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Ravera F, Cirmena G, Dameri M, Gallo M, Vellone VG, Fregatti P, Friedman D, Calabrese M, Ballestrero A, Tagliafico A, Ferrando L, Zoppoli G. Development of a hoRizontal data intEgration classifier for NOn-invasive early diAgnosis of breasT cancEr: the RENOVATE study protocol. BMJ Open 2021; 11:e054256. [PMID: 34972769 PMCID: PMC8720992 DOI: 10.1136/bmjopen-2021-054256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
INTRODUCTION Standard procedures aimed at the early diagnosis of breast cancer (BC) present suboptimal accuracy and imply the execution of invasive and sometimes unnecessary tissue biopsies. The assessment of circulating biomarkers for diagnostic purposes, together with radiomics, is of great potential in BC management. METHODS AND ANALYSIS This is a prospective translational study investigating the accuracy of the combined assessment of multiple circulating analytes together with radiomic variables for early BC diagnosis. Up to 750 patients will be recruited at their presentation at the Diagnostic Senology Unit of Ospedale Policlinico San Martino (Genoa, IT) for the execution of a diagnostic biopsy after the detection of a suspect breast lesion (t0). Each recruited patient will be asked to donate peripheral blood and urine before undergoing breast biopsy. Blood and urine samples will also be collected from a cohort of 100 patients with negative mammography. For cases with histological diagnosis of invasive BC, a second sample of blood and urine will be collected after breast surgery. Circulating tumour DNA, cell-free methylated DNA and circulating proteins will be assessed in samples collected at t0 from patients with stage I-IIA BC at surgery together with those collected from patients with histologically confirmed benign lesions of similar size and from healthy controls with negative mammography. These analyses will be combined with radiomic variables extracted with freeware algorithms applied to cases and matched controls for which digital mammography is available. The overall goal of the present study is to develop a horizontal data integration classifier for the early diagnosis of BC. ETHICS AND DISSEMINATION This research protocol has been approved by Regione Liguria Ethics Committee (reference number: 2019/75, study ID: 4452). Patients will be required to provide written informed consent. Results will be published in international peer-reviewed scientific journals. TRIAL REGISTRATION NUMBER NCT04781062.
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Affiliation(s)
- Francesco Ravera
- Department of Internal Medicine, Università degli Studi di Genova, Genova, Italy
| | - Gabriella Cirmena
- Department of Internal Medicine, Università degli Studi di Genova, Genova, Italy
| | - Martina Dameri
- Ospedale Policlinico San Martino Istituto di Ricovero e Cura a Carattere Scientifico per l'Oncologia, Genova, Italy
| | - Maurizio Gallo
- Department of Internal Medicine, Università degli Studi di Genova, Genova, Italy
| | - Valerio Gaetano Vellone
- Department of Surgical Sciences and Integrated Diagnostic, Università degli Studi di Genova, Genova, Italy
| | - Piero Fregatti
- Ospedale Policlinico San Martino Istituto di Ricovero e Cura a Carattere Scientifico per l'Oncologia, Genova, Italy
| | - Daniele Friedman
- Ospedale Policlinico San Martino Istituto di Ricovero e Cura a Carattere Scientifico per l'Oncologia, Genova, Italy
| | - Massimo Calabrese
- Ospedale Policlinico San Martino Istituto di Ricovero e Cura a Carattere Scientifico per l'Oncologia, Genova, Italy
| | - Alberto Ballestrero
- Department of Internal Medicine, Università degli Studi di Genova, Genova, Italy
| | - Alberto Tagliafico
- Department of Health Sciences, Università degli Studi di Genova, Genova, Italy
| | - Lorenzo Ferrando
- Ospedale Policlinico San Martino Istituto di Ricovero e Cura a Carattere Scientifico per l'Oncologia, Genova, Italy
| | - Gabriele Zoppoli
- Department of Internal Medicine, Università degli Studi di Genova, Genova, Italy
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Forouhari S, Beygi Z, Mansoori Z, Hajsharifi S, Heshmatnia F, Gheibihayat SM. Liposomes: Ideal drug delivery systems in breast cancer. Biotechnol Appl Biochem 2021; 69:1867-1884. [PMID: 34505736 DOI: 10.1002/bab.2253] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 09/06/2021] [Indexed: 12/15/2022]
Abstract
Breast cancer (BC) has been recognized as the most common type of cancer in females across the world, accounting for 12% of each cancer case. In this sense, better diagnosis and screening have been thus far proven to contribute to higher survival rates. Moreover, traditional (or standard) chemotherapy is still known as one of the several prominent therapeutic options available, though it suffers from unsuitable cell selectivity, severe consequences, as well as resistance. In this regard, nanobased drug delivery systems (DDSs) are likely to provide promising grounds for BC treatment. Liposomes are accordingly effective nanosystems, having the benefits of multiple formulations verified to treat different diseases. Such systems possess specific features, including smaller size, biodegradability, hydrophobic/hydrophilic characteristics, biocompatibility, lower toxicity, as well as immunogenicity, which can all lead to considerable efficacy in treating various types of cancer. As chemotherapy uses drugs to target tumors, generates higher drug concentrations in tumors, which can provide for their slow release, and enhances drug stability, it can be improved via liposomes in DDSs for BC treatment. Therefore, the present study aims to review the existing issues regarding BC treatment and discuss liposome-based targeting in order to overcome barriers to conventional drug therapy.
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Affiliation(s)
- Sedighe Forouhari
- Infertility Research Center, Research Center of Quran, Hadith, and Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Beygi
- Department of Nursing and Midwife, Maybod Branch, Islamic Azad University, Maybod, Iran
| | - Zahra Mansoori
- Faculty of Educational Sciences and Psychology, Department of Sports Sciences, Shiraz University, Shiraz, Iran
| | - Sara Hajsharifi
- Student Research Committee, Department of Midwifery, Fatemeh (PBUH) School of Nursing and Midwifery, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Fatemeh Heshmatnia
- Student Research Committee, Department of Midwifery, Fatemeh (PBUH) School of Nursing and Midwifery, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Mohammad Gheibihayat
- Department of Medical Biotechnology, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
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Bae GE, Kim SH, Choi MK, Kim JM, Yeo MK. Targeted Sequencing of Ascites and Peritoneal Washing Fluid of Patients With Gastrointestinal Cancers and Their Clinical Applications and Limitations. Front Oncol 2021; 11:712754. [PMID: 34336700 PMCID: PMC8319747 DOI: 10.3389/fonc.2021.712754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 06/28/2021] [Indexed: 12/13/2022] Open
Abstract
Cytology from gastrointestinal (GI) cancers is frequently obtained from ascites and peritoneal washing fluids. Examination of ascites and peritoneal washing fluids from patients with GI cancers can help in the tumor staging and prognosis. Tumor-derived DNA in these cytology samples can be a target for next generation sequencing (NGS). Targeted NGS was evaluated in ascites and peritoneal washing samples obtained from 33 patients with GI cancers. These sequences were compared with those from tumor tissue samples, and correlated with cytopathologic findings of the ascites and peritoneal fluid samples. The correlation between fluid and tissue genotyping results was 25%, with a sensitivity of 21.43%. The volume of tumor contained within the fluid samples was low, ranging from ~0 to 10%. Importantly, the sensitivity of detection of somatic mutations in the fluid samples could be increased to 69.2% by assessing samples containing >2% tumor volume. Evaluation of cells from ascitic fluid showed the presence of KRAS, TP53, and CDH1 mutations in 33, 13, and 7%, respectively, of patients with pancreatic cancer, and the presence of KRAS, TP53, and APC mutations in 25, 12, and 13%, respectively, of patients with gastric cancer. Ascites of one of the latter patients acquired KRAS mutation, which was a novel mutation during metastasis. Targeted NGS of ascites and peritoneal washing fluid have clinical implications, as well as limitations, in patients with GI cancers. NGS-based cytology examination may expand cytomolecular practices in GI cancer patients.
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Affiliation(s)
- Go Eun Bae
- Department of Pathology, Chungnam National University School of Medicine, Daejeon, South Korea
| | - Seok-Hwan Kim
- Department of Surgery, Chungnam National University School of Medicine, Daejeon, South Korea
| | - Min Kyung Choi
- Department of Pathology, Chungnam National University School of Medicine, Daejeon, South Korea
| | - Jin-Man Kim
- Department of Pathology, Chungnam National University School of Medicine, Daejeon, South Korea
| | - Min-Kyung Yeo
- Department of Pathology, Chungnam National University School of Medicine, Daejeon, South Korea
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Park HJ, Lee SH, Chang YS. Recent advances in diagnostic technologies in lung cancer. Korean J Intern Med 2020; 35:257-268. [PMID: 32131569 PMCID: PMC7060993 DOI: 10.3904/kjim.2020.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 02/24/2020] [Indexed: 12/14/2022] Open
Abstract
The increase in lung cancer incidence of Korea has been dampened since 2000; however, increased human lifespan, interest in health care and the widespread implementation of health examinations have resulted in a considerable rise in detection of small lesions that need to be differentiated from lung cancer. Detection of lung cancer at an early stage rather than at a symptomatic advanced stage is also increasing, suggesting that there are increasing diagnostic demands for small peripheral lung lesions. The development of new molecular diagnostics, including next generation sequencing, companion diagnostics that accompany development of new anti-cancer drugs, and re-biopsy for application of new therapeutic modality accelerate the development of lung cancer diagnostics. In this review, we extensively describe the current available diagnostic tools in lung cancer.
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Affiliation(s)
- Hye Jung Park
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Sang Hoon Lee
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Yoon Soo Chang
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
- Correspondence to Yoon Soo Chang, M.D. Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, 211 Eonju-ro, Gangnam-gu, Seoul 06273, Korea Tel: +82-2-2019-3310 Fax: +82-2-3463-3882 E-mail:
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Precision Medicine Tumor Boards: Clinical Applicability of Personalized Treatment Concepts in Ovarian Cancer. Cancers (Basel) 2020; 12:cancers12030548. [PMID: 32120793 PMCID: PMC7139570 DOI: 10.3390/cancers12030548] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/14/2020] [Accepted: 02/20/2020] [Indexed: 11/26/2022] Open
Abstract
Background: Treating cancer according to its molecular alterations (i.e., targeted treatment, TT) is the goal of precision medicine tumor boards (PTBs). Their clinical applicability has been evaluated for ovarian cancer patients in this analysis. Methods: All consecutive ovarian cancer patients discussed in a PTB at the Medical University of Vienna, Austria, from April 2015 to April 2019 were included (n = 44). Results: In 38/44 (86%) cases, at least one mutation, deletion or amplification was detected. The most frequently altered genes were p53 (64%), PI3K pathway (18%), KRAS (14%), BRCA1 (11%) and BRCA2 (2%). In 31 patients (70%) a TT was recommended. A total of 12/31 patients (39%) received the recommended therapy. Median time from indication for PTB to TT start was 65 days (15–216). Median time to treatment failure was 2.7 months (0.2–13.2). Clinical benefit rate (CBR) was 42%. Reasons for treatment discontinuation were disease progression (42%), poor performance status (PS > 2; 25%), death (17%) or treatment related side effects (8%). In 61% the TT was not administered—mainly due to PS > 2. Conclusion: Even though a TT recommendation can be derived frequently, clinical applicability remains limited due to poor patients’ general condition after exploitation of standard treatment. However, we observed antitumor activity in a substantial number of heavily pretreated patients.
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Clinical application of genomic high-throughput data: Infrastructural, ethical, legal and psychosocial aspects. Eur Neuropsychopharmacol 2020; 31:1-15. [PMID: 31866110 DOI: 10.1016/j.euroneuro.2019.09.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 11/03/2018] [Accepted: 09/20/2019] [Indexed: 12/28/2022]
Abstract
Genomic high-throughput technologies (GHTT) such as next-generation sequencing represent a fast and cost-effective tool toward a more comprehensive understanding of the molecular background of complex diseases. However, technological advances contrast with insufficient application in clinical practice. Thus, patients, physicians, and other professionals are faced with tough challenges that forestall the efficient and effective implementation. With the increasing application of genetic testing, it is of paramount importance that physicians and other professionals in healthcare recognize the restrictions and potential of GHTT, in order to understand and interpret the complex data in the context of health and disease. At the same time, the growing volume and complexity of data is forever increasing the need for sustainable infrastructure and state-of-the-art tools for efficient data management, including their analysis and integration. The large pool of sensitive information remains difficult to interpret and fundamental questions spanning from billing to legal, social, and ethical issues have still not been resolved. Here we summarize and discuss these obstacles in an interdisciplinary context and suggest ways to overcome them. Continuous discussion with clinicians, data managers, biostatisticians, systems medicine experts, ethicists, legal scholars, and patients illuminates the strengths, weakness, and current practices in the pipeline from biomaterial to sequencing and data management. This discussion also highlights the new, cross-disciplinary working collaborations to realize the wide-ranging challenges in clinical genomics including the exceptional demands placed on the staff preparing and presenting the data, as well as the question as to how to report the data and results to patients.
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Exome sequencing of oral leukoplakia and oral squamous cell carcinoma implicates DNA damage repair gene defects in malignant transformation. Oral Oncol 2019; 96:42-50. [PMID: 31422212 DOI: 10.1016/j.oraloncology.2019.07.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/28/2019] [Accepted: 07/05/2019] [Indexed: 12/19/2022]
Abstract
OBJECTIVES To map the genomic pathways of patients with oral leukoplakia (OLK) which transformed to cancer (progressive) and those which did not (non-progressive), and to compare their exomic profiles. MATERIALS AND METHODS Whole exome sequencing was performed on 42 sequential samples from five progressive and eight non-progressive patients. Association of genomic variant frequencies with progression or lesion severity were analysed by non-parametric tests (Kruskal-Wallis and Mann-Whitney-Wilcoxon) and multivariate sparse partial least squares discriminant analysis (sPLS-DA). Enrichment analysis was used to characterise the effect of mutations upon biological pathways. Confirmatory studies used qPCR and immunohistochemistry. RESULTS Using sPLS-DA, the variant frequency of a small number of genes could be used to classify the samples based on lesion severity or progressive status. Enrichment analysis showed that DNA damage repair gene related pathways were highly impacted in lesions which progressed to cancer. Multivariate analysis of a set of 148 DNA damage repair genes could be used to classify progressive lesions using mutation frequency. BRCA1, BRCA2 and other double strand break (DSB) repair Fanconi anaemia (FA)/BRCA pathway genes were prominent contributors to this classification. CONCLUSION Patients with progressive and non-progressive OLK can be differentiated using the frequency of exomic variants, particularly in DNA damage repair pathway genes. To our knowledge, this is the first report of FA/BRCA (DSB) pathway involvement in malignant transformation of OLK to oral squamous cell carcinoma (OSCC).
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Phylogenomic Pipeline Validation for Foodborne Pathogen Disease Surveillance. J Clin Microbiol 2019; 57:JCM.01816-18. [PMID: 30728194 DOI: 10.1128/jcm.01816-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Foodborne pathogen surveillance in the United States is transitioning from strain identification using restriction digest technology (pulsed-field gel electrophoresis [PFGE]) to shotgun sequencing of the entire genome (whole-genome sequencing [WGS]). WGS requires a new suite of analysis tools, some of which have long histories in academia but are new to the field of public health and regulatory decision making. Although the general workflow is fairly standard for collecting and analyzing WGS data for disease surveillance, there are a number of differences in how the data are collected and analyzed across public health agencies, both nationally and internationally. This impedes collaborative public health efforts, so national and international efforts are underway to enable direct comparison of these different analysis methods. Ultimately, the harmonization efforts will allow the (mutually trusted and understood) production and analysis of WGS data by labs and agencies worldwide, thus improving outbreak response capabilities globally. This review provides a historical perspective on the use of WGS for pathogen tracking and summarizes the efforts underway to ensure the major steps in phylogenomic pipelines used for pathogen disease surveillance can be readily validated. The tools for doing this will ensure that the results produced are sound, reproducible, and comparable across different analytic approaches.
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Zhang X, Liang Z, Wang S, Lu S, Song Y, Cheng Y, Ying J, Liu W, Hou Y, Li Y, Liu Y, Hou J, Liu X, Shao J, Tai Y, Wang Z, Fu L, Li H, Zhou X, Bai H, Wang M, Lu Y, Yang J, Zhong W, Zhou Q, Yang X, Wang J, Huang C, Liu X, Zhou X, Zhang S, Tian H, Chen Y, Ren R, Liao N, Wu C, Zhu Z, Pan H, Gu Y, Wang L, Liu Y, Zhang S, Liu T, Chen G, Shao Z, Xu B, Zhang Q, Xu R, Shen L, Wu Y, Tumor Biomarker Committee OBOCSOCO(CSCO. Application of next-generation sequencing technology to precision medicine in cancer: joint consensus of the Tumor Biomarker Committee of the Chinese Society of Clinical Oncology. Cancer Biol Med 2019; 16:189-204. [PMID: 31119060 PMCID: PMC6528448 DOI: 10.20892/j.issn.2095-3941.2018.0142] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 12/20/2018] [Indexed: 02/05/2023] Open
Abstract
Next-generation sequencing (NGS) technology is capable of sequencing millions or billions of DNA molecules simultaneously. Therefore, it represents a promising tool for the analysis of molecular targets for the initial diagnosis of disease, monitoring of disease progression, and identifying the mechanism of drug resistance. On behalf of the Tumor Biomarker Committee of the Chinese Society of Clinical Oncology (CSCO) and the China Actionable Genome Consortium (CAGC), the present expert group hereby proposes advisory guidelines on clinical applications of NGS technology for the analysis of cancer driver genes for precision cancer therapy. This group comprises an assembly of laboratory cancer geneticists, clinical oncologists, bioinformaticians, pathologists, and other professionals. After multiple rounds of discussions and revisions, the expert group has reached a preliminary consensus on the need of NGS in clinical diagnosis, its regulation, and compliance standards in clinical sample collection. Moreover, it has prepared NGS criteria, the sequencing standard operation procedure (SOP), data analysis, report, and NGS platform certification and validation.
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Affiliation(s)
- Xuchao Zhang
- Guangdong Lung Cancer Institute, Medical Research Center, Cancer Center of Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou 510080, China
- Affiliated Guangdong Provincial People's Hospital, South China University of Technology, Guangzhou 510630, China
| | - Zhiyong Liang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100006, China
| | - Shengyue Wang
- National Research Center for Translational Medicine, Shanghai, RuiJin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Shun Lu
- Lung Tumor Clinical Medical Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yong Song
- Division of Respiratory Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing 210029, China
| | - Ying Cheng
- Department of Oncology, Jilin Cancer Hospital, Changchun 132002, China
| | - Jianming Ying
- Department of Pathology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100006, China
| | - Weiping Liu
- Department of Pathology, West China Hospital, Sichuan University, Chengdu 610065, China
| | - Yingyong Hou
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Yangqiu Li
- Department of Hematology, First Affiliated Hospital, Institute of Hematology, School of Medicine, Jinan University, Guangzhou 519000, China
| | - Yi Liu
- Laboratory of Oncology, Affiliated Hospital of the Academy of Military Medical Sciences, Beijing 100071, China
| | - Jun Hou
- Department of Oncology, First Clinical College of South China University of Technology/Guangdong Lung Cancer Institute, Guangzhou 510060, China
| | - Xiufeng Liu
- People's Liberation Army Cancer Center of Bayi Hospital Affiliated to Nanjing University of Chinese Medicine, Nanjing 210046, China
| | - Jianyong Shao
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou 519000, China
| | - Yanhong Tai
- Department of Pathology, Affiliated Hospital of the Academy of Military Medical Sciences, Beijing 100071, China
| | - Zheng Wang
- Department of Pathology, Beijing Hospital, Beijing 100071, China
| | - Li Fu
- Department of Breast Cancer Pathology and Research Laboratory of Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin’s Clinical Research Center for Cancer, Tianjin 300060, China
| | - Hui Li
- Department of Oncology, Jilin Cancer Hospital, Changchun 132002, China
| | - Xiaojun Zhou
- Department of Pathology, Jinling Hospital Nanjing University School of Medicine, Nanjing 210029, China
| | - Hua Bai
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100006, China
| | - Mengzhao Wang
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100006, China
| | - You Lu
- Department of Oncology, West China Hospital, Sichuan University, Chengdu 610065, China
| | - Jinji Yang
- Guangdong Lung Cancer Institute, Guangdong Provincical Prople's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Wenzhao Zhong
- Guangdong Lung Cancer Institute, Guangdong Provincical Prople's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Qing Zhou
- Guangdong Lung Cancer Institute, Guangdong Provincical Prople's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Xuening Yang
- Guangdong Lung Cancer Institute, Guangdong Provincical Prople's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Jie Wang
- Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100006, China
| | - Cheng Huang
- Department of Thoracic Oncology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou 350001, China
| | - Xiaoqing Liu
- Department of Oncology, Affiliated Hospital of the Academy of Military Medical Sciences, Beijing 100071, China
| | - Xiaoyan Zhou
- Department of Pathology, Shanghai Cancer Center, Fudan University, Shanghai 200433, China
| | - Shirong Zhang
- Center for Translational Medicine, Hangzhou First People's Hospital, Nanjing Medical University, Nanjing 210029, China
| | - Hongxia Tian
- Guangdong Lung Cancer Institute, Medical Research Center, Cancer Center of Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou 510080, China
- Affiliated Guangdong Provincial People's Hospital, South China University of Technology, Guangzhou 510630, China
| | - Yu Chen
- Guangdong Lung Cancer Institute, Medical Research Center, Cancer Center of Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou 510080, China
- Affiliated Guangdong Provincial People's Hospital, South China University of Technology, Guangzhou 510630, China
| | - Ruibao Ren
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, RuiJin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Ning Liao
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangzhou 510080, China
| | - Chunyan Wu
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200240, China
| | - Zhongzheng Zhu
- Department of Oncology, No. 113 Hospital of People's Liberation Army, Ningbo 315040, China
| | - Hongming Pan
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou 310020, China
| | - Yanhong Gu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing 210029, China
| | - Liwei Wang
- Department of Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Yunpeng Liu
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang 110016, China
| | - Suzhan Zhang
- Department of Oncology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310020, China
| | - Tianshu Liu
- Department of Oncology, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Gong Chen
- Department of Colorectal, Sun Yat-sen University Cancer Center, Guangzhou 519000, China
| | - Zhimin Shao
- Department of Breast Surgery, Shanghai Cancer Center, Fudan University, Shanghai 200433, China
| | - Binghe Xu
- Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100006, China
| | - Qingyuan Zhang
- Department of Internal Medicine, The Third Affiliated Hospital of Harbin Medical University, Harbin 150030, China
| | - Ruihua Xu
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou 519000, China
| | - Lin Shen
- Department of Gastrointestinal Oncology, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Yilong Wu
- Guangdong Lung Cancer Institute, Medical Research Center, Cancer Center of Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou 510080, China
- Affiliated Guangdong Provincial People's Hospital, South China University of Technology, Guangzhou 510630, China
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Abstract
Large-scale tumor profiling studies have generated massive amounts of data that have been instrumental for the detection of recurrent driver mutations in many tumor types. These driver mutations as well as the concurrent passenger mutations are now being used for a more accurate diagnosis of the tumor and prognosis for the patient. Moreover, therapeutic inhibitors toward specific mutations are already on the market and many clinical trials are ongoing to approve novel therapeutic drugs. The broad-range identification of these somatic mutations is key to this tailored personalized medicine approach, which preferentially has to be performed by a multigene multihotspot method such as massive parallel sequencing, also called next generation sequencing (NGS). The implementation of NGS in molecular diagnostics of tumor profiling however, requires a firm validation to minimize the occurrence of false positives and false negatives, thereby yielding highly accurate and robust clinical data.Here, we describe the different performance characteristics as well as quality metrics that should be analyzed for the robust diagnostic validation of tumor profiling in order to meet the requirements of international standards specific for medical laboratories, such as the ISO15189:2012 standard. These metrics include assays that assess the precision, limit of detection, accuracy, sensitivity, specificity, and robustness of the entire workflow from DNA enrichment up to the final report.
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Affiliation(s)
- Guy Froyen
- Laboratory for Molecular Diagnostics, Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium.
| | - Brigitte Maes
- Laboratory for Molecular Diagnostics, Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium
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Garinet S, Laurent-Puig P, Blons H, Oudart JB. Current and Future Molecular Testing in NSCLC, What Can We Expect from New Sequencing Technologies? J Clin Med 2018; 7:E144. [PMID: 29890761 PMCID: PMC6024886 DOI: 10.3390/jcm7060144] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 06/05/2018] [Accepted: 06/06/2018] [Indexed: 12/17/2022] Open
Abstract
Recent changes in lung cancer care, including new approvals in first line and the introduction of high-throughput molecular technologies in routine testing led us to question ourselves on how deeper molecular testing may be helpful for the optimal use of targeted drugs. In this article, we review recent results in the scope of personalized medicine in lung cancer. We discuss biomarkers that have a therapeutic predictive value in lung cancer with a focus on recent changes and on the clinical value of large scale sequencing strategies. We review the use of second- and third-generation EGFR and ALK inhibitors with a focus on secondary resistance alterations. We discuss anti-BRAF and anti-MEK combo, emerging biomarkers as NRG1 and NTRKs fusions and immunotherapy. Finally, we discuss the different technical issues of comprehensive molecular profiling and show how large screenings might refine the prediction value of individual markers. Based on a review of recent publications (2012⁻2018), we address promising approaches for the treatment of patients with lung cancers and the technical challenges associated with the identification of new predictive markers.
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Affiliation(s)
- Simon Garinet
- INSERM UMR-S1147, Paris Sorbonne Cite University, 75270 Paris Cedex 06, France.
- Department of Biochemistry, Unit of Pharmacogenetics and Molecular Oncology, Georges Pompidou European Hospital, Assistance Publique-Hôpitaux de Paris, 75015 Paris, France.
| | - Pierre Laurent-Puig
- INSERM UMR-S1147, Paris Sorbonne Cite University, 75270 Paris Cedex 06, France.
- Department of Biochemistry, Unit of Pharmacogenetics and Molecular Oncology, Georges Pompidou European Hospital, Assistance Publique-Hôpitaux de Paris, 75015 Paris, France.
| | - Hélène Blons
- INSERM UMR-S1147, Paris Sorbonne Cite University, 75270 Paris Cedex 06, France.
- Department of Biochemistry, Unit of Pharmacogenetics and Molecular Oncology, Georges Pompidou European Hospital, Assistance Publique-Hôpitaux de Paris, 75015 Paris, France.
| | - Jean-Baptiste Oudart
- Department of Biochemistry, Unit of Pharmacogenetics and Molecular Oncology, Georges Pompidou European Hospital, Assistance Publique-Hôpitaux de Paris, 75015 Paris, France.
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12
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Validity of Targeted Next-Generation Sequencing in Routine Care for Identifying Clinically Relevant Molecular Profiles in Non-Small-Cell Lung Cancer: Results of a 2-Year Experience on 1343 Samples. J Mol Diagn 2018; 20:550-564. [PMID: 29787863 DOI: 10.1016/j.jmoldx.2018.04.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 03/15/2018] [Accepted: 04/11/2018] [Indexed: 11/22/2022] Open
Abstract
Theranostic assays are based on single-gene testing, but the ability of next-generation sequencing (NGS) to interrogate numerous genetic alterations will progressively replace single-gene assays. Although NGS was evaluated to screen for theranostic mutations, its usefulness in clinical practice on large series of samples remains to be demonstrated. NGS performance was assessed following guidelines. TaqMan probes and NGS were compared for their ability to detect EGFR and KRAS mutations, and NGS mutation profiles were analyzed on a large series of non-small-cell lung cancers (n = 1343). The R2 correlation between expected and measured allelic ratio, using commercial samples, was >0.96. Mutation detection threshold was 2% for 10 ng of DNA input. κ Scores for TaqMan versus NGS were 0.99 (95% CI, 0.97-1.00) for EGFR and 0.98 (95% CI, 0.97-1.00) for KRAS after exclusion of rare EGFR (n = 40) and KRAS (n = 60) mutations. NGS identified 693 and 292 mutations in validated and potential oncogenic drivers, respectively. Significant associations were found between EGFR and PI3KCA or CTNNB1 and between KRAS and STK11. Potential oncogenic driver mutations or gene amplifications were more frequent in validated oncogenic driver nonmutated samples. This work is a proof of concept that targeted NGS is accessible in routine screening, including large screening, at reasonable cost. Clinical data should be collected and implemented in specific databases to make molecular data meaningful for direct patients' benefit.
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13
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Bonde GV, Yadav SK, Chauhan S, Mittal P, Ajmal G, Thokala S, Mishra B. Lapatinib nano-delivery systems: a promising future for breast cancer treatment. Expert Opin Drug Deliv 2018. [DOI: 10.1080/17425247.2018.1449832] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Gunjan Vasant Bonde
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi, India
| | - Sarita Kumari Yadav
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi, India
- Department of Pharmacy, Moti Lal Nehru Medical College, Allahabad, India
| | - Sheetal Chauhan
- Department of Pharmacology, Melaka Manipal Medical College, Manipal University, Manipal, India
| | - Pooja Mittal
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi, India
| | - Gufran Ajmal
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi, India
| | - Sathish Thokala
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi, India
| | - Brahmeshwar Mishra
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi, India
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14
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Kotelnikova EA, Pyatnitskiy M, Paleeva A, Kremenetskaya O, Vinogradov D. Practical aspects of NGS-based pathways analysis for personalized cancer science and medicine. Oncotarget 2018; 7:52493-52516. [PMID: 27191992 PMCID: PMC5239569 DOI: 10.18632/oncotarget.9370] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 04/18/2016] [Indexed: 12/17/2022] Open
Abstract
Nowadays, the personalized approach to health care and cancer care in particular is becoming more and more popular and is taking an important place in the translational medicine paradigm. In some cases, detection of the patient-specific individual mutations that point to a targeted therapy has already become a routine practice for clinical oncologists. Wider panels of genetic markers are also on the market which cover a greater number of possible oncogenes including those with lower reliability of resulting medical conclusions. In light of the large availability of high-throughput technologies, it is very tempting to use complete patient-specific New Generation Sequencing (NGS) or other "omics" data for cancer treatment guidance. However, there are still no gold standard methods and protocols to evaluate them. Here we will discuss the clinical utility of each of the data types and describe a systems biology approach adapted for single patient measurements. We will try to summarize the current state of the field focusing on the clinically relevant case-studies and practical aspects of data processing.
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Affiliation(s)
- Ekaterina A Kotelnikova
- Personal Biomedicine, Moscow, Russia.,A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.,Institute Biomedical Research August Pi Sunyer (IDIBAPS), Hospital Clinic of Barcelona, Barcelona, Spain
| | - Mikhail Pyatnitskiy
- Personal Biomedicine, Moscow, Russia.,Orekhovich Institute of Biomedical Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - Olga Kremenetskaya
- Personal Biomedicine, Moscow, Russia.,Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
| | - Dmitriy Vinogradov
- Personal Biomedicine, Moscow, Russia.,A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.,Lomonosov Moscow State University, Moscow, Russia
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15
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Yang A, Troup M, Ho JWK. Scalability and Validation of Big Data Bioinformatics Software. Comput Struct Biotechnol J 2017; 15:379-386. [PMID: 28794828 PMCID: PMC5537105 DOI: 10.1016/j.csbj.2017.07.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 06/30/2017] [Accepted: 07/17/2017] [Indexed: 12/20/2022] Open
Abstract
This review examines two important aspects that are central to modern big data bioinformatics analysis – software scalability and validity. We argue that not only are the issues of scalability and validation common to all big data bioinformatics analyses, they can be tackled by conceptually related methodological approaches, namely divide-and-conquer (scalability) and multiple executions (validation). Scalability is defined as the ability for a program to scale based on workload. It has always been an important consideration when developing bioinformatics algorithms and programs. Nonetheless the surge of volume and variety of biological and biomedical data has posed new challenges. We discuss how modern cloud computing and big data programming frameworks such as MapReduce and Spark are being used to effectively implement divide-and-conquer in a distributed computing environment. Validation of software is another important issue in big data bioinformatics that is often ignored. Software validation is the process of determining whether the program under test fulfils the task for which it was designed. Determining the correctness of the computational output of big data bioinformatics software is especially difficult due to the large input space and complex algorithms involved. We discuss how state-of-the-art software testing techniques that are based on the idea of multiple executions, such as metamorphic testing, can be used to implement an effective bioinformatics quality assurance strategy. We hope this review will raise awareness of these critical issues in bioinformatics.
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Affiliation(s)
- Andrian Yang
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia.,St. Vincent's Clinical School, University of New South Wales, Darlinghurst, NSW 2010, Australia
| | - Michael Troup
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Joshua W K Ho
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia.,St. Vincent's Clinical School, University of New South Wales, Darlinghurst, NSW 2010, Australia
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16
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Comparison of Next-Generation Sequencing Panels and Platforms for Detection and Verification of Somatic Tumor Variants for Clinical Diagnostics. J Mol Diagn 2017; 18:842-850. [PMID: 27770852 DOI: 10.1016/j.jmoldx.2016.06.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 05/07/2016] [Accepted: 06/03/2016] [Indexed: 11/22/2022] Open
Abstract
Use of next-generation sequencing to detect somatic variants in DNA extracted from formalin-fixed, paraffin-embedded tumor tissues poses a challenge for clinical molecular diagnostic laboratories because of variable DNA quality and quantity, and the potential to detect low allele frequency somatic variants difficult to verify by non-next-generation sequencing methods. We evaluated somatic variant detection performance of the MiSeq and Ion Proton benchtop sequencers using two commercially available panels, the TruSeq Amplicon Cancer Panel and the AmpliSeq Cancer Hotspot Panel Version 2. Both the MiSeq-TruSeq Amplicon Cancer Panel and Ion Proton-AmpliSeq Cancer Hotspot Panel Version 2 were comparable in terms of detection of somatic variants and allele frequency determination using DNA extracted from tumor tissue. Concordance was 100% between the panels for detection of somatic variants in genomic regions tested by both panels, including 27 variants present at low somatic allele frequency (<15%). Use of both the MiSeq and Ion Proton platforms in a combined workflow enabled detection of potentially actionable variants with importance for patient diagnosis, prognosis, or treatment in 49% (305/621) of cases. Overall, a combined workflow using both platforms enabled successful molecular profiling of 96% (621/644) of tumor samples, and provided an approach for verification of somatic variants not amenable to verification by Sanger sequencing (<15% variant allele frequency).
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17
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Bertier G, Sénécal K, Borry P, Vears DF. Unsolved challenges in pediatric whole-exome sequencing: A literature analysis. Crit Rev Clin Lab Sci 2017; 54:134-142. [PMID: 28132577 DOI: 10.1080/10408363.2016.1275516] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Whole-exome sequencing (WES) has been instrumental in the discovery of novel genes and mechanisms causing Mendelian diseases. While this technology is now being successfully applied in a number of clinics, particularly to diagnose patients with rare diseases, it also raises a number of ethical, legal and social issues. In order to identify what challenges were directly foreseen by technology users, we performed a systematic review of the literature. In this paper, we focus on recent publications related to the use of WES in the pediatric context and analyze the most prominent challenges raised by technology users. This is particularly relevant considering that a) most patients currently undergoing testing using WES to identify the genetic basis for rare diseases are children and b) their lack of capacity to consent for themselves makes them a vulnerable population and generates the need for specific ethical, legal and regulatory procedures. We identified key challenges that related to four main categories: (1) intake; (2) sequence production and analysis; (3) reporting of results and counseling considerations and (4) collaborative data interpretation and data sharing. We then contextualize these challenges in light of the recent recommendations and guidelines, published by professional societies that have significant potential to impact the field.
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Affiliation(s)
- Gabrielle Bertier
- a Department of Human Genetics , Centre of Genomics and Policy, McGill University , Montreal , QC , Canada.,b UMR 1027, Inserm, Université Toulouse III - Paul Sabatier , Toulouse , France
| | - Karine Sénécal
- a Department of Human Genetics , Centre of Genomics and Policy, McGill University , Montreal , QC , Canada
| | - Pascal Borry
- c Department of Public Health and Primary Care , Leuven Institute for Human Genomics and Society , KU Leuven , Leuven , Belgium and
| | - Danya F Vears
- c Department of Public Health and Primary Care , Leuven Institute for Human Genomics and Society , KU Leuven , Leuven , Belgium and.,d Center for Biomedical Ethics and Law , KU Leuven , Leuven , Belgium
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18
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Kadri S, Long BC, Mujacic I, Zhen CJ, Wurst MN, Sharma S, McDonald N, Niu N, Benhamed S, Tuteja JH, Seiwert TY, White KP, McNerney ME, Fitzpatrick C, Wang YL, Furtado LV, Segal JP. Clinical Validation of a Next-Generation Sequencing Genomic Oncology Panel via Cross-Platform Benchmarking against Established Amplicon Sequencing Assays. J Mol Diagn 2016; 19:43-56. [PMID: 27836695 DOI: 10.1016/j.jmoldx.2016.07.012] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 06/10/2016] [Accepted: 07/19/2016] [Indexed: 10/20/2022] Open
Abstract
Next-generation sequencing (NGS) genomic oncology profiling assays have emerged as key drivers of personalized cancer care and translational research. However, validation of these assays to meet strict clinical standards has been historically problematic because of both significant assay complexity and a scarcity of optimal validation samples. Herein, we present the clinical validation of 76 genes from a novel 1212-gene large-scale hybrid capture cancer sequencing assay (University of Chicago Medicine OncoPlus) using full-data comparisons against multiple clinical NGS amplicon-based assays to yield dramatic increases in per-sample data comparison efficiency compared with previously published validations. Using a sample set of 104 normal, solid tumor, and hematopoietic malignancy specimens, head-to-head NGS data analyses allowed for 6.8 million individual clinical base call comparisons, including 2729 previously confirmed variants, with 100% sensitivity and specificity. University of Chicago Medicine OncoPlus showed excellent performance for detection of single-nucleotide variants, insertions/deletions up to 52 bp, and FLT3 internal tandem duplications of up to 102 bp or larger. Highly concordant copy number variant and ALK/RET/ROS1 gene fusion detection were also observed. In addition to underlining the efficiency of NGS validation via full-data benchmarking against existing clinical NGS assays, this study also highlights the degree of performance similarity between hybrid capture and amplicon assays that is attainable with the application of strict quality control parameters and optimized computational analytics.
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Affiliation(s)
- Sabah Kadri
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Bradley C Long
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Ibro Mujacic
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Chao J Zhen
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Michelle N Wurst
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Shruti Sharma
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Nadia McDonald
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Nifang Niu
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Sonia Benhamed
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Jigyasa H Tuteja
- Department of Pathology, the Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois
| | - Tanguy Y Seiwert
- Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Kevin P White
- Department of Pathology, the Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois
| | - Megan E McNerney
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Carrie Fitzpatrick
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Y Lynn Wang
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Larissa V Furtado
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Jeremy P Segal
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois.
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19
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Bertier G, Carrot-Zhang J, Ragoussis V, Joly Y. Integrating precision cancer medicine into healthcare-policy, practice, and research challenges. Genome Med 2016; 8:108. [PMID: 27776531 PMCID: PMC5075982 DOI: 10.1186/s13073-016-0362-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Precision medicine (PM) can be defined as a predictive, preventive, personalized, and participatory healthcare service delivery model. Recent developments in molecular biology and information technology make PM a reality today through the use of massive amounts of genetic, ‘omics’, clinical, environmental, and lifestyle data. With cancer being one of the most prominent public health threats in developed countries, both the research community and governments have been investing significant time, money, and efforts in precision cancer medicine (PCM). Although PCM research is extremely promising, a number of hurdles still remain on the road to an optimal integration of standardized and evidence-based use of PCM in healthcare systems. Indeed, PCM raises a number of technical, organizational, ethical, legal, social, and economic challenges that have to be taken into account in the development of an appropriate health policy framework. Here, we highlight some of the more salient issues regarding the standards needed for integration of PCM into healthcare systems, and we identify fields where more research is needed before policy can be implemented. Key challenges include, but are not limited to, the creation of new standards for the collection, analysis, and sharing of samples and data from cancer patients, and the creation of new clinical trial designs with renewed endpoints. We believe that these issues need to be addressed as a matter of priority by public health policymakers in the coming years for a better integration of PCM into healthcare.
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Affiliation(s)
- Gabrielle Bertier
- Center of Genomics and Policy, McGill University, 740 Dr. Penfield Avenue, Montreal, QC, H3A 0G1, Canada. .,Université Toulouse III Paul Sabatier and Inserm UMR 102, 37 allées Jules Guesde, F-31000, Toulouse, France.
| | - Jian Carrot-Zhang
- Center of Genomics and Policy, McGill University, 740 Dr. Penfield Avenue, Montreal, QC, H3A 0G1, Canada
| | - Vassilis Ragoussis
- Sargent College, Boston University, One Silber Way, Boston, MA, 02215, USA
| | - Yann Joly
- Center of Genomics and Policy, McGill University, 740 Dr. Penfield Avenue, Montreal, QC, H3A 0G1, Canada
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20
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Choi S, Go JH, Kim EK, Lee H, Lee WM, Cho CS, Han K. Mutational Analysis of Extranodal NK/T-Cell Lymphoma Using Targeted Sequencing with a Comprehensive Cancer Panel. Genomics Inform 2016; 14:78-84. [PMID: 27729836 PMCID: PMC5056900 DOI: 10.5808/gi.2016.14.3.78] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 08/10/2016] [Accepted: 08/11/2016] [Indexed: 02/06/2023] Open
Abstract
Extranodal natural killer (NK)/T-cell lymphoma, nasal type (NKTCL), is a malignant disorder of cytotoxic lymphocytes of NK or T cells. It is an aggressive neoplasm with a very poor prognosis. Although extranodal NKTCL reportedly has a strong association with Epstein-Barr virus, the molecular pathogenesis of NKTCL has been unexplored. The recent technological advancements in next-generation sequencing (NGS) have made DNA sequencing cost- and time-effective, with more reliable results. Using the Ion Proton Comprehensive Cancer Panel, we sequenced 409 cancer-related genes to identify somatic mutations in five NKTCL tissue samples. The sequencing analysis detected 25 mutations in 21 genes. Among them, KMT2D, a histone modification-related gene, was the most frequently mutated gene (four of the five cases). This result was consistent with recent NGS studies that have suggested KMT2D as a novel driver gene in NKTCL. Mutations were also found in ARID1A, a chromatin remodeling gene, and TP53, which also recurred in recent NGS studies. We also found mutations in 18 novel candidate genes, with molecular functions that were potentially implicated in cancer development. We suggest that these genes may result in multiple oncogenic events and may be used as potential bio-markers of NKTCL in the future.
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Affiliation(s)
- Seungkyu Choi
- Department of Pathology, Dankook University College of Medicine, Cheonan 31116, Korea
| | - Jai Hyang Go
- Department of Pathology, Dankook University College of Medicine, Cheonan 31116, Korea
| | - Eun Kyung Kim
- Department of Pathology, Eulji Medical Center, Eulji University School of Medicine, Seoul 01830, Korea
| | - Hojung Lee
- Department of Pathology, Eulji Medical Center, Eulji University School of Medicine, Seoul 01830, Korea
| | - Won Mi Lee
- Department of Pathology, Eulji Medical Center, Eulji University School of Medicine, Seoul 01830, Korea
| | - Chun-Sung Cho
- Department of Neurosurgery, Dankook University College of Medicine, Cheonan 31116, Korea
| | - Kyudong Han
- Department of Nanobiomedical Science, BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Korea
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21
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Aguilar H, Sanchez E, Braña I, Vivancos A, Rodon J. Molecular screening programmes for precision medicine: lessons learned from personalized medicine trials. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2016. [DOI: 10.1080/23808993.2016.1238285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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22
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Endrullat C, Glökler J, Franke P, Frohme M. Standardization and quality management in next-generation sequencing. Appl Transl Genom 2016; 10:2-9. [PMID: 27668169 PMCID: PMC5025460 DOI: 10.1016/j.atg.2016.06.001] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 05/13/2016] [Accepted: 06/29/2016] [Indexed: 11/30/2022]
Abstract
DNA sequencing continues to evolve quickly even after > 30 years. Many new platforms suddenly appeared and former established systems have vanished in almost the same manner. Since establishment of next-generation sequencing devices, this progress gains momentum due to the continually growing demand for higher throughput, lower costs and better quality of data. In consequence of this rapid development, standardized procedures and data formats as well as comprehensive quality management considerations are still scarce. Here, we listed and summarized current standardization efforts and quality management initiatives from companies, organizations and societies in form of published studies and ongoing projects. These comprise on the one hand quality documentation issues like technical notes, accreditation checklists and guidelines for validation of sequencing workflows. On the other hand, general standard proposals and quality metrics are developed and applied to the sequencing workflow steps with the main focus on upstream processes. Finally, certain standard developments for downstream pipeline data handling, processing and storage are discussed in brief. These standardization approaches represent a first basis for continuing work in order to prospectively implement next-generation sequencing in important areas such as clinical diagnostics, where reliable results and fast processing is crucial. Additionally, these efforts will exert a decisive influence on traceability and reproducibility of sequence data.
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Key Words
- ABRF, Association of Biomolecular Resource Facilities
- BAM, binary alignment/map
- CAP, College of American Pathologist's
- CEN, European Committee for Standardization
- CLIA, Clinical Laboratory Improvement Amendments
- Data quality
- ERCC, External RNA Controls Consortium
- FDA, Food and Drug Administration
- FFPE, formalin-fixed, paraffin-embedded
- FMEA, failure mode and effects analysis
- GATK, genome analysis toolkit
- GSC, Genomic Standards Consortium
- Guideline
- HGP, Human Genome Project
- Indel, insertion or deletion
- MAQC, MicroArray Quality Control Project
- MIGS, minimum information about a genome sequence
- MOL, molecular pathology checklist
- NGS, next-generation sequencing
- NIST, National Institute of Standards and Technology
- NTC, no-template control
- Nex-StoCT, next generation sequencing — standardization of clinical testing
- Next-generation sequencing
- PT, proficiency testing
- QA, quality assurance
- QC, quality control
- QM, quality management
- QMS, quality management system
- Quality management
- RIN, RNA integrity number
- SAM, sequence alignment/map
- SEQC, sequencing quality control
- SNP, single nucleotide polymorphism
- SOP, standard operating procedure
- Standardization
- TN, technical note
- VCF, variant call format
- Validation
- ddPCR, digital droplet PCR
- mtDNA, mitochondrial DNA
- qPCR, quantitative PCR
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Affiliation(s)
- Christoph Endrullat
- Molecular Biotechnology and Functional Genomics, Institute of Applied Biosciences, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
| | - Jörn Glökler
- Molecular Biotechnology and Functional Genomics, Institute of Applied Biosciences, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
| | - Philipp Franke
- Molecular Biotechnology and Functional Genomics, Institute of Applied Biosciences, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
| | - Marcus Frohme
- Molecular Biotechnology and Functional Genomics, Institute of Applied Biosciences, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
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23
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Roy-Chowdhuri S, Stewart J. Preanalytic Variables in Cytology: Lessons Learned From Next-Generation Sequencing—The MD Anderson Experience. Arch Pathol Lab Med 2016; 140:1191-1199. [DOI: 10.5858/arpa.2016-0117-ra] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Context.—
As our understanding of genomic alterations underlying solid tumor malignancies continues to evolve, molecular testing of tumor samples is increasingly used to guide therapeutic management. Next-generation sequencing (NGS) provides a novel platform for the simultaneous screening of multiple genes using small amounts of DNA. Several recent studies have described NGS mutational analysis using cytologic specimens. The cytopathologist's role in specimen assessment and triaging is critical to effectively implementing NGS in routine cytology practice.
Objectives.—
To review the NGS experience and a variety of preanalytic factors that affect NGS success rates of cytologic specimens at our institution.
Data Sources.—
To evaluate cytology specimen adequacy rates for NGS, we reviewed a 14-month period of image-guided fine-needle aspiration and core needle biopsies used for testing. In addition, we reviewed data from our previously published studies to evaluate preanalytic factors affecting NGS success in these specimens.
Conclusions.—
Identifying factors that affect NGS success rates in cytology specimens is crucial for a better understanding of specimen adequacy requirements and for proper use of limited-volume tissue samples. In our practice, which uses direct smears as well as cell block sections, NGS success rates in core needle biopsy and fine-needle aspiration samples are comparable. The chance of successful testing is further increased by procuring concurrent fine-needle aspiration and core needle biopsy samples. The type of glass slides used for direct smears and the method of tissue extraction affect our DNA yield. Validating a DNA input for cytology samples that is lower than that recommended by the manufacturer has significantly increased our NGS success rate.
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Affiliation(s)
- Sinchita Roy-Chowdhuri
- From the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston
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24
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Grissom AA, Friend PJ. Multigene Panel Testing for Hereditary Cancer Risk. J Adv Pract Oncol 2016; 7:394-407. [PMID: 29225998 PMCID: PMC5679029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Alyssa A Grissom
- Loyola University Chicago, Marcella Niehoff School of Nursing, Chicago, Illinois
| | - Patricia J Friend
- Loyola University Chicago, Marcella Niehoff School of Nursing, Chicago, Illinois
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25
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Abstract
Context.—Precision medicine is the promise of individualized therapy and management of patients based on their personal biology. There are now multiple global initiatives to perform whole-genome sequencing on millions of individuals. In the United States, an early program was the Million Veteran Program, and a more recent proposal in 2015 by the president of the United States is the Precision Medicine Initiative. To implement precision medicine in routine oncology care, genetic variants present in tumors need to be matched with effective clinical therapeutics. When we focus on the current state of precision medicine for gastrointestinal malignancies, it becomes apparent that there is a mixed history of success and failure.
Objective.—To present the current state of precision medicine using gastrointestinal oncology as a model. We will present currently available targeted therapeutics, promising new findings in clinical genomic oncology, remaining quality issues in genomic testing, and emerging oncology clinical trial designs.
Data Sources.—Review of the literature including clinical genomic studies on gastrointestinal malignancies, clinical oncology trials on therapeutics targeted to molecular alterations, and emerging clinical oncology study designs.
Conclusions.—Translating our ability to sequence thousands of genes into meaningful improvements in patient survival will be the challenge for the next decade.
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Affiliation(s)
| | - Jason Y. Park
- From the Department of Internal Medicine, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center and Dallas Veterans Affairs Medical Center, Dallas (Dr Wang)
- and the Department of Pathology, Eugene McDermott Center for Human Growth and Development, Children's Medical Center, and University of Texas Southwestern Medical Center, Dallas (Dr Park)
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26
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Froyen G, Broekmans A, Hillen F, Pat K, Achten R, Mebis J, Rummens JL, Willemse J, Maes B. Validation and Application of a Custom-Designed Targeted Next-Generation Sequencing Panel for the Diagnostic Mutational Profiling of Solid Tumors. PLoS One 2016; 11:e0154038. [PMID: 27101000 PMCID: PMC4839685 DOI: 10.1371/journal.pone.0154038] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/07/2016] [Indexed: 01/15/2023] Open
Abstract
The inevitable switch from standard molecular methods to next-generation sequencing for the molecular profiling of tumors is challenging for most diagnostic laboratories. However, fixed validation criteria for diagnostic accreditation are not in place because of the great variability in methods and aims. Here, we describe the validation of a custom panel of hotspots in 24 genes for the detection of somatic mutations in non-small cell lung carcinoma, colorectal carcinoma and malignant melanoma starting from FFPE sections, using 14, 36 and 5 cases, respectively. The targeted hotspots were selected for their present or future clinical relevance in solid tumor types. The target regions were enriched with the TruSeq approach starting from limited amounts of DNA. Cost effective sequencing of 12 pooled libraries was done using a micro flow cell on the MiSeq and subsequent data analysis with MiSeqReporter and VariantStudio. The entire workflow was diagnostically validated showing a robust performance with maximal sensitivity and specificity using as thresholds a variant allele frequency >5% and a minimal amplicon coverage of 300. We implemented this method through the analysis of 150 routine diagnostic samples and identified clinically relevant mutations in 16 genes including KRAS (32%), TP53 (32%), BRAF (12%), APC (11%), EGFR (8%) and NRAS (5%). Importantly, the highest success rate was obtained when using also the low quality DNA samples. In conclusion, we provide a workflow for the validation of targeted NGS by a custom-designed pan-solid tumor panel in a molecular diagnostic lab and demonstrate its robustness in a clinical setting.
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Affiliation(s)
- Guy Froyen
- Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium
- * E-mail:
| | - An Broekmans
- Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium
| | - Femke Hillen
- Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium
| | - Karin Pat
- Department of Pneumology, Jessa Hospital, Hasselt, Belgium
| | - Ruth Achten
- Department of Pathology, Jessa Hospital, Hasselt, Belgium
| | - Jeroen Mebis
- Department of Medical Oncology, Jessa Hospital, Hasselt, Belgium
| | - Jean-Luc Rummens
- Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium
| | - Johan Willemse
- Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium
- Department of Clinical Biology, AZ Turnhout, Turnhout, Belgium
| | - Brigitte Maes
- Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium
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27
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Van Krieken JHJM, Rouleau E, Ligtenberg MJL, Normanno N, Patterson SD, Jung A. RAS testing in metastatic colorectal cancer: advances in Europe. Virchows Arch 2016; 468:383-96. [PMID: 26573425 PMCID: PMC4830882 DOI: 10.1007/s00428-015-1876-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 10/20/2015] [Accepted: 10/22/2015] [Indexed: 12/22/2022]
Abstract
Personalized medicine shows promise for maximizing efficacy and minimizing toxicity of anti-cancer treatment. KRAS exon 2 mutations are predictive of resistance to epidermal growth factor receptor-directed monoclonal antibodies in patients with metastatic colorectal cancer. Recent studies have shown that broader RAS testing (KRAS and NRAS) is needed to select patients for treatment. While Sanger sequencing is still used, approaches based on various methodologies are available. Few CE-approved kits, however, detect the full spectrum of RAS mutations. More recently, "next-generation" sequencing has been developed for research use, including parallel semiconductor sequencing and reversible termination. These techniques have high technical sensitivities for detecting mutations, although the ideal threshold is currently unknown. Finally, liquid biopsy has the potential to become an additional tool to assess tumor-derived DNA. For accurate and timely RAS testing, appropriate sampling and prompt delivery of material is critical. Processes to ensure efficient turnaround from sample request to RAS evaluation must be implemented so that patients receive the most appropriate treatment. Given the variety of methodologies, external quality assurance programs are important to ensure a high standard of RAS testing. Here, we review technical and practical aspects of RAS testing for pathologists working with metastatic colorectal cancer tumor samples. The extension of markers from KRAS to RAS testing is the new paradigm for biomarker testing in colorectal cancer.
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Affiliation(s)
- J Han J M Van Krieken
- Department of Pathology, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, Netherlands.
| | | | - Marjolijn J L Ligtenberg
- Department of Pathology, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, Netherlands
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, INT-Fondazione Pascale, Naples, Italy
| | - Scott D Patterson
- Amgen Inc., Thousand Oaks, CA, USA
- Gilead Sciences, Inc., Foster City, CA, USA
| | - Andreas Jung
- Institute of Pathology, University of Munich, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
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28
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Kanagal-Shamanna R, Singh RR, Routbort MJ, Patel KP, Medeiros LJ, Luthra R. Principles of analytical validation of next-generation sequencing based mutational analysis for hematologic neoplasms in a CLIA-certified laboratory. Expert Rev Mol Diagn 2016; 16:461-72. [PMID: 26765348 DOI: 10.1586/14737159.2016.1142374] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Targeted therapy based on mutational profiles is the current standard of practice for the management of patients with hematologic malignancies. Next-generation sequencing (NGS)- based analysis has been adopted by clinical laboratories for high-throughput mutational profiling of myeloid and lymphoid neoplasms. The technology is fairly novel and complex, hence both validation and test implementation in a CLIA-certified laboratory differ substantially from traditional sequencing platforms. Recently, organizations such as the American College of Medical Genetics, Centers for Disease Control and Prevention and College of American Pathologists have published principles and guidelines for NGS test development to ensure standardization of testing across institutions. Summarized here are the recommendations from these organizations as they pertain to targeted NGS-based testing of hematologic malignancies ('liquid tumors'), with particular emphasis on myeloid neoplasms.
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Affiliation(s)
- Rashmi Kanagal-Shamanna
- a Department of Hematopathology , The University of Texas at M.D. Anderson Cancer Center , Houston , TX , USA
| | - Rajesh R Singh
- a Department of Hematopathology , The University of Texas at M.D. Anderson Cancer Center , Houston , TX , USA
| | - Mark J Routbort
- a Department of Hematopathology , The University of Texas at M.D. Anderson Cancer Center , Houston , TX , USA
| | - Keyur P Patel
- a Department of Hematopathology , The University of Texas at M.D. Anderson Cancer Center , Houston , TX , USA
| | - L Jeffrey Medeiros
- a Department of Hematopathology , The University of Texas at M.D. Anderson Cancer Center , Houston , TX , USA
| | - Rajyalakshmi Luthra
- a Department of Hematopathology , The University of Texas at M.D. Anderson Cancer Center , Houston , TX , USA
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29
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McDonald ES, Clark AS, Tchou J, Zhang P, Freedman GM. Clinical Diagnosis and Management of Breast Cancer. J Nucl Med 2016; 57 Suppl 1:9S-16S. [DOI: 10.2967/jnumed.115.157834] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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30
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Ballester LY, Luthra R, Kanagal-Shamanna R, Singh RR. Advances in clinical next-generation sequencing: target enrichment and sequencing technologies. Expert Rev Mol Diagn 2016; 16:357-72. [PMID: 26680590 DOI: 10.1586/14737159.2016.1133298] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The huge parallel sequencing capabilities of next generation sequencing technologies have made them the tools of choice to characterize genomic aberrations for research and diagnostic purposes. For clinical applications, screening the whole genome or exome is challenging owing to the large genomic area to be sequenced, associated costs, complexity of data, and lack of known clinical significance of all genes. Consequently, routine screening involves limited markers with established clinical relevance. This process, referred to as targeted genome sequencing, requires selective enrichment of the genomic areas comprising these markers via one of several primer or probe-based enrichment strategies, followed by sequencing of the enriched genomic areas. Here, the authors review current target enrichment approaches and next generation sequencing platforms, focusing on the underlying principles, capabilities, and limitations of each technology along with validation and implementation for clinical testing.
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Affiliation(s)
- Leomar Y Ballester
- a Department of Pathology and Immunology , Baylor College of Medicine , Houston , TX , USA
| | - Rajyalakshmi Luthra
- b Department of Hematopathology , The University of Texas MD Anderson Cancer Center , Houston , TX , USA
| | - Rashmi Kanagal-Shamanna
- b Department of Hematopathology , The University of Texas MD Anderson Cancer Center , Houston , TX , USA
| | - Rajesh R Singh
- b Department of Hematopathology , The University of Texas MD Anderson Cancer Center , Houston , TX , USA
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31
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Dickson DJ, Pfeifer JD. Real-world data in the molecular era-finding the reality in the real world. Clin Pharmacol Ther 2016; 99:186-97. [PMID: 26565654 DOI: 10.1002/cpt.300] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 11/10/2015] [Indexed: 01/06/2023]
Abstract
Real-world data (RWD) promises to provide a pivotal element to the understanding of personalized medicine. However, without true representation (or the reality) of the patient-disease biosystem and its molecular contributors, RWD may hamper rather than help this advancement. In this review article, we discuss RWD vs. clinical reality and the disconnects that exist currently (emphasizing molecular medicine), and methods of closing the gaps between RWD and reality.
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Affiliation(s)
- D J Dickson
- Molecular Evidence Development Consortium, Rexburg, Idaho, USA
| | - J D Pfeifer
- Department of Pathology, Washington University School of Medicine, St. Louis, Missouri, USA
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Abstract
The past several years can be considered a renaissance era in the treatment of metastatic melanoma. Following a 30-year stretch in which oncologists barely put a dent in a very grim overall survival (OS) rate for these patients, things have rapidly changed course with the recent approval of three new melanoma drugs by the FDA. Both oncogene-targeted therapy and immune checkpoint blockade approaches have shown remarkable efficacy in a subset of melanoma patients and have clearly been game-changers in terms of clinical impact. However, most patients still succumb to their disease, and thus, there remains an urgent need to improve upon current therapies. Fortunately, innovations in molecular medicine have led to many silent gains that have greatly increased our understanding of the nature of cancer biology as well as the complex interactions between tumors and the immune system. They have also allowed for the first time a detailed understanding of an individual patient's cancer at the genomic and proteomic level. This information is now starting to be employed at all stages of cancer treatment, including diagnosis, choice of drug therapy, treatment monitoring, and analysis of resistance mechanisms upon recurrence. This new era of personalized medicine will foreseeably lead to paradigm shifts in immunotherapeutic treatment approaches such as individualized cancer vaccines and adoptive transfer of genetically modified T cells. Advances in xenograft technology will also allow for the testing of drug combinations using in vivo models, a truly necessary development as the number of new drugs needing to be tested is predicted to skyrocket in the coming years. This chapter will provide an overview of recent technological developments in cancer research, and how they are expected to impact future diagnosis, monitoring, and development of novel treatments for metastatic melanoma.
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Affiliation(s)
| | | | | | - Patrick Hwu
- University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Gregory Lizée
- University of Texas MD Anderson Cancer Center, Houston, TX, USA
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33
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Le Tourneau C, Kamal M, Tsimberidou AM, Bedard P, Pierron G, Callens C, Rouleau E, Vincent-Salomon A, Servant N, Alt M, Rouzier R, Paoletti X, Delattre O, Bièche I. Treatment Algorithms Based on Tumor Molecular Profiling: The Essence of Precision Medicine Trials. J Natl Cancer Inst 2015; 108:djv362. [PMID: 26598514 PMCID: PMC4830395 DOI: 10.1093/jnci/djv362] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/26/2015] [Indexed: 12/13/2022] Open
Abstract
With the advent of high-throughput molecular technologies, several precision medicine (PM) studies are currently ongoing that include molecular screening programs and PM clinical trials. Molecular profiling programs establish the molecular profile of patients' tumors with the aim to guide therapy based on identified molecular alterations. The aim of prospective PM clinical trials is to assess the clinical utility of tumor molecular profiling and to determine whether treatment selection based on molecular alterations produces superior outcomes compared with unselected treatment. These trials use treatment algorithms to assign patients to specific targeted therapies based on tumor molecular alterations. These algorithms should be governed by fixed rules to ensure standardization and reproducibility. Here, we summarize key molecular, biological, and technical criteria that, in our view, should be addressed when establishing treatment algorithms based on tumor molecular profiling for PM trials.
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Affiliation(s)
- Christophe Le Tourneau
- Affiliations of authors:Department of Medical Oncology, Institut Curie , Paris & Saint-Cloud , France (CLT, MK, MA); EA7285 Versailles-St-Quentin-en-Yvelines University , France (CLT, RR); Investigational Cancer Therapeutics, M. D. Anderson Cancer Center , Houston, TX (AMT); Drug Development Program, Department of Medical Oncology and Hematology, Princess Margaret Hospital , Toronto , Canada (PB); Department of Genetics, Institut Curie , Paris , France (GP, CC, ER, IB); Department of Pathology, Institut Curie , Paris , France (AVS); Institut Curie / INSERM U900 , Paris , France (NS, XP); Department of Surgery, Institut Curie , Paris & Saint-Cloud , France (RR); Institut Curie, INSERM U830 , Paris , France (OD); EA7331, University of Paris-Descartes , Paris , France (IB)
| | - Maud Kamal
- Affiliations of authors:Department of Medical Oncology, Institut Curie , Paris & Saint-Cloud , France (CLT, MK, MA); EA7285 Versailles-St-Quentin-en-Yvelines University , France (CLT, RR); Investigational Cancer Therapeutics, M. D. Anderson Cancer Center , Houston, TX (AMT); Drug Development Program, Department of Medical Oncology and Hematology, Princess Margaret Hospital , Toronto , Canada (PB); Department of Genetics, Institut Curie , Paris , France (GP, CC, ER, IB); Department of Pathology, Institut Curie , Paris , France (AVS); Institut Curie / INSERM U900 , Paris , France (NS, XP); Department of Surgery, Institut Curie , Paris & Saint-Cloud , France (RR); Institut Curie, INSERM U830 , Paris , France (OD); EA7331, University of Paris-Descartes , Paris , France (IB)
| | - Apostolia-Maria Tsimberidou
- Affiliations of authors:Department of Medical Oncology, Institut Curie , Paris & Saint-Cloud , France (CLT, MK, MA); EA7285 Versailles-St-Quentin-en-Yvelines University , France (CLT, RR); Investigational Cancer Therapeutics, M. D. Anderson Cancer Center , Houston, TX (AMT); Drug Development Program, Department of Medical Oncology and Hematology, Princess Margaret Hospital , Toronto , Canada (PB); Department of Genetics, Institut Curie , Paris , France (GP, CC, ER, IB); Department of Pathology, Institut Curie , Paris , France (AVS); Institut Curie / INSERM U900 , Paris , France (NS, XP); Department of Surgery, Institut Curie , Paris & Saint-Cloud , France (RR); Institut Curie, INSERM U830 , Paris , France (OD); EA7331, University of Paris-Descartes , Paris , France (IB)
| | - Philippe Bedard
- Affiliations of authors:Department of Medical Oncology, Institut Curie , Paris & Saint-Cloud , France (CLT, MK, MA); EA7285 Versailles-St-Quentin-en-Yvelines University , France (CLT, RR); Investigational Cancer Therapeutics, M. D. Anderson Cancer Center , Houston, TX (AMT); Drug Development Program, Department of Medical Oncology and Hematology, Princess Margaret Hospital , Toronto , Canada (PB); Department of Genetics, Institut Curie , Paris , France (GP, CC, ER, IB); Department of Pathology, Institut Curie , Paris , France (AVS); Institut Curie / INSERM U900 , Paris , France (NS, XP); Department of Surgery, Institut Curie , Paris & Saint-Cloud , France (RR); Institut Curie, INSERM U830 , Paris , France (OD); EA7331, University of Paris-Descartes , Paris , France (IB)
| | - Gaëlle Pierron
- Affiliations of authors:Department of Medical Oncology, Institut Curie , Paris & Saint-Cloud , France (CLT, MK, MA); EA7285 Versailles-St-Quentin-en-Yvelines University , France (CLT, RR); Investigational Cancer Therapeutics, M. D. Anderson Cancer Center , Houston, TX (AMT); Drug Development Program, Department of Medical Oncology and Hematology, Princess Margaret Hospital , Toronto , Canada (PB); Department of Genetics, Institut Curie , Paris , France (GP, CC, ER, IB); Department of Pathology, Institut Curie , Paris , France (AVS); Institut Curie / INSERM U900 , Paris , France (NS, XP); Department of Surgery, Institut Curie , Paris & Saint-Cloud , France (RR); Institut Curie, INSERM U830 , Paris , France (OD); EA7331, University of Paris-Descartes , Paris , France (IB)
| | - Céline Callens
- Affiliations of authors:Department of Medical Oncology, Institut Curie , Paris & Saint-Cloud , France (CLT, MK, MA); EA7285 Versailles-St-Quentin-en-Yvelines University , France (CLT, RR); Investigational Cancer Therapeutics, M. D. Anderson Cancer Center , Houston, TX (AMT); Drug Development Program, Department of Medical Oncology and Hematology, Princess Margaret Hospital , Toronto , Canada (PB); Department of Genetics, Institut Curie , Paris , France (GP, CC, ER, IB); Department of Pathology, Institut Curie , Paris , France (AVS); Institut Curie / INSERM U900 , Paris , France (NS, XP); Department of Surgery, Institut Curie , Paris & Saint-Cloud , France (RR); Institut Curie, INSERM U830 , Paris , France (OD); EA7331, University of Paris-Descartes , Paris , France (IB)
| | - Etienne Rouleau
- Affiliations of authors:Department of Medical Oncology, Institut Curie , Paris & Saint-Cloud , France (CLT, MK, MA); EA7285 Versailles-St-Quentin-en-Yvelines University , France (CLT, RR); Investigational Cancer Therapeutics, M. D. Anderson Cancer Center , Houston, TX (AMT); Drug Development Program, Department of Medical Oncology and Hematology, Princess Margaret Hospital , Toronto , Canada (PB); Department of Genetics, Institut Curie , Paris , France (GP, CC, ER, IB); Department of Pathology, Institut Curie , Paris , France (AVS); Institut Curie / INSERM U900 , Paris , France (NS, XP); Department of Surgery, Institut Curie , Paris & Saint-Cloud , France (RR); Institut Curie, INSERM U830 , Paris , France (OD); EA7331, University of Paris-Descartes , Paris , France (IB)
| | - Anne Vincent-Salomon
- Affiliations of authors:Department of Medical Oncology, Institut Curie , Paris & Saint-Cloud , France (CLT, MK, MA); EA7285 Versailles-St-Quentin-en-Yvelines University , France (CLT, RR); Investigational Cancer Therapeutics, M. D. Anderson Cancer Center , Houston, TX (AMT); Drug Development Program, Department of Medical Oncology and Hematology, Princess Margaret Hospital , Toronto , Canada (PB); Department of Genetics, Institut Curie , Paris , France (GP, CC, ER, IB); Department of Pathology, Institut Curie , Paris , France (AVS); Institut Curie / INSERM U900 , Paris , France (NS, XP); Department of Surgery, Institut Curie , Paris & Saint-Cloud , France (RR); Institut Curie, INSERM U830 , Paris , France (OD); EA7331, University of Paris-Descartes , Paris , France (IB)
| | - Nicolas Servant
- Affiliations of authors:Department of Medical Oncology, Institut Curie , Paris & Saint-Cloud , France (CLT, MK, MA); EA7285 Versailles-St-Quentin-en-Yvelines University , France (CLT, RR); Investigational Cancer Therapeutics, M. D. Anderson Cancer Center , Houston, TX (AMT); Drug Development Program, Department of Medical Oncology and Hematology, Princess Margaret Hospital , Toronto , Canada (PB); Department of Genetics, Institut Curie , Paris , France (GP, CC, ER, IB); Department of Pathology, Institut Curie , Paris , France (AVS); Institut Curie / INSERM U900 , Paris , France (NS, XP); Department of Surgery, Institut Curie , Paris & Saint-Cloud , France (RR); Institut Curie, INSERM U830 , Paris , France (OD); EA7331, University of Paris-Descartes , Paris , France (IB)
| | - Marie Alt
- Affiliations of authors:Department of Medical Oncology, Institut Curie , Paris & Saint-Cloud , France (CLT, MK, MA); EA7285 Versailles-St-Quentin-en-Yvelines University , France (CLT, RR); Investigational Cancer Therapeutics, M. D. Anderson Cancer Center , Houston, TX (AMT); Drug Development Program, Department of Medical Oncology and Hematology, Princess Margaret Hospital , Toronto , Canada (PB); Department of Genetics, Institut Curie , Paris , France (GP, CC, ER, IB); Department of Pathology, Institut Curie , Paris , France (AVS); Institut Curie / INSERM U900 , Paris , France (NS, XP); Department of Surgery, Institut Curie , Paris & Saint-Cloud , France (RR); Institut Curie, INSERM U830 , Paris , France (OD); EA7331, University of Paris-Descartes , Paris , France (IB)
| | - Roman Rouzier
- Affiliations of authors:Department of Medical Oncology, Institut Curie , Paris & Saint-Cloud , France (CLT, MK, MA); EA7285 Versailles-St-Quentin-en-Yvelines University , France (CLT, RR); Investigational Cancer Therapeutics, M. D. Anderson Cancer Center , Houston, TX (AMT); Drug Development Program, Department of Medical Oncology and Hematology, Princess Margaret Hospital , Toronto , Canada (PB); Department of Genetics, Institut Curie , Paris , France (GP, CC, ER, IB); Department of Pathology, Institut Curie , Paris , France (AVS); Institut Curie / INSERM U900 , Paris , France (NS, XP); Department of Surgery, Institut Curie , Paris & Saint-Cloud , France (RR); Institut Curie, INSERM U830 , Paris , France (OD); EA7331, University of Paris-Descartes , Paris , France (IB)
| | - Xavier Paoletti
- Affiliations of authors:Department of Medical Oncology, Institut Curie , Paris & Saint-Cloud , France (CLT, MK, MA); EA7285 Versailles-St-Quentin-en-Yvelines University , France (CLT, RR); Investigational Cancer Therapeutics, M. D. Anderson Cancer Center , Houston, TX (AMT); Drug Development Program, Department of Medical Oncology and Hematology, Princess Margaret Hospital , Toronto , Canada (PB); Department of Genetics, Institut Curie , Paris , France (GP, CC, ER, IB); Department of Pathology, Institut Curie , Paris , France (AVS); Institut Curie / INSERM U900 , Paris , France (NS, XP); Department of Surgery, Institut Curie , Paris & Saint-Cloud , France (RR); Institut Curie, INSERM U830 , Paris , France (OD); EA7331, University of Paris-Descartes , Paris , France (IB)
| | - Olivier Delattre
- Affiliations of authors:Department of Medical Oncology, Institut Curie , Paris & Saint-Cloud , France (CLT, MK, MA); EA7285 Versailles-St-Quentin-en-Yvelines University , France (CLT, RR); Investigational Cancer Therapeutics, M. D. Anderson Cancer Center , Houston, TX (AMT); Drug Development Program, Department of Medical Oncology and Hematology, Princess Margaret Hospital , Toronto , Canada (PB); Department of Genetics, Institut Curie , Paris , France (GP, CC, ER, IB); Department of Pathology, Institut Curie , Paris , France (AVS); Institut Curie / INSERM U900 , Paris , France (NS, XP); Department of Surgery, Institut Curie , Paris & Saint-Cloud , France (RR); Institut Curie, INSERM U830 , Paris , France (OD); EA7331, University of Paris-Descartes , Paris , France (IB)
| | - Ivan Bièche
- Affiliations of authors:Department of Medical Oncology, Institut Curie , Paris & Saint-Cloud , France (CLT, MK, MA); EA7285 Versailles-St-Quentin-en-Yvelines University , France (CLT, RR); Investigational Cancer Therapeutics, M. D. Anderson Cancer Center , Houston, TX (AMT); Drug Development Program, Department of Medical Oncology and Hematology, Princess Margaret Hospital , Toronto , Canada (PB); Department of Genetics, Institut Curie , Paris , France (GP, CC, ER, IB); Department of Pathology, Institut Curie , Paris , France (AVS); Institut Curie / INSERM U900 , Paris , France (NS, XP); Department of Surgery, Institut Curie , Paris & Saint-Cloud , France (RR); Institut Curie, INSERM U830 , Paris , France (OD); EA7331, University of Paris-Descartes , Paris , France (IB)
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Verigos J, Magklara A. Revealing the Complexity of Breast Cancer by Next Generation Sequencing. Cancers (Basel) 2015; 7:2183-200. [PMID: 26561834 PMCID: PMC4695885 DOI: 10.3390/cancers7040885] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Revised: 10/18/2015] [Accepted: 10/26/2015] [Indexed: 02/06/2023] Open
Abstract
Over the last few years the increasing usage of "-omic" platforms, supported by next-generation sequencing, in the analysis of breast cancer samples has tremendously advanced our understanding of the disease. New driver and passenger mutations, rare chromosomal rearrangements and other genomic aberrations identified by whole genome and exome sequencing are providing missing pieces of the genomic architecture of breast cancer. High resolution maps of breast cancer methylomes and sequencing of the miRNA microworld are beginning to paint the epigenomic landscape of the disease. Transcriptomic profiling is giving us a glimpse into the gene regulatory networks that govern the fate of the breast cancer cell. At the same time, integrative analysis of sequencing data confirms an extensive intertumor and intratumor heterogeneity and plasticity in breast cancer arguing for a new approach to the problem. In this review, we report on the latest findings on the molecular characterization of breast cancer using NGS technologies, and we discuss their potential implications for the improvement of existing therapies.
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Affiliation(s)
- John Verigos
- Laboratory of Clinical Chemistry, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina 45110, Greece.
- Department of Biomedical Research, Institute of Molecular Biology & Biotechnology,Foundation for Research & Technology-Hellas, Ioannina 45110, Greece.
| | - Angeliki Magklara
- Laboratory of Clinical Chemistry, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina 45110, Greece.
- Department of Biomedical Research, Institute of Molecular Biology & Biotechnology,Foundation for Research & Technology-Hellas, Ioannina 45110, Greece.
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35
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Analysis of Pre-Analytic Factors Affecting the Success of Clinical Next-Generation Sequencing of Solid Organ Malignancies. Cancers (Basel) 2015; 7:1699-715. [PMID: 26343728 PMCID: PMC4586792 DOI: 10.3390/cancers7030859] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 08/20/2015] [Accepted: 08/21/2015] [Indexed: 01/28/2023] Open
Abstract
Application of next-generation sequencing (NGS) technology to routine clinical practice has enabled characterization of personalized cancer genomes to identify patients likely to have a response to targeted therapy. The proper selection of tumor sample for downstream NGS based mutational analysis is critical to generate accurate results and to guide therapeutic intervention. However, multiple pre-analytic factors come into play in determining the success of NGS testing. In this review, we discuss pre-analytic requirements for AmpliSeq PCR-based sequencing using Ion Torrent Personal Genome Machine (PGM) (Life Technologies), a NGS sequencing platform that is often used by clinical laboratories for sequencing solid tumors because of its low input DNA requirement from formalin fixed and paraffin embedded tissue. The success of NGS mutational analysis is affected not only by the input DNA quantity but also by several other factors, including the specimen type, the DNA quality, and the tumor cellularity. Here, we review tissue requirements for solid tumor NGS based mutational analysis, including procedure types, tissue types, tumor volume and fraction, decalcification, and treatment effects.
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Endorsing good quality assurance practices in molecular pathology: risks and recommendations for diagnostic laboratories and external quality assessment providers. Virchows Arch 2015; 468:31-41. [PMID: 26306715 DOI: 10.1007/s00428-015-1839-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 08/06/2015] [Accepted: 08/17/2015] [Indexed: 12/13/2022]
Abstract
Quality assurance is an indispensable element in a molecular diagnostic laboratory. The ultimate goal is to warrant patient safety. Several risks that can compromise high quality procedures are at stake, from sample collection to the test performed by the laboratory, the reporting of test results to clinicians, and the organization of effective external quality assessment schemes. Quality assurance should therefore be safeguarded at each level and should imply a holistic multidisciplinary approach. This review aims to provide an overview of good quality assurance practices and discusses certain risks and recommendations to promote and improve quality assurance for both diagnostic laboratories and for external quality assessment providers. The number of molecular targets is continuously rising, and new technologies are evolving. As this poses challenges for clinical implementation and increases the demand for external quality assessment, the formation of an international association for improving quality assurance in molecular pathology is called for.
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Abstract
MicroRNAs (miRNAs) control physiological and fundamental processes in cellular development and differentiation by modulating the expression of their target genes. They have been found to participate in cell transformation and multiplication by functioning as oncomiRs and tumor suppressors in diverse cancers. Introduction of antisense miRNAs (antagomiRs) into primary cells such as immune cells by lipofection, viral vectors or electroporation can achieve the specific silencing of individual miRNAs. Therefore, harnessing miRNAs may lead to promising cancer therapeutics. There is emerging evidence demonstrating the involvement of miRNAs in combined cancer therapies, including chemotherapy, radiotherapy and immunotherapy combining with miRNA therapy.
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Affiliation(s)
- Hong W Yu
- Hong Kong Polytechnic University, Department of Health Technology and Informatics , Kowloon, Hong Kong , China
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