CNA Detection Performance Evaluation

For CNA detection performance, cell-line DNA from MCF7 (Lot #60540387), HCC2218 (Lot #64097142), and HCC827 (Lot #64216187; all obtained from ATCC) and the HapMap cell-line NA24143 were used following acoustic shearing to 200 bp on an ME220 Focused-ultrasonicator. The HCC827 cell-line harbors a 32.6-fold increase in EGFR copy number over the diploid number, as verified by the manufacturers via ddPCR. Fragmented HCC2218 DNA was mixed with fragmented NA24143 DNA to generate cell-line DNA admixtures containing EGFR copy numbers of 30, 20, 10, 4, 3, and 2.4. The HCC2218 cell-line harbors a 16.32-fold increase in ERBB2 (HER2) copy number [30 (link)], and the MCF7 cell-line harbors an estimated 4.46-fold increase in NRAS copy number, 3.34-fold increase in MYC copy number, and a 1.80-fold increase in CDK6 copy number [31 (link),32 (link)]. Fragmented MCF7 DNA was mixed with fragmented NA24143 DNA to generate cell-line DNA admixtures containing 4.3 copies of NRAS and 3.6 copies of MYC, and 3.2 copies of NRAS and 2.8 copies of MYC. The HD786 reference standard harbors focal MET and MYC amplification at 4.5 and 9.5 copies respectively.