KAPA Library Prep Kits achieve ultra-low detection limit and broad patient coverage

A team of researchers from Stanford University found the combination of the KAPA Library Preparation Kits and the Roche NimbleGen sequence capture products to be an economical and ultrasensitive method for quantifying and enriching circulating tumor DNA (ctDNA). The study, published recently in Nature Medicine, validated the complementary workflow of the two products and demonstrated the ability to increase recovery efficiency by more than 300% and decrease bias for NGS libraries constructed from as little as 4 ng of ctDNA.

As part of the study, the team at Stanford University introduced a new detection method for quantifying ctDNA called cancer personalized profiling by deep sequencing (CAPP-Seq). This method was applied to non–small-cell lung cancer (NSCLC) with a design covering multiple classes of somatic alterations that identified mutations in more than 95% of tumors. The team of researchers detected ctDNA in 100% of patients with stage II–IV NSCLC and in 50% of patients with stage I, with 96% specificity and ultra-low mutant allele frequency detection limit of approximately 0.02%.

The ability to detect mutations from ctDNA has the potential to significantly reduce the number of invasive tissue biopsies and accelerate research in multiple types of cancers. However, ctDNA is challenging due to limited quantities, so researchers must use sample prep methods that are highly sensitive and specific and that do not introduce bias in the results. The CAPP-Seq method proved to be a very effective way of enriching and quantifying libraries from ctDNA, with high specificity and ultra-low detection limits.

Publication Details Newman, A. M. et al. (2014). An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage. Nature Medicine, DOI: 10.1038/nm.3519