title: Quantitative identification of mutant alleles derived from lung cancer in plasma cell-free DNA via anomaly detection using deep sequencing data.
abstract: The detection of rare mutants using next generation sequencing has considerable potential for diagnostic applications. Detecting circulating tumor DNA is the foremost application of this approach. The major obstacle to its use is the high read error rate of next-generation sequencers. Rather than increasing the accuracy of final sequences, we detected rare mutations using a semiconductor sequencer and a set of anomaly detection criteria based on a statistical model of the read error rate at each error position. Statistical models were deduced from sequence data from normal samples. We detected epidermal growth factor receptor (EGFR) mutations in the plasma DNA of lung cancer patients. Single-pass deep sequencing (>100,000 reads) was able to detect one activating mutant allele in 10,000 normal alleles. We confirmed the method using 22 prospective and 155 retrospective samples, mostly consisting of DNA purified from plasma. A temporal analysis suggested potential applications for disease management and for therapeutic decision making to select epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKI).
authors.affiliation: Research Institute, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Osaka, Japan.
authors.forename: Yoji
authors.initials: Y
authors.lastname: Kukita
authors.forename: Junji
authors.initials: J
authors.lastname: Uchida
authors.forename: Shigeyuki
authors.initials: S
authors.lastname: Oba
authors.forename: Kazumi
authors.initials: K
authors.lastname: Nishino
authors.forename: Toru
authors.initials: T
authors.lastname: Kumagai
authors.forename: Kazuya
authors.initials: K
authors.lastname: Taniguchi
authors.forename: Takako
authors.initials: T
authors.lastname: Okuyama
authors.forename: Fumio
authors.initials: F
authors.lastname: Imamura
authors.forename: Kikuya
authors.initials: K
authors.lastname: Kato
mesh_terms: D000483:Alleles; D000970:Antineoplastic Agents / Q000494:pharmacology / Q000627:therapeutic use; D004252:DNA Mutational Analysis; D004273:DNA, Neoplasm / Q000097:blood*; D019008:Drug Resistance, Neoplasm; D066246:ErbB Receptors / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008175:Lung Neoplasms / Q000175:diagnosis / Q000188:drug therapy / Q000235:genetics*; D009154:Mutation; D047428:Protein Kinase Inhibitors / Q000494:pharmacology / Q000627:therapeutic use; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity
chemical_list: D000970:Antineoplastic Agents; D004273:DNA, Neoplasm; D047428:Protein Kinase Inhibitors; D066246:ErbB Receptors