Comprehensive Panel

Intended Use

The AmoyDx® Comprehensive Panel is a next-generation sequencing (NGS) based assay intended for the qualitative detection of single nucleotide variants (SNVs), insertions and deletions (InDels), gene fusions, and copy number variations (CNVs) in 110 genes, single nucleotide polymorphisms (SNPs) in 19 genes, and tumor MSI status. The assay allows the detection of SNVs, InDels, fusions, CNVs, SNPs and MSI using DNA isolated from formalin-fixed paraffin-embedded (FFPE) tissue specimens, and the detection of SNVs, InDels, fusions and SNPs using circulating cell-free DNA (cfDNA) isolated from plasma derived from anti-coagulated peripheral whole blood specimens.

The kit is intended to be used by trained professionals in a laboratory environment.

Principles of the Procedure

The test kit is based on dual-directional capture (ddCAP) technology which is a targeted next-generation sequencing method that uses biotinylated oligonucleotide baits (probes) to hybridize to the target regions. The test kit is designed for use with fragmented genomic DNA (gDNA) or cfDNA. During the library construction process, each individual DNA molecule is tagged with a unique molecular index (UMI) at both ends, which allows high sensitivity in variant detection by eliminating any library amplification and sequencing bias.

For FFPE tissue samples, the extracted DNA should be sheared into short fragments, using either mechanical methods (e.g.,ultrasonication shearing) or enzymatic digestion, then the purified fragmented DNA can be used for downstream library preparation. For plasma samples, the extracted cfDNA can be used directly to downstream library preparation.

The test kit includes the reagents and enzymes needed for library preparation. First, the fragmented DNA or cfDNA are incubated with end repair enzyme and reagents to get the blunt-ended fragments with dA-tails, then the DNA fragments are ligated to adaptors with complementary dT-overhangs, then the adaptor-ligated DNA fragments are size-selected through AMPure beads, then the PCR amplification is performed to enrich the libraries and each library is tagged with unique dual index. Next, the library is performed with target enrichment, the process including denature the double-strand library, hybridize biotinylated probes to the complementary target DNA, and enrich the captured target DNA using streptavidin beads. Finally, the universal PCR amplification is performed to enrich the target libraries.

After quality control (QC), the qualified libraries could be sequenced on Illumina sequencing platform. The sequencing data can be analyzed by AmoyDx NGS data analysis system (ANDAS) to detect the genomic variants in the target region.

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