KAPA HyperCap Catalog Panels and Kits

KAPA HyperCap Oncology Panel

• Sequences low quantity and low quality FFPET DNA samples by achieving high percentage of error-free positions over the target (>94%)
• Achieves uniform and deep sequencing coverage with greater than 92% of bases covered within 0.5x – 2x of the median and greater than 88% of exon bases covered by more than 300x

KAPA HyperCap Heredity Panel

• Achieves a fine balance of high specificity (80.9% reads on-target), high uniformity (1.42 Fold-80 base penalty), and low PCR duplication (2.2%)
• Maximizes sequencing efficiency to cover 98.5% of the target bases by 30x and achieve a mean coverage of 92.6x

Figure 1: Key sequencing metrics with the KAPA HyperCap Oncology Panel.

Two real-world low-quality FFPET DNA samples were compared with the Horizon™ HD789 control FFPE DNA sample. Sample libraries (in duplicates) were prepared following the KAPA HyperCap FFPET DNA Workflow from 10 ng FFPE DNA with the KAPA HyperPlus Kit. Following single library hybridization and capture, the final libraries were sequenced on a NextSeq™ 550 system and downsampled to 10 M HQ filtered clusters (2 x 150 bp) prior to analysis.

Figure 2: Key sequencing metrics of the KAPA HyperCap cfDNA Workflow.

Five healthy donor cfDNA samples were tested in duplicate (average is shown), in parallel with SeraSeq® ctDNA Complete™ Reference Material AF0.5% (duplicates) starting from 10 ng of input.
The KAPA HyperCap cfDNA Workflow was followed using the KAPA HyperPrep Kit and single sample library hybridization and captures. Final libraries were sequenced on a NovaSeq™ 6000 system. Fifty (50) million high-quality filtered clusters (2 x 150 bp) were analyzed per sample.

Figure 3: Key sequencing metrics with the KAPA HyperCap Heredity Panel.

Eight-plex pre-capture multiplexing with the standard KAPA HyperCap Workflow v3 including the KAPA HyperPlus Kit from 100 ng gDNA (16 coriell cell lines in duplicate). Final libraries were sequenced on a NovaSeq™ 6000 system and downsampled to 10 M HQ filtered clusters (2 x 100 bp) prior to analysis.

Figure 4: KAPA HyperCap DS NHL panel met key sequencing performance criteria and exhibited high sequencing efficiency, as exhibited by the unique sequencing depth per sample.

In this study, commercial reference samples were used to prepare “contrived” samples that mimic NHL samples, with known variants at allele frequencies (AFs) ranging from 0% to 5%. Next-generation sequencing (NGS) libraries were prepared using the KAPA HyperPrep Kit and KAPA HyperCap cfDNA Workflow v1.1 or the KAPA HyperPlus Kit and KAPA HyperCap Workflow v3.4. Libraries were enriched by hybridization to the KAPA HyperCap DS NHL Panel. Sequencing was performed on an Illumina® NextSeqTM 500/550 instrument using standard protocols. Data analysis was performed using open source bioinformatic tools.² The KAPA HyperCap DS NHL panel sequencing metrics met expectations for a 8-sample run on Illumina® NextSeqTM 500/550 flow-cell with an average number of reads > 88M per sample. After unique molecular identifier (UMI) deduplication, the median number of reads returned for Complete Mutation Mix (Seraseq®) libraries was 44 M, compared to the median of 33 M reads for Pan-cancer Reference Standard libraries. This translated to a median coverage.

KAPA HyperCap Oncology Panel

• Unlocks the potential of challenging samples with the extensively optimized KAPA HyperCap FFPET DNA Workflow and the accuracy provided by the KAPA Universal UMI Adapter
• Streamlined targeted sequencing with the Roche HyperCap Evolved Workflow, driven by KAPA EvoPrep Boost or KAPA EvoPlus Boost Kits

KAPA HyperCap Heredity Panel

• Uncover efficiencies across the sample preparation process with the streamlined and automation-friendly KAPA HyperCap Workflow, driven by KAPA EvoPrep Boost or KAPA EvoPlus Boost Kits

KAPA HyperCap Oncology Panel

Captures 13 genes strongly associated with somatic oncology, along with additional hotspot variants commonly included in commercial FFPET and cfDNA controls.

KAPA HyperCap Heredity Panel

• Covers more than 85% of the total ClinVar Pathogenic and likely pathogenic content at >30x by targeting those carefully selected 3332 genes in a sequencing efficient 10 Mb capture target
• Achieves high percentage of bases covered by 30x for the ACMG 73 genes and the ENSEMBL and RefSeq transcripts of the 3332 genes targeted by the KAPA HyperCap Heredity Panel

Figure 5: Percent bases covered at 30x and above in key genomic databases using the KAPA HyperCap Heredity Panel.

Twelve-plex precapture multiplexing with the standard KAPA HyperCap Workflow v3 and the KAPA HyperPrep Kit from 100 ng gDNA (96 replicates, NA12878). Final libraries were sequenced on a NovaSeq™ 6000 system and downsampled to 10 M high-quality filtered clusters (2 x 100 bp) prior to analysis.