​世界肺癌大会是全球肺癌领域影响力最大的国际会议，每年有一百多个国家超过七千人的临床专家参会研讨胸部恶性肿瘤的治疗、诊断和科研方向上的最新进展。今年第16届世界肺癌大会在美国丹佛市召开，邀请北京协和医院病理科的梁智勇主任团队参会并做口头报告“在非小细胞肺癌里使用NGS方法开展临床检测有诊疗指导意义的基因突变”。协和病理科师晓华老师在大会上汇报了使用雅康博公司的NGS诊断产品科吉安肺癌试剂盒（NextDaySeq Lung Panel）开展的临床验证工作。

       在该研究中，协和病理科平行使用NGS，qPCR和Sanger测序三种方法，用200多例非小细胞肺癌病人FFPE样本检测了对肺癌临床诊疗有重要指导的基因突变。验证结果显示，NGS方法（科吉安肺癌试剂盒）的灵敏度和特异性均显著优于Sanger测序；在热点突变检测上，NGS方法和qPCR方法的检测结果完全一致；而NGS检出了一批非热点突变。本研究的检测对比数据已经整理成文，目前已被国际临床检测杂志Clinical Laboratory接受并发表。

        该报告得到了参会临床专家的广泛认可，能够检测7个肺癌临床诊疗指导基因的科吉安肺癌NGS诊断试剂盒也引起了专家们的极大兴趣。科吉安肺癌试剂盒基于LIFE的Ion Torrent平台，采用独有的文库制备技术，结合专有的生物信息学分析软件，全面提升插入缺失突变判读的精度，并可在48小时内完成从FFPE样本到7个基因（EGFR, KRAS, BRAF, PIK3CA, ALK, DDR2和PDGFRA）突变检测的报告。

 

 

 

附2015年肺癌大会摘要：

 

Title:

 

Clinical implementation of the NextDaySeq Lung Panel for identification of clinically actionable variants in non-small cell lung cancer

 

Author:

 

Gao Jie (GaoJie@pumch.cn), Wu Huanwen (whw14093@163.com,PhD), Shi Xiaohua (shixiaohua3762@hotmail.com,PhD),  Huo Zhen(huozhen1976@126.com,BS), Zhang Jing (jingzhangsmile@163.com,MD), Liang Zhiyong (liangzhiyong1220@yahoo.com, MD, PhD, correspongding author).

Department of pathology,Peking Union Medical College Hospital, Chinese Academy of Medical Science,Beijing100730,China)

 

Background:

 

    Molecular testing-directed targeted therapies are transforming treatment paradigms for non-small cell lung cancer (NSCLC). The clinical application of next-generation sequencing (NGS) technologies has offered a more comprehensive understanding of the mutational landscape.  Efforts have been made in the past three years in the Department of pathology at the Peking Union Medical College Hospital, to adopt NGS in the clinical setting allowing rapid and reliable detection of actionable mutations that facilitate therapeutic decision making and disease prediction for at-risk patients.

 

Methods:

 

    The NextDaySeq Lung panel on Ion TorrentTM System and DanPA bioinformatics pipeline have been implemented in our clinical laboratory.  The workflow employs novel chemistry in library preparation and innovation in informatics, which allows a 48-hour turnaround from FFPE samples to identification of variants with demonstrated clinical importance.  The test sequences 16 exons in EGFR, KRAS, BRAF, PIK3CA, ALK, DDR2 and PDGFRA, covering 82 well recognized hotspots.  The end-to-end test performance has been established with analytical sensitivity and specificity as well as the assay’s repeatability and reproducibility.  Up to date, more than 200 samples have been examined including both lung adenocarcinoma and lung squamous carcinoma.  To characterize the analytical performance, the NGS results have been compared with Sanger sequencing that covers the same exons, as well as QPCR assays (CFDA approved IVD kits) that cover a majority of hotspots within these exons.

 

Results:

 

    Analysis of 200 cases indicated 100% concordance for reportable variants mutually covered in both NGS and QPCR assays.  Eight cases reported at least one additional potentially clinically relevant variant, for example, in EGFR and PIK3CA, that would not have been identified in previously implemented QPCR assays.  The mutation rates reported in 200 cases ranged from 2.4% to 84.3% according to DanPA analysis, while Sanger sequencing failed to detect variants in 32 cases with mutation rates lower than 20%.  The Indel analysis had been a challenge for previous NGS tests in the lab, and the current test resolved the issue with the DanPA pipeline, demonstrating 100% PPV and NPV values compared with QPCR, and Sanger when mutation rates higher than 20%.  Additionally, we documented multiple cases that carry double and triple mutations, which were rare in lung cancer, and also identified several novel mutations.

 

Conclusion:

 

    Therefore, we reported the validation of NextDaySeq Lung panel for high throughput detection of mutations in NSCLC, and the development of a wet-bench and informatics workflow enabling timely and informative molecular diagnosis.  The implementation of the test offers significantly improved information benefit over previous tests, and holds the promise to impact patient management.