Detection of somatic copy number deletion of the CDKN2A gene by quantitative multiplex PCR for clinical practice

A feasible method to detect somatic copy number deletion (SCND) of genes is still absent to date. Interstitial base-resolution deletion/fusion coordinates for were extracted from published articles and our whole genome sequencing (WGS) datasets. The copy number of the gene was measured with a quantitative multiplex PCR assay P16-Light and confirmed with whole genome sequencing (WGS). Estimated common deletion regions (CDRs) were observed in many tumor suppressor genes, such as , , , , , and , in the SNP array-based COSMIC datasets. A 5.1 kb base-resolution CDR could be identified in >90% of cancer samples with deletion by sequencing. The CDR covers exon-2, which is essential for P16 and P14 synthesis. Using the true CDR as a PCR target, a quantitative multiplex PCR assay P16-Light was programmed to detect gene copy number. P16-Light was further confirmed with WGS as the gold standard among cancer tissue samples from 139 patients. The 5.1 kb CDR was found in >90% of cancers containing deletion. The CDR was used as a potential target for developing the P16-Light assay to detect SCND and amplification for routine clinical practices.