Noninvasive genotyping and monitoring of anaplastic lymphoma kinase (ALK) rearranged non-small cell lung cancer by capture-based next-generation sequencing

Abstract

Noninvasive genotyping of driver genes and monitoring of tumor dynamics help make better personalized therapeutic decisions. However, neither PCR-based assays nor amplicon-based targeted sequencing can detect fusion genes like anaplastic lymphoma kinase (ALK) rearrangements in blood samples. To investigate the feasibility and performance of capture-based sequencing on ALK fusion detection, we developed a capture-based targeted sequencing panel to detect and quantify rearrangement events, along with other driver mutation variants in plasma. In this perspective study, we screened 364 patients with advanced non-small cell lung cancer (NSCLC) for ALK rearrangements, and collected blood samples from 24 of them with confirmed ALK rearrangements based on their tissue biopsies. ALK rearrangements were successfully detected in 19 of 24 patients at baseline with 79.2% (95% CI 57.9%, 92.9%) sensitivity and 100% (36/36) specificity. Among the 24 patients, we obtained longitudinal blood samples from 7 of them after either chemotherapy and/or Crizotinib treatment for disease monitoring. The by-sample detection rate of ALK rearrangements after treatment drops to 69.2% (9 of 13). In addition to detecting ALK rearrangements, we also detected 3 Crizotinib resistant mutations, ALK L1152R, ALK I1171T and ALK L1196M from patient P4. ctDNA concentration correlates with responses and disease progression, reflecting its ability as a biomarker. Our findings suggest capture-based sequencing can detect and quantify ALK rearrangements as well as other somatic mutations, including mutations mediated drug resistance, in plasma with high sensitivity, paving the way for its application in identifying driver fusion genes and monitoring tumor dynamics in the clinic.

A field guide for cancer diagnostics using cell‐free DNA: From principles to practice and clinical applications

“…Whole‐genome sequencing or targeted hybrid capture approaches may be used for broad detection of oncogenic gene fusions across tumor entities. Indeed, single cases of ALK ‐fusion detection in liquid biopsies by DNA capture methods have already been described in the literature . Data on RNA‐based screening for gene fusions as routinely done in FFPE are still preliminary and limited but maybe equally effective.…”

“…Indeed, single cases of ALK-fusion detection in liquid biopsies by DNA capture methods have already been described in the literature. 56,104,[202][203][204][205][206] Data on RNA-based screening for gene fusions as routinely done in FFPE 207…”

Treatment of ALK‐rearranged non‐small cell lung cancer: A review of the landscape and approach to emerging patterns of treatment resistance in the Australian context

“…Currently, in 25% of cases, the cause for resistance remains unknown. An attempt to obtain repeat tissue or liquid biopsy upon progression is recommended especially as NGS testing is becoming increasingly available and less expensive (Figure ) …”

Lung Cancer Management: where are we in 2017?

“…2017;3 patient's emergent secondary mutations 46 . In order to do this, liquid biopsies are currently being investigated in ALK-positive patients with some interesting preliminary reports 47 .…”