TCRbeta Profiling - TCRsafe™

HSDiagnomics provides a complex service to customers, starting normally from genomic DNA extracted from blood, tissues or FFPE samples. Using our proprietary primer sets covering all 44 V-segments and 14 J-segments for the T-cell Receptor beta (TCRbeta) CDR3 locus, plus an inbuilt contamination protection system, we amplify the T-cell repertoire and perform a deep sequencing step: Typically 1-2 million read-pairs per sample are generated.

In the 2nd part of the TCRsafe-service, with an in-house developed software package HSDiagnomics processes and assembles raw reads into clusters and assigns V/J-segment IDs and CDR3 DNA and amino acid sequences. The result of our analysis sent out to customers is a table of clusters and frequencies, i.e. a high-resolution profile of TCRbeta.

At a glance, our TCRsafe™ service comprises the following steps:

  • 2-step multiplex PCR with contamination protection
  • Generation of barcoded sequencing library
  • Ultra-deep sequencing (HiSEQ, MiSEQ) with typically 1-2 million read-pairs per sample
  • Highly-sensitive clustering of reads
  • Assignment of V/J-segment IDs according to the IMGT annotation system
  • Generation of comprehensive TCRbeta frequency tables (spreadsheets), see an example here

 


 

TCRsafe – Research Projects

HSDiagnomics has processed hundreds of samples using its TCRsafe technology in research projects carried out with partners from academia.

We are always interested in partnerships with research projects, both in academia and industry. As a service provider and partner we can offer our well tested technology for fast delivery of results and systematic tools to monitor and store results in a user-friendly way.

The following features will help your project to get robust and relevant data in a very short period of time:

  • Data quality and safety: Contamination protection will be active from project start to end
  • Data mining packages by HSDiagnomics will help you to find common motifs in large sample cohorts – easy and precise
  • Specific questions and needs of customer projects can be addressed by customized software modules.
  • HSDiagnomics will organize your data storage

We are happy to discuss all relevant details with you – just give us a call!

 


 

Product under development: Mouse TCRsafe™

There are strong interests by researchers in academic and industry labs to perform analysis of T-cell response under various treatments in the mouse model system. HSDiagnomics will address these needs by a proprietary mouse TCRsafe kit. It will be equipped with the same contamination protection system as the human TCRsafe kit. Interested customers are welcome to contact us in advance for more details.