KAPA HyperCap DS NHL Panel

Overview

The KAPA HyperCap Design Share (DS) non-Hodgkin lymphoma (NHL) panel enables highly sensitive detection and longitudinal analysis of ctDNA in blood-derived NHL samples for research use purposes. Existing methods such as the radiological and nuclear imaging methods are unable to provide key information on clonal evolution and minimal residual disease (MRD).¹

Cell-free circulating tumor DNA (cfDNA/ctDNA), typically assessed using targeted deep sequencing, has emerged as an important non-invasive and highly sensitive biomarker in the monitoring of NHL patient status.^2,3 To unlock the full potential of ctDNA as a biomarker more research needs to be done to better understand where it can make the most impact. Now clinical researchers have the flexibility to develop their in-house workflows using the KAPA HyperCap DS NHL panel along with the robust KAPA HyperCap workflows⁵ and customizable bioinformatics.⁶                                                

Features and benefits of the KAPA HyperCap DS NHL panel

• Insights from ctDNA NHL research now within your reach - Pioneer advances in NHL research by using a unique panel developed for ctDNA monitoring.
• Unique panel design used in a large pivotal study - Leverage a panel based on years of rigorous research and panel design that was used in the POLARIX study to validate ctDNA as a prognostic biomarker.⁷
• Simplified and reliable NHL research workflows - Utilize robust and streamlined KAPA workflows with the new KAPA HyperCap DS NHL panel and customizable open-source bioinformatics analysis.
  

Figure 2. High sensitivity was exhibited across samples with 0.5%, 1% and 5% AFs

Each blue dot represents a replicate. SNV calling sensitivity was demonstrated by using a blended sample of gDNA NA24631 (98%) & NA24149 (2%), targeting 1% AF, with characterized variants covered by the KAPA HyperCap DS NHL Panel to assess variant calling performance for the germline workflow  (DNA blend 1%: 10 true positive (TP); 8 replicates) and pre-fragmented reference cfDNA samples with known variants at specific AF covered by the KAPA HyperCap DS NHL Panel to assess somatic variant calling performance for the plasma cfDNA workflowKAPA HyperCap DS NHL Panel (Seraseq® ctDNA complete mix AF 0.5% and AF 5% from SeraCare: 3 SNVs, 2 replicates each; cfDNA Pan-cancer Reference Standard AF 0.5% and 5% from Twist: 12 SNVs, 4 replicates each). For the germline workflow, 10 out of 10 (100%) TP were observed in all gDNA replicates. For the plasma cfDNA workflow, all expected SNVs were found in all cfDNA replicates that were investigated.

*High SNV calling specificity demonstrated by 0.06 errors every 10 Kb of the panel (as calculated by a set of 23 healthy donor samples). In the gDNA NA24149/NA24631 blend, 53 out of 53 true negative (TN) were observed in all eight replicates.

Table 1. Summary of longitudinal mutation analysis results for contrived cfDNA Pan-cancer  reference standard samples

Data generated from samples were subsequently processed using the three-stage KAPA bioinformatics analysis for longitudinal detection of ctDNA to demonstrate the use of the KAPA HyperCap DS NHL Panel for longitudinal analysis of NHL-associated variants in circulating tumor DNA. Reporter variants were successfully detected in all contrived T_N (subsequent samples after baseline) Pan-cancer samples. The Monte Carlo p-value^8,9 threshold for ctDNA positivity in simulated longitudinal samples was set at 0.003 since this was the lowest value observed in the wild type sample. The number of reporter variants with non-zero supporting reads, as well as the total number of supporting alt reads, drops as the expected AF % decreases from 0.5% to 0.01%. Mutation positivity was accurately called in all replicates of the AF 0.5%, AF 0.1%, and AF 0.05% samples (Monte Carlo p-values <0.003). For the AF 0.01% sample, mutation positivity was accurately called in five out of six replicates. All replicates of the wild type sample were called negative.