ULTRA-Peptide Libraries for Sequence Diversity

JPT’s PepMix™ peptide pools, PepTrack™ peptide libraries and PepStar™ peptide microarrays are widely used for immune monitoring of T- and B-cell response, the stimulation of effector cells in immunotherapy and the development of vaccines. These products can represent one or several antigens with defined protein sequences. As sequence diversity among viruses and in humans is gaining more attention in research and development efforts, we created a new algorithm to reflect sequence diversity within our peptide libraries, peptide pools and peptide microarrays.

Sequence Diversity in Viruses

Sequence diversity among populations is a hallmark of many pathogenic viruses including HIV, HBV and Influenza, representing a great challenge for vaccine development, biomarker discovery and immune monitoring. Although sequence variations are observed in all viral proteins, the greatest sequence diversity has been found in viral envelope proteins, reflecting the important role of these proteins in eliciting host immune recognition. Therefore, sequence diversity has to be taken into account in the design of antigen-based products, intended for immune monitoring and vaccination. 

Sequence Diversity in Tumors

Recent advancements in DNA-sequencing technology have facilitated the sequencing of thousands of complete genomes. The 1000 Genomes and other projects have provided information on the genetic variability between individuals within and across different ethnic groups. On average 10000 to 12000 sites with coding mutations have been identified per individual. With approximately 20K genes per individual, this translates into a sequence alteration in one of every two genes. These germline mutations are observed uniformly in each cell of an organism. Furthermore, somatic mutations cause sequence heterogeneity within individuals which are of special significance in the pathological mechanisms of cancer. Exemplarily, for one of the most important tumor driver genes TP53, 767 germline and 29881 somatic mutations have been identified. 

Solutions with ULTRA-Peptide Libraries

Peptides are ideally suited to accommodate sequence diversity as peptides can be produced in high numbers by controlled, automated chemical synthesis at relatively low cost and with reliable quality. Peptide libraries ideally reflect the sequence of the actual infecting virus or tumor mutanome. Although in principle it is possible to identify the sequences of each patient for a personalized diagnosis and treatment, this is often not feasible and quite expensive. Therefore, targeting the full spectrum of sequence variation within a virus or type of cancer with one comprehensive peptide library saves precious time and resources.

JPT’s ULTRA-Peptide Libraries are generic, all-inclusive peptide libraries with an optimized coverage of all sequence variations in a given genetically heterogeneous population. Standard products make use of a common peptide library format. Often a single antigen is represented by 15 amino acid peptides with 11 amino acid overlaps or an offset of 4. We invented a new algorithm creating all possible peptide variations and scoring these according to their frequency of occurrence across all sequences. We can then define the optimal overlap required to provide homogeneous overall coverage.

Available ULTRA-Peptide Libraries

Find a list of ULTRA products in our online shop. 

Customized ULTRA-Peptide Libraries

Please inquire via email

Applications for JPT’s ULTRA-Peptide Libraries

  • Immune monitoring of T- and B-cell response
  • T-cell stimulation in immunotherapy
  • Biomarker discovery
  • Development of vaccines

Read Application Notes:
Application Note on the Generation of ULTRA Libraries
by Pawlowski et al. (2015)
Application Note on the Use of HIV Ultra-Peptide Pools to Generate Multi-HIV Antigen T-Cells as a Component for a Cure Strategy
by Lam et al. (2015)

Benefits of ULTRA-Peptide Libraries

  • Allows high coverage even of complex sequence spaces
  • Proprietary bioinformatic algorithm to design your optimal peptide library
  • Fast chemical assembly of complex peptide libraries, pools, and microarrays
  • Maximum diversity at minimum number of peptides

References on ULTRA-Peptide Libraries

"Antibody Responses After Analytic Treatment Interruption in Human Immunodeficiency Virus-1-Infected Individuals on Early Initiated Antiretroviral Therapy"
Stephenson et al., Open Forum Infectious Diseases (2016) - PMID: n.a.
"A Global Reference for Human Genetic Variation"
The 1000 Genomes Project Consortium, Nature (2015) - PMID: 26432245
"Impact of Mutant p53 Functional Properties on TP53 Mutation Patterns and Tumor Phenotype: Lessons From Recent Developments in the IARC TP53 Database"
Petitjean et al., Hum. Mut. (2007) - PMID: 17311302
"Broadly-specific Cytotoxic T Cells Targeting Multiple HIV Antigens Are Expanded From HIV+ Patients: Implications for Immunotherapy"
Lam. et al., Mol. Ther. (2015) - PMID: 25366030
"Quantification of the Epitope Diversity of HIV-1-Specific Binding Antibodies by Peptide Microarrays for Global HIV-1 Vaccine Development"
Stephenson et al., J. Immunol. Methods (2015) - PMID: 25445329
"Comprehensive Characterization of Antibodies Directed towards Epigenetic Histone Modifications"
Masch. et al., Application Note (2015)

Read More References

ULTRA-Peptide Libraries for Sequence Diversity
Stay in touch and be the first to receive the latest news!