The Network Genomic Medicine Lung Cancer was set up to rapidly translate scientific advances into early clinical trials of targeted therapies in lung cancer, performing molecular analyses of more than 3500 patients annually. Their aim was to analyze all therapeutically relevant mutations in lung cancer samples in a high-throughput fashion while significantly reducing turnaround time and amount of input DNA compared with conventional dideoxy-sequencing of single polymerase chain reaction amplicons.
In a recent study published in Journal of Thoracic Oncology, the Network Genomic Medicine Lung Cancer demonstrates the feasibility of using an Ion AmpliSeq Custom DNA Panel containing 102 amplicons of 12 different genes for multiplex polymerase chain reaction, followed by sequencing on an Illumina sequencer, in routine diagnostics. 10 – 50 ng of DNA was isolated from formalin-fixed paraffin-embedded tissue. After the gene targets were amplified using the Ion AmpliSeq Custom DNA Panels (Life Tech), the PCR products were incubated with NEXTflex DNA Adenylation Mix. NEXTflex DNA Barcode adapters were ligated to the fragments using Switch Solution and T4 DNA Ligase. Then 10 cycles of PCR were run and the samples were sequenced on an Illumina MiSeq.
The researchers observed that comprehensive biomarker testing provided novel information in addition to histological diagnosis and clinical staging. In 2657 consecutively analyzed lung cancer samples, the Network Genomic Medicine Lung Cancer identified driver mutations at the expected prevalence. Furthermore they found potentially targetable DDR2 mutations at a frequency of 3% in both adenocarcinomas and squamous cell carcinomas.
Overall, these data demonstrate the utility of NGS analysis in a clinical routine setting and highlight the dramatic impact of such an approach on the availability of therapeutic strategies for the targeted treatment of individual cancer patients.
König, K. et al. (2015) Implementation of Amplicon Parallel Sequencing Leads to Improvement of Diagnosis and Therapy of Lung Cancer Patients. Journal of Thoracic Oncology. 10:7, 1049–1057. doi: 10.1097/JTO.0000000000000570.