ACE ImmunoID is an all-in-one immunogenomics platform. It combines our analytically validated ACE (Accuracy & Content Enhanced) Cancer Exome and ACE Cancer Transcriptome assays, in a tumor/normal configuration, to provide robust genomic data. Additionally, through NeoantigenID, ACE ImmunoID provides analytics to elucidate the tumor’s neoantigen landscape.
ACE ImmunoID uses our patented ACE Technology which improves processes from nucleic acid extraction, through sequencing, to analytics. ACE ImmunoID stands apart by:
- Performing dual DNA/RNA extraction from FFPE samples: Maximizes the use of precious patient samples
- Providing augmented coverage to enhance neoantigen detection: Missed mutations lead to downstream inaccuracies in neoantigen predicitions
- Identifying neoantigens not only from SNVs, but also fusions and indels: Fusions and indels are a rich source of potential immunogenic peptides (Turajlic et al., 2017)
- Reporting HLA Class I and Class II typing: Validated in silico prediction from exome data to save time and sample
- Listing putative peptides which bind to the sample’s MHC Class I and Class II: Both are important in eliciting a sustained T-cell response as has been recently shown in first-human neoantigen-based vaccine trials (Sahin et al., 2017, Ott et al., 2017 )
ACE Cancer Exome
The ACE Cancer Exome assay provides high-coverage, high-accuracy sequencing of >20,000 genes, with improved coverage of > 1,400 cancer related genes, for superior neoantigen identification.
Gene-wide analysis of SYN1 (Figure 1, Panel B) shows the sequencing coverage provided by standard exome (blue regions) as well as the ACE-augmented coverage (green regions). ACE Cancer Exome coverage encompasses both the standard blue and the augmented green regions.
Positional analysis of peptide mutations and binding potential across the SYN1 genes (Figure 1, Panel A, highlighted region) indicates the number of predicted binding peptides that are captured in the augmented green region only (ACE supplementation)— these peptides would have been missed by the standard offering.
Figure 1. Superior coverage provided by the ACE Cancer Exome results in the identification of neoantigens that would have otherwise been missed by the standard exome.
ACE Cancer Transcriptome
The same accuracy and coverage are delivered with our ACE Cancer Transcriptome enrichment protocol. When compared to a standard exome enrichment protocol, the ACE Cancer Transcriptome shows more uniform and deeper coverage across the entire gene (see Figure 2). In addition, because we use the most current gene definitions, the ACE Cancer Transcriptome covers exons that are missing in the standard annotation and other exon capture methods (Figure 3).
Figure 2: Deeper, more even coverage. Samples were prepared with both a standard exome capture method (A) and the ACE Cancer Transcriptome protocol (B). Five exons of the BCR gene are shown. The ACE Cancer Transcriptome protocol shows deeper and more even coverage across all five exon regions.
Figure 3: Missing annotation. Samples were prepared with both a standard exome capture method (A) and the ACE Cancer Transcriptome protocol (B). Two exons of the AFF3 gene are shown. The standard exome capture method misses the second exon while the ACE Cancer Transcriptome protocol shows deeper and more even coverage of both.