title: Multiplexed deep sequencing analysis of ALK kinase domain identifies resistance mutations in relapsed patients following crizotinib treatment.
abstract: The recently approved ALK kinase inhibitor crizotinib has demonstrated successful treatment of metastatic and late stage ALK fusion positive non-small cell lung cancer (NSCLC). However, the median duration of clinical benefit is ~10-11months due to the emergence of multiple and simultaneous resistance mechanisms in these tumors. Mutations in the ALK kinase domain confer resistance to crizotinib in about one-third of these patients. We developed a multiplex deep sequencing method using semiconductor sequencing technology to quickly detect resistance mutations within the ALK kinase domain from tumor biopsies. By applying a base-pair specific error-weighted mutation calling algorithm (BASCA) that we developed for this assay, genomic DNA analysis from thirteen relapsed patients revealed three known crizotinib resistance mutations, C1156Y, L1196M and G1269A. Our assay demonstrates robust and sensitive detection of ALK kinase mutations in NSCLC tumor samples and aids in the elucidation of resistance mechanisms pertinent to the clinical setting.
authors: Pfizer Oncology, San Diego, CA, USA. donghuistephen.huang@pfizer.com
authors: Donghui
authors: D
authors: Huang
authors: Dong-Wan
authors: DW
authors: Kim
authors: Athanasios
authors: A
authors: Kotsakis
authors: Shibing
authors: S
authors: Deng
authors: Paul
authors: P
authors: Lira
authors: Steffan N
authors: SN
authors: Ho
authors: Nathan V
authors: NV
authors: Lee
authors: Pamela
authors: P
authors: Vizcarra
authors: Joan Q
authors: JQ
authors: Cao
authors: James G
authors: JG
authors: Christensen
authors: Tae Min
authors: TM
authors: Kim
authors: Jong-Mu
authors: JM
authors: Sun
authors: Jin Seok
authors: JS
authors: Ahn
authors: Myung-Ju
authors: MJ
authors: Ahn
authors: Keunchil
authors: K
authors: Park
authors: Mao
authors: M
authors: Mao
mesh_terms: D000465:Algorithms; D000077548:Anaplastic Lymphoma Kinase; D000970:Antineoplastic Agents / Q000627:therapeutic use; D002289:Carcinoma, Non-Small-Cell Lung / Q000188:drug therapy* / Q000201:enzymology / Q000235:genetics; D045744:Cell Line, Tumor; D000077547:Crizotinib; D019008:Drug Resistance, Neoplasm / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008175:Lung Neoplasms / Q000188:drug therapy* / Q000201:enzymology / Q000235:genetics; D009154:Mutation; D009364:Neoplasm Recurrence, Local; D047428:Protein Kinase Inhibitors / Q000627:therapeutic use; D011720:Pyrazoles / Q000627:therapeutic use*; D011725:Pyridines / Q000627:therapeutic use*; D020794:Receptor Protein-Tyrosine Kinases / Q000037:antagonists & inhibitors / Q000235:genetics* / Q000378:metabolism; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D000970:Antineoplastic Agents; D047428:Protein Kinase Inhibitors; D011720:Pyrazoles; D011725:Pyridines; D000077547:Crizotinib; C000626173:ALK protein, human; D000077548:Anaplastic Lymphoma Kinase; D020794:Receptor Protein-Tyrosine Kinases
keywords: Crizotinib; Deep sequencing; Mutation; Resistance