Powerful spike-in standard technology for ctDNA-based NGS hotspot assays
The problem:
NGS-based assays measuring ctDNA variant allele frequencies exhibit increased sequencing errors and false positives at low variant allele frequencies (VAF) (<0.5%). Moreover, emerging ctDNA applications such as minimum residual disease (MRD) monitoring require consistent performance of the assay and assurance that absence of detection is not due to sensitivity drift of the assay. The use of a standardized run control is critical to the proper assurance of the clinical results.
The product:
Accukit™ ONCO1LB contains a blend of 13 synthetic DNA internal standards (IS) to clinically actionable oncogenic regions of the genome (Table 1). The mixtures are physically and enzymatically fragmented to an average size of ~165bp and are suitable for use as routine spike-in controls for cell-free DNA assays. Accukit Onco1LB internal standards are spiked into each specimen prior to library prep. Being biochemically identical to the target sequence, the standards will co-vary with the sample and provide highly accurate control for the sample.
Why does it help?
Sequence Accuracy (Limit of Blank):
As the VAF of the target variants decrease below 1%, there is an increase in technical and systemic (sequencing) errors that can create false positives in the sequence measurements. The use of SNAQ™-SEQ standardization technology in the Accukit Onco1LB provides an accurate measurement of the background error for EACH reaction and enables the sample to dictate the sensitivity and cutoffs of a true positive vs. a false positive.
Sensitivity control (Limit of Detection)
For applications such as MRD, the Accukit Onco1LB can be spiked into each sample at the limit of detection for the assay to ensure that the assay’s performance specifications are being met. The Accukit standards should be detectable in each assay—even in the absence of detectable target. A positive control for a negative result.
Table 1: Gene targets in the Accukit Onco1LB
Additional SNAQ-SEQ internal standards available as custom mixes:
Table 2: Individual internal standard constructs available
Custom Design Service:
SNAQ-SEQ is a highly customizable and flexible technology with custom spike-in controls in as little as 6 weeks. Create from 6 to 66 (or more) unique custom control regions for your assay. There are virtually no limits to the number of targets to develop your controls. AccuGenomics will take care of the designs and guide you to the best approach based on your control needs.