Next generation analysis of breast cancer genomes for precision medicine

For many years breast cancer classification has been based on histology and immune-histochemistry. New techniques, more strictly related to cancer biology, partially succeeded in fractionating patients, correlated to survival and better predicted the patient response to therapy. Nowadays, great expectations arise from massive parallel or high throughput next generation sequencing. Cancer genomics has already revolutionized our knowledge of breast cancer molecular pathology, paving the way to the development of new and more effective clinical protocols. This review is focused on the most recent advances in the field of cancer genomics and epigenomics, including DNA alterations and driver gene mutations, gene fusions, DNA methylation and miRNA expression.     

Predictive molecular pathology of lung cancer in Germany with focus on gene fusion testing: Methods and quality assurance

Predictive molecular testing has become an important part of the diagnosis of any patient with lung cancer. Using reliable methods to ensure timely and accurate results is inevitable for guiding treatment decisions. In the past few years, parallel sequencing has been established for mutation testing, and its use is currently broadened for the detection of other genetic alterations, such as gene fusion and copy number variations. In addition, conventional methods such as immunohistochemistry and in situ hybridization are still being used, either for formalin-fixed, paraffin-embedded tissue or for cytological specimens. For the development and broad implementation of such complex technologies, interdisciplinary and regional networks are needed. The Network Genomic Medicine (NGM) has served as a model of centralized testing and decentralized treatment of patients and incorporates all German comprehensive cancer centers. Internal quality control, laboratory accreditation, and participation in external quality assessment is mandatory for the delivery of reliable results. Here, we provide a summary of current technologies used to identify patients who have lung cancer with gene fusions, briefly describe the structures of NGM and the national NGM (nNGM), and provide recommendations for quality assurance.     

Quality assurance and quality control for radiotherapy/medical oncology in Europe: Guideline development and implementation

The past two decades have brought tremendous changes to the practice of radiation oncology and medical oncology. To manage all the complexities related to the new technologies and the new drugs, the radiation and medical oncologists have to enhance their clinical action and professional skill profile. To accomplish this they have to find reliable tools in the quality of their medical practice and in future research activities. Quality assurance (QA) and quality control (QC) for radiation and medical oncologists mean to clarify the different components of the clinical decision, to supervise with proper methodology the required steps needed to accomplish the agreed outcomes and to control them. Quality for radiation and medical oncology means to supervise each clinical and technical component of the whole process to guarantee that all steps together will arrive at the final and best possible outcome. Key components are guidelines, specialization and a multidisciplinary approach. The research of global quality could represent a further complexity, but it is the best tool to give a perspective and a chance to further improvements of our disciplines and to promote better outcome in all cancer patients.     

下一代测序技术引领下的血液系统恶性肿瘤研究新进展：第55届美国血液学会年会报道

第55届美国血液学会（ASH）年会最大亮点是在下一代测序技术（NGS）引领下,血液系统恶性肿瘤诊断、发病机制、疗效评价、预后分析和微小残留病（MRD）监测等领域出现一系列革命性进步.文章仅将第55届Best ASH中应用NGS技术取得重要突破的7篇论文介绍给国内读者.     

Multiple Biomarker Testing Tissue Consumption and Completion Rates With Single-gene Tests and Investigational Use of Oncomine Dx Target Test for Advanced Non–Small-cell Lung Cancer: A Single-center Analysis

Introduction

First-line targeted therapies have been developed for advanced non–small-cell lung cancer (NSCLC). However, small biopsy samples pose a challenge to testing all relevant biomarkers. The present study characterized clinician-ordered single-gene lung cancer testing and evaluated tissue stewardship and the ability to successfully determine mutation status with single-gene testing or investigational use of the Oncomine Dx Target Test.

非小细胞肺癌分子病理学的研究

目的　探讨上海地区人肺癌发生及发展过程中的分子病理学模式。方法　采用DNAslotblot、PCR、PCR SSCP等方法 ,先后检测 2 0 0例NSCLC组织DNA标本中C erbB2、C myc、EGFR癌基因扩增 ,抑癌基因中p5 3基因外显子 5～ 8点突变、p15基因的纯合性丢失 ,以及某些与肺癌相关的染色体 3p及 17p13 .3位点的杂合性丢失 (LOH)。结果　多种癌基因共扩增率与肺癌TNM分期呈正相关 (P <0 .0 0 1)。p5 3基因外显子 5～8点突变率为 49.2 % ( 3 1/63 ) ,其中以外显子 8为主。肺癌组织中p15基因出现高频率纯合性丢失 ,并与肺癌TNM分期密切相关 (P <0 .0 0 5 )。 17p13 .3杂合性丢失率为 40 % ( 8/2 0 ) ,并与p5 3基因的点突变相关联。 3p14及 3p2 5位点处的杂合性总丢失率可高达 66.7% ( 10 8/162 ) ,其中肺腺癌中 3p14及 3p2 5二位点的共丢失率明显高于鳞癌 (P <0 .0 5 )。结论　根据上述结果 ,提出上海市区居民的非小细胞肺癌分子病理学的初步模式 :癌前期病变时已可出现 3p丢失 ,原位癌时以p5 3基因突变及 17p13 .3丢失为主 ,浸润癌及向转移性癌过渡时有多种癌基因C myc、C erbB2及EGFR癌基因共扩增 ,并出现p15基因纯合性丢失。     

Error in the delivery of radiation therapy: results of a quality assurance review

PURPOSE: To examine error rates in the delivery of radiation therapy (RT), technical factors associated with RT errors, and the influence of a quality improvement intervention on the RT error rate. METHODS AND MATERIALS: We undertook a review of all RT errors that occurred at the Princess Margaret Hospital (Toronto) from January 1, 1997, to December 31, 2002. Errors were identified according to incident report forms that were completed at the time the error occurred. Error rates were calculated per patient, per treated volume (>/=1 volume per patient), and per fraction delivered. The association between tumor site and error was analyzed. Logistic regression was used to examine the association between technical factors and the risk of error. RESULTS: Over the study interval, there were 555 errors among 28,136 patient treatments delivered (error rate per patient = 1.97%, 95% confidence interval [CI], 1.81-2.14%) and among 43,302 treated volumes (error rate per volume = 1.28%, 95% CI, 1.18-1.39%). The proportion of fractions with errors from July 1, 2000, to December 31, 2002, was 0.29% (95% CI, 0.27-0.32%). Patients with sarcoma or head-and-neck tumors experienced error rates significantly higher than average (5.54% and 4.58%, respectively); however, when the number of treated volumes was taken into account, the head-and-neck error rate was no longer higher than average (1.43%). The use of accessories was associated with an increased risk of error, and internal wedges were more likely to be associated with an error than external wedges (relative risk = 2.04; 95% CI, 1.11-3.77%). Eighty-seven errors (15.6%) were directly attributed to incorrect programming of the "record and verify" system. Changes to planning and treatment processes aimed at reducing errors within the head-and-neck site group produced a substantial reduction in the error rate. CONCLUSIONS: Errors in the delivery of RT are uncommon and usually of little clinical significance. Patient subgroups and technical factors associated with errors can be identified. The introduction of new technology can produce new ways for errors to occur, necessitating ongoing evaluation of RT errors for quality assurance. Modifications to processes of care can produce important reductions in error rates.     

External quality assessment for KRAS testing is needed: setup of a European program and report of the first joined regional quality assessment rounds

The use of epidermal growth factor receptor-targeting antibodies in metastatic colorectal cancer has been restricted to patients with wild-type KRAS tumors by the European Medicines Agency since 2008, based on data showing a lack of efficacy and potential harm in patients with mutant KRAS tumors. In an effort to ensure optimal, uniform, and reliable community-based KRAS testing throughout Europe, a KRAS external quality assessment (EQA) scheme was set up. The first large assessment round included 59 laboratories from eight different European countries. For each country, one regional scheme organizer prepared and distributed the samples for the participants of their own country. The samples included unstained sections of 10 invasive colorectal carcinomas with known KRAS mutation status. The samples were centrally validated by one of two reference laboratories. The laboratories were allowed to use their own preferred method for histological evaluation, DNA isolation, and mutation analysis. In this study, we analyze the setup of the KRAS scheme. We analyzed the advantages and disadvantages of the regional scheme organization by analyzing the outcome of genotyping results, analysis of tumor percentage, and written reports. We conclude that only 70% of laboratories correctly identified the KRAS mutational status in all samples. Both the false-positive and false-negative results observed negatively affect patient care. Reports of the KRAS test results often lacked essential information. We aim to further expand this program to more laboratories to provide a robust estimate of the quality of KRAS testing in Europe, and provide the basis for remedial measures and harmonization.     

Cervical cancer screening in Europe: Quality assurance and organisation of programmes

BackgroundCervical screening programmes have reduced cervical cancer incidence and mortality but the level of success is highly variable between countries. Organisation of programmes is essential for equity and cost-effectiveness. However, there are differences in effectiveness, also among organised programmes. In order to identify the key organisational components that determine effectiveness, we performed a Europe-wide survey on the current status of organisation and organised quality assurance (QA) measures in cervical cancer prevention programmes, as well as organisation-associated costs.MethodsA comprehensive questionnaire was developed through systematic review of literature and existing guidelines. The survey was sent to programme organisers, Ministries of Health and experts in 34 European Union (EU) and European Free Trade Agreement (EFTA) countries. Detailed aspects of programme organisation, quality assurance, monitoring, evaluation and corresponding line-item costs were recorded. Documentation of programme guidelines, protocols and publications was requested.ResultsTwenty-nine of 34 countries responded. The results showed that organised efforts for QA, monitoring and evaluation were carried out to a differing extent and were not standardised, making it difficult to compare the cost-effectiveness of organisation and QA strategies. Most countries found it hard to estimate the costs associated with launching and operating the organised programme.ConclusionsTo our knowledge, this is the first questionnaire to request detailed information on the actual organisation and QA of programmes. The results of this survey can be used as a basis for further development of standardised guidelines on organisation and QA of cervical cancer screening programmes in Europe.     

“去重”在肺癌NGS数据分析中的重要作用

目的 探讨“不去重”和“去重”两种方法分析后各NGS相关指标间的差异,研究“去重”在靶向捕获NGS数据分析中的重要作用。方法 通过对58例肺癌患者的DNA样本进行靶向286基因探针杂交方法建库并进行NGS检测,每例NGS检测数据分别进行“去重”和“不去重”两种方法的生物信息学分析,比较两种方法分析得到的NGS相关指标Mapped Reads（可比对上reads比例）、On Target（靶向区域reads比例）、Mean Depth（平均测序深度）以及Uniformity（均一性）等数据之间的差异。结果 “不去重”和“去重”两种方法分析得到平均Mapped Reads、On Target、Mean Depth和Uniformity值,各组指标间差异均有统计学意义（P<0.001）。“去重”方法分析时,Mapped Reads、On Target和MeanDepth 3个指标均呈现出血浆样本与其他3种类型样本间（FFPE、穿刺和手术）差异有统计学意义,在Uniformity指标上则呈现出4种类型样本间差异均无统计学意义。而“不去重”方法分析后结果正好相反。结论 去除PCR扩增所致重复序列的“去重”步骤在NGS数据分析中具有重要的作用,能够改善结果均一性,真实反映所测样本的DNA模板数量及等位基因频率（AF值,allele frequency）。“去重”后结果更有助于临床决策。     

机器学习在调强放疗质量保证中的应用研究进展

近年来随着大数据分析与人工智能技术的发展,机器学习在放疗领域的应用研究逐渐增多。通过既往计划训练,机器学习可预测计划质量及剂量验证结果。机器学习也可以预测MLC位置误差、加速器性能。机器学习用于调强放疗质量保证能提高治疗计划和实施的质量和效率,增加患者获益并降低风险。机器学习用于调强放疗质量保证目前尚存在特征值选择、提取和计算复杂,要求训练样本量大,预测精度不够等问题,阻碍了其临床转化和应用。本文综述其研究进展。     

Challenges to quality assurance of surgical interventions in clinical oncology trials: A systematic review

Where surgery forms the primary curative modality in surgical oncology trials the quality of this intervention has the potential to directly influence outcomes. Many trials however lack a robust framework to ensure surgical quality. We aim to report existing published challenges to quality assurance of surgical interventions within oncological trials. A systematic on-line literature search of Embase and Medline identified 34 relevant studies, including 19 RCTs, 11 further analyses of the primary RCTs, and 4 trial protocols. Inclusion criteria: oncological RCTs with a surgical intervention and/or associated publications relevant to the research question; ‘Challenges to quality assurance of surgery in clinical oncology trials’. Selected articles were assessed by two reviewers to identify reported challenges to quality assurance of surgical intervention within these trials. Reported challenges to surgical quality could be classified as those affecting credentialing, standardisation and monitoring of surgical interventions. Constraints of using case volume for credentialing surgeons; inter-centre variation in the definition and execution of interventions; insufficient training, and monitoring of surgical quality, were the most commonly encountered challenges within each of these three domains. Findings confirmed an inadequacy in the implementation and reporting of effective surgical quality assurance measures. The surgical community should enable implementation of agreed upon mitigating strategies to overcome challenges to surgical quality in oncology trials.     

Time and motion study of radiotherapy delivery: Economic burden of increased quality assurance and IMRT

Time measurements were performed on daily treatment delivery with the aim to quantify the impact of quality assurance (QA) using an electronic portal imaging device (EPID) on RT delivery time and to validate the time burden of intensity modulated radiation therapy (IMRT) as an example of advanced technology.Both increased QA and the delivery of IMRT were found to be significant parameters determining daily treatment time (TT), which in turn translates in increased treatment costs.     

Development of an electronic database for quality assurance of radiotherapy in the International Society of Paediatric Oncology (Europe) high risk neuroblastoma study

Quality assurance of radiotherapy is an important determinant of outcome in some cancers. SIOPEN-R-NET developed a computerised remote data entry system for recording imaging and treatment parameters for its multimodality high risk neuroblastoma study. This will enable investigation of the relationship between radiotherapy quality and local control.     

Molecular pathology quality control in Southeast Asia: Results of a multiregional quality assurance study from MASTER KEY Asia

Tissue specimen quality assurance is a major issue of precision medicine for rare cancers. However, the laboratory standards and quality of pathological specimens prepared in Asian hospitals remain unknown. To understand the methods in Southeast Asian oncology hospitals and to clarify how pre-analytics affect the quality of formalin-fixed paraffin-embedded (FFPE) specimens, a questionnaire surveying pre-analytical procedures (Part I) was administered, quality assessment of immunohistochemistry (IHC) staining and DNA/RNA extracted from the representative FFPE specimens from each hospital (Part II) was conducted, and the quality of DNA/RNA extracted from FFPE of rare-cancer patients for genomic sequencing (Part III) was examined. Quality measurements for DNA/RNA included ΔΔCt, DV200, and cDNA yield. Six major cancer hospitals from Malaysia, Philippines, and Vietnam participated. One hospital showed unacceptable quality for the DNA/RNA assessment, but improved by revising laboratory procedures. Only 57% (n = 73) of the 128 rare-cancer patients' specimens met both DNA and RNA quality criteria for next-generation sequencing. Median DV200 was 80.7% and 64.3% for qualified and failed RNA, respectively. Median ΔΔCt was 1.25 for qualified and 4.89 for failed DNA. Longer storage period was significantly associated with poor DNA (fail to qualify ratio = 1579:321 days, p < 0.001) and RNA (fail to qualify ratio = 1070:280 days, p < 0.001). After improvement of pre-analytical factors, the qualification rate increased for hospitals A and E from 41.5% to 70.5% and 62.5% to 86%, respectively. This is the first report to elucidate the pre-analytical laboratory procedures of main Southeast Asian oncology hospitals. An external quality assessment program may improve factors associated with tumor FFPE specimen quality.