Clinical application of amplicon-based next-generation sequencing to therapeutic decision making in lung cancer

Takeda, Masayuki; Sakai, Kazuko; Terashima, Masato; Kaneda, Hiroyasu; Hayashi, Hidetoshi; Tanaka, Kumiko; Okamoto, Kentaro; Takahama, Takayuki; Yoshida, Teruhiko; Iwasa, Tsutomu; Shimizu, Tsuneo; Nonagase, Yoshikane; Kudo, Kenichiro; Tomida, Shuta; Mitsudomi, Tetsuya; Saigo, Kazumasa; Ito, Akihiko; Nakagawa, Kazuhiko; Nishio, Kazuto

doi:10.1093/annonc/mdv475

Cited by 75 publications

(62 citation statements)

References 19 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Together with several recent reports [2–8, 14–16], our clinical validation and implementation of a commercial DNA amplicon-based NGS assay support the usage of this technique in routine clinical diagnostics of NSCLC compared to previous single gene diagnostics also in smaller regional healthcare regions, based on concordance between techniques (99% in this study), turnaround time, sample success rate over time, accuracy, limit of detection, and cost. In agreement with both Fisher et al [5] and Hagemann et al [2], the success rate and clinical feasibility of our NGS framework is highly dependent on central pathological review by experienced diagnostic pathologists together with standardized and quality controlled tissue handling, to ensure sufficiently high proportions of malignant cells in specimens with adequate nucleic acid quality.…”

Section: Discussionsupporting

confidence: 81%

Clinical framework for next generation sequencing based analysis of treatment predictive mutations and multiplexed gene fusion detection in non-small cell lung cancer

Lindquist¹,

Karlsson

Leveén³

et al. 2017

Oncotarget

View full text Add to dashboard Cite

Precision medicine requires accurate multi-gene clinical diagnostics. We describe the implementation of an Illumina TruSight Tumor (TST) clinical NGS diagnostic framework and parallel validation of a NanoString RNA-based ALK, RET, and ROS1 gene fusion assay for combined analysis of treatment predictive alterations in non-small cell lung cancer (NSCLC) in a regional healthcare region of Sweden (Scandinavia). The TST panel was clinically validated in 81 tumors (99% hotspot mutation concordance), after which 533 consecutive NSCLCs were collected during one-year of routine clinical analysis in the healthcare region (˜90% advanced stage patients). The NanoString assay was evaluated in 169 of 533 cases. In the 533-sample cohort 79% had 1-2 variants, 12% >2 variants and 9% no detected variants. Ten gene fusions (five ALK, three RET, two ROS1) were detected in 135 successfully analyzed cases (80% analysis success rate). No ALK or ROS1 FISH fusion positive case was missed by the NanoString assay. Stratification of the 533-sample cohort based on actionable alterations in 11 oncogenes revealed that 66% of adenocarcinomas, 13% of squamous carcinoma (SqCC) and 56% of NSCLC not otherwise specified harbored ≥1 alteration. In adenocarcinoma, 10.6% of patients (50.3% if including KRAS) could potentially be eligible for emerging therapeutics, in addition to the 15.3% of patients eligible for standard EGFR or ALK inhibitors. For squamous carcinoma corresponding proportions were 4.4% (11.1% with KRAS) vs 2.2%. In conclusion, multiplexed NGS and gene fusion analyses are feasible in NSCLC for clinical diagnostics, identifying notable proportions of patients potentially eligible for emerging molecular therapeutics.

show abstract

Section: Discussionsupporting

confidence: 81%

Clinical framework for next generation sequencing based analysis of treatment predictive mutations and multiplexed gene fusion detection in non-small cell lung cancer

Lindquist¹,

Karlsson

Leveén³

et al. 2017

Oncotarget

View full text Add to dashboard Cite

show abstract

“…The ratio was lower than one previous report (49%) (25), but was similar to that of a recent study (26). The frequencies of EML4/ KIF5b-ALK and KIF5b/CCDC6-RET were in total 2.2% among these patients, which was lower than that of a previous study (3.8%) (13). The ratios of EGFR-TKI sensitizing mutations among smokers (58%) and non-smokers (22%) were also less than that of a previous report (68% and 31%, respectively) (25).…”

Section: Discussioncontrasting

confidence: 82%

Routine genetic testing of lung cancer specimens derived from surgery, bronchoscopy and fluid aspiration by next generation sequencing

Yamamoto

Kikuchi

Kobayashi

et al. 2017

International Journal of Oncology

View full text Add to dashboard Cite

After the development of EGFR tyrosine kinase inhibitors (TKIs), genetic testing of EGFR became required for effective treatment of lung cancer. Initially, the testing was conducted separately for each mutated region. However, many EGFR mutations have since been identified that determine the efficacy of EGFR-TKIs. Therefore, genetic testing of EGFR by next generation sequencing (NGS) may be a suitable strategy for lung cancer. Here we examined the applicability of the NGS method in regard to sensitivity, time and cost. A total of 939 specimens were obtained from 686 lung cancer patients at our hospital. DNA and RNA were simultaneously extracted from specimens derived from surgery, bronchoscopy, and fluid aspiration. Specimens included cerebrospinal fluid, pleural effusion, abdominal fluid, and pericardial effusion. From RNA, target regions (EGFR, KRAS, ALK fusion and RET fusion) were enriched by RT-PCR and sequenced with MiSeq. From DNA, PCR or PCR-RFLP conventional methods were performed. NGS and conventional methods were carried out routinely per week. Among the total 939 specimens, 38 specimens could not be examined with NGS. Among these, 34 specimens were analyzed by conventional testing with simultaneously extracted DNA. The remaining four specimens could not be tested with either method. Compared with the conventional method, the concordance rate of mutations was 99% (892/901), excluding specimens with NGS failure. The time period required from processing of specimens to results was 4 days, and the cost per sample was sufficiently low. In conclusion, the genetic testing with NGS method was useful for lung cancer treatment. The cost, sensitivity and time were able to tolerate routine examinations.

show abstract

“…Such multiplex genomic testing will assist physicians to identify actionable mutations with available targeted treatments or new target agents for clinical trials 16. One limitation of this study was its retrospective nature.…”

Section: Discussionmentioning

confidence: 99%

A retrospective analysis of the clinicopathological and molecular characteristics of pulmonary blastoma

Zhao¹,

Liu²,

Zhou³

et al. 2016

OTT

View full text Add to dashboard Cite

PurposeThe aim of this study was to analyze and summarize the clinicopathological and molecular characteristics of classic biphasic pulmonary blastoma (PB) to improve its diagnosis and treatment.Patients and methodsA retrospective analysis was performed in patients who were diagnosed with PB at Sun Yat-Sen University Cancer Center from March 1995 to March 2015. Genomic DNA was profiled using a capture-based targeted sequencing panel.ResultsSixteen patients with an average age of 40 years were included in this study. Accurate preoperative diagnosis was very challenging as surgically resected tissues with immunohistochemical staining were required for the diagnosis. Surgery was the optimal treatment for localized disease and there was no standard management for metastatic disease. Mutations were detected among 9 out of the 56 genes profiled, including BRCA2, ERBB4, ALK, MET, BRAF, RAF1, PTEN, EGFR, and PIK3CA.ConclusionDue to the low incidence rate and the reclassification of PB, no standard treatment is available. Although the numbers of cases are few with varying individual experiences, it is important to improve our understanding regarding this rare lung cancer. Targeted DNA sequencing may be of clinical use for molecular testing and the effects of targeted therapy need to be confirmed.

show abstract

Clinical application of amplicon-based next-generation sequencing to therapeutic decision making in lung cancer

Cited by 75 publications

References 19 publications

Clinical framework for next generation sequencing based analysis of treatment predictive mutations and multiplexed gene fusion detection in non-small cell lung cancer

Clinical framework for next generation sequencing based analysis of treatment predictive mutations and multiplexed gene fusion detection in non-small cell lung cancer

Routine genetic testing of lung cancer specimens derived from surgery, bronchoscopy and fluid aspiration by next generation sequencing

A retrospective analysis of the clinicopathological and molecular characteristics of pulmonary blastoma

Contact Info

Product

Resources

About