feasible for microorganisms with many published sequences, e.g. Staphylococcus aureus (S. aureus).

Next generation sequencing makes the problem even more evident as the number of public genome sequences increase very rapidly. Ideally, the validation process should be continued after implementation of the assay into routine diagnostic use, by testing the assay against new available sequences to secure optimal detection of new types or variants of the microorganism of interest. This is rarely done.

In order to allow continuous validation of RT-PCR assays a plug-in module handling thousands of sequences and checking for assay matches and mismatches have been developed. In addition the software has incorporated BLAST features enabling analysis of cross reaction with other microorganisms than intended.



Pathogen Characterization

Sequencing-based pathogen detection and characterization applications are absolutely necessary within human public health, biodefense, vaccine research, microbial surveillance, agricultural infection control and epidemiology around the globe. Viral pathogens like Influenza A or resistant-bacteria like MRSA and VRE cause fear in the general population and clinical staff regardless of geography, race or class.

Rapid and accurate detection and characterization of these agents and many more is absolutely necessary to be able to identify, anticipate and react to rapidly spreading epidemics in hospitals or pandemics that could lead to millions of deaths across the globe. At CLC bio, we are working with top public health laboratories and pharma to quickly develop and validate specialized solutions to detect and characterize a variety of pathogens based on the latest technologies in DNA sequencing.

These ongoing efforts and the flexible framework and technology of CLC bio Enterprise platform are ideal for implementation of complete pathogen-detection and identification and management solutions for small labs or for a National infrastructure deploying small-scale Sanger sequencing or large-scale high-throughput sequencing platforms involving analysis of millions of reads and thousands of samples. New technologies, microbiology and the CLC bio platform are joining together for human and animal health.

Contact us to discuss how we can rapidly tailor this important application for your laboratory, organizational or country’s needs.

Immunoinformatics

Antibody analysis

Automated, high-throughput tool for detailed analysis of antibody sequences

Our Antibody Analysis tool allows automatic annotation of antibody heavy and light variable domains and performs alignments in both DNA and amino acid space to proprietary or public databases of germline DNA sequences or rearranged variable domain sequences. Details regarding V, D, and J allele usage, mutations found compared to these, junction sequences, FR and CDR region lengths and sequences are presented in tables and visual displays for further investigation, such as multiple alignments across selected input sequences.

Read the technical note