Targeted Next-Generation Sequencing at Copy-Number Breakpoints for Personalized Analysis of Rearranged Ends in Solid Tumors

Abstract

BackgroundThe concept of the utilization of rearranged ends for development of personalized biomarkers has attracted much attention owing to its clinical applicability. Although targeted next-generation sequencing (NGS) for recurrent rearrangements has been successful in hematologic malignancies, its application to solid tumors is problematic due to the paucity of recurrent translocations. However, copy-number breakpoints (CNBs), which are abundant in solid tumors, can be utilized for identification of rearranged ends.MethodAs a proof of concept, we performed targeted next-generation sequencing at copy-number breakpoints (TNGS-CNB) in nine colon cancer cases including seven primary cancers and two cell lines, COLO205 and SW620. For deduction of CNBs, we developed a novel competitive single-nucleotide polymorphism (cSNP) microarray method entailing CNB-region refinement by competitor DNA.ResultUsing TNGS-CNB, 19 specific rearrangements out of 91 CNBs (20.9%) were identified, and two polymerase chain reaction (PCR)-amplifiable rearrangements were obtained in six cases (66.7%). And significantly, TNGS-CNB, with its high positive identification rate (82.6%) of PCR-amplifiable rearrangements at candidate sites (19/23), just from filtering of aligned sequences, requires little effort for validation.ConclusionOur results indicate that TNGS-CNB, with its utility for identification of rearrangements in solid tumors, can be successfully applied in the clinical laboratory for cancer-relapse and therapy-response monitoring.

Textbook of Personalized Medicine

“…After fi nding such rearrangements in breast and colorectal cancer (CRC) samples, further studies have used PARE to track cancer treatment response, recurrence, and metastasis in CRC patients. Targeted NGS at copy-number breakpoints (TNGS-CNB) has been used in CRC (Kim et al 2014a ). For deduction of CNBs, a novel competitive SNP (cSNP) microarray method was developed entailing CNB-region refi nement by competitor DNA.…”