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Murciano-Goroff YR, Uppal M, Chen M, Harada G, Schram AM. Basket Trials: Past, Present, and Future. ANNUAL REVIEW OF CANCER BIOLOGY 2024; 8:59-80. [PMID: 38938274 PMCID: PMC11210107 DOI: 10.1146/annurev-cancerbio-061421-012927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
Large-scale tumor molecular profiling has revealed that diverse cancer histologies are driven by common pathways with unifying biomarkers that can be exploited therapeutically. Disease-agnostic basket trials have been increasingly utilized to test biomarker-driven therapies across cancer types. These trials have led to drug approvals and improved the lives of patients while simultaneously advancing our understanding of cancer biology. This review focuses on the practicalities of implementing basket trials, with an emphasis on molecularly targeted trials. We examine the biologic subtleties of genomic biomarker and patient selection, discuss previous successes in drug development facilitated by basket trials, describe certain novel targets and drugs, and emphasize practical considerations for participant recruitment and study design. This review also highlights strategies for aiding patient access to basket trials. As basket trials become more common, steps to ensure equitable implementation of these studies will be critical for molecularly targeted drug development.
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Affiliation(s)
| | - Manik Uppal
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Monica Chen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Guilherme Harada
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alison M Schram
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
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Kang DW, Park SK, Yu YL, Lee Y, Lee DH, Kang S. Effectiveness of next-generation sequencing for patients with advanced non-small-cell lung cancer: a population-based registry study. ESMO Open 2024; 9:102200. [PMID: 38194884 PMCID: PMC10820286 DOI: 10.1016/j.esmoop.2023.102200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 10/25/2023] [Accepted: 11/17/2023] [Indexed: 01/11/2024] Open
Abstract
BACKGROUND Despite the growing use of next-generation sequencing (NGS) in the management of advanced non-small-cell lung cancer (NSCLC), there is little evidence that its use leads to improved clinical outcomes. This study aimed to compare the effectiveness of NGS with that of single-gene testing (SGT) alone in patients with advanced NSCLC. MATERIALS AND METHODS This was a retrospective cohort study conducted on patients diagnosed with advanced lung adenocarcinoma between 2017 and 2018 from a nationwide, population-based database. We identified patients who had SGT exclusively (SGT group) or underwent upfront NGS or NGS following SGT as an initial evaluation (NGS group). Patients were followed up until death or the end of the study (31 December 2019). The adjusted hazard ratio (aHR) for death was estimated using the Cox proportional hazards model. The factors affecting the adoption of NGS were identified. RESULTS Of 8566 patients diagnosed with advanced lung adenocarcinoma, 402 and 6932 patients were assigned to the NGS and SGT groups, respectively. More NGS was carried out in younger patients, those with higher incomes, and those living in urban areas. After balancing these confounders through matching, no difference was observed in the median overall survival and risk of death between the NGS and SGT groups [18.5 versus 19.7 months, log-rank P = 0.783; aHR 0.98, 95% confidence interval (CI) 0.84-1.14, respectively]. Only in a subgroup for whom epidermal growth factor receptor (EGFR) or anaplastic lymphoma kinase (ALK) inhibitors were not indicated, NGS was associated with better survival outcomes (14.1 versus 9.0 months, log-rank P = 0.006; aHR 0.82, 95% CI 0.69-0.97). CONCLUSIONS In the real world, NGS for all-comers in patients with advanced NSCLC did not increase survival outcomes. When health care resources to support equal access to NGS are limited, upfront SGT followed by NGS may be a more efficient strategy.
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Affiliation(s)
- D-W Kang
- School of Pharmacy, Sungkyunkwan University, Suwon
| | - S-K Park
- College of Pharmacy, The Catholic University of Korea, Bucheon
| | - Y L Yu
- Center for Gynecologic Cancer, Research Institute and Hospital, National Cancer Center, Goyang
| | - Y Lee
- Department of Internal Medicine, National Cancer Center, Goyang
| | - D H Lee
- Department of Oncology, University of Ulsan College of Medicine, Asan Medical Center, Seoul
| | - S Kang
- Center for Gynecologic Cancer, Research Institute and Hospital, National Cancer Center, Goyang; Department of Cancer Control and Policy, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Republic of Korea.
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Samlowski W, Adajar C. Cautious addition of targeted therapy to PD-1 inhibitors after initial progression of BRAF mutant metastatic melanoma on checkpoint inhibitor therapy. BMC Cancer 2021; 21:1187. [PMID: 34743688 PMCID: PMC8573907 DOI: 10.1186/s12885-021-08906-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 10/25/2021] [Indexed: 12/11/2022] Open
Abstract
Background Virtually all metastatic patients with metastatic melanoma who progress after initial treatment with PD-1 or CTLA-4 directed antibodies will die of their disease. Salvage options are urgently needed. It is theoretically attractive to combine immunotherapy with targeted agents in progressing patients with BRAF mutation positive melanoma, but the toxicity of combined treatment has proven challenging. Methods We performed a retrospective analysis of our patient database and identified 23 patients who progressed on initial checkpoint inhibitor treatment, who subsequently had cautious addition of BRAF±MEK inhibitor therapy to continued PD-1 antibody treatment. Results We found an objective response rate of 55% in second line therapy, with a median progression-free survival of 33.4 months and median overall survival of 34.1 months, with 40% of patients in unmaintained remission at over 3 years. Ten of 12 responding patients were able to discontinue all therapy and continue in unmaintained remission. Toxicity of this approach was generally manageable (21.7% grade 3–5 toxicity). There was 1 early sudden death for unknown reasons in a responding patient. Discussion Our results suggest that 2nd line therapy with PD-1 inhibitors plus BRAF±MEK inhibitors has substantial activity and manageable toxicity. This treatment can induce additional durable complete responses in patients who have progressed on initial immunotherapy. These results suggest further evaluation be performed of sequential PD-1 antibody treatment with cautious addition of targeted therapy in appropriate patients.
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Affiliation(s)
- Wolfram Samlowski
- Comprehensive Cancer Centers of Nevada, 9280 W. Sunset Rd., Suite 100, Las Vegas, NV, 89148, USA. .,University of Nevada Las Vegas, (UNLV) Kerkorian School of Medicine, Las Vegas, NV, USA. .,University of Nevada School of Medicine, Reno, NV, USA.
| | - Camille Adajar
- University of Nevada Las Vegas, (UNLV) Kerkorian School of Medicine, Las Vegas, NV, USA
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Zhu L, Xie S, Yang C, Hua N, Wu Y, Wang L, Ni W, Tong X, Fei M, Wang S. Current Progress in Investigating Mature T- and NK-Cell Lymphoma Gene Aberrations by Next-Generation Sequencing (NGS). Cancer Manag Res 2021; 13:5275-5286. [PMID: 34239326 PMCID: PMC8259727 DOI: 10.2147/cmar.s299505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 06/14/2021] [Indexed: 11/23/2022] Open
Abstract
Despite efforts to abrogate the severe threat to life posed by the profound malignancy of mature natural killer/T-cell lymphoma (NKTCL), therapeutic advances still require further investigation of its inherent regulatory biochemical processes. Next-generation sequencing (NGS) is an increasingly developing gene detection technique, which has been widely used in lymphoma genetic research in recent years. Targeted therapy based on the above studies has also generated a series of advances, making genetic mutation a new research hotspot in lymphoma. Advances in NKTCL-related gene mutations are reviewed in this paper.
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Affiliation(s)
- Lifen Zhu
- Molecular diagnosis laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
| | - Shufang Xie
- Molecular diagnosis laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, People’s Republic of China
| | - Chen Yang
- Molecular diagnosis laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
- Department of Clinical Medicine, Qingdao University, Qingdao, Shandong, People’s Republic of China
| | - Nanni Hua
- Molecular diagnosis laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, People’s Republic of China
| | - Yi Wu
- Phase I clinical research center, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
| | - Lei Wang
- Molecular diagnosis laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
| | - Wanmao Ni
- Molecular diagnosis laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
| | - Xiangmin Tong
- Molecular diagnosis laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
| | - Min Fei
- Center of Health Management, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
| | - Shibing Wang
- Molecular diagnosis laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
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Shimazawa R, Ikeda M. Regulatory perspectives on next-generation sequencing and complementary diagnostics in Japan. Expert Rev Mol Diagn 2020; 20:601-610. [DOI: 10.1080/14737159.2020.1728256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Rumiko Shimazawa
- Department of Clinical Pharmacology, Tokai University School of Medicine, Isehara, Japan
| | - Masayuki Ikeda
- Department of Medical Informatics, Kagawa University Hospital, Takamatsu, Japan
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Pennell NA, Mutebi A, Zhou ZY, Ricculli ML, Tang W, Wang H, Guerin A, Arnhart T, Dalal A, Sasane M, Wu KY, Culver KW, Otterson GA. Economic Impact of Next-Generation Sequencing Versus Single-Gene Testing to Detect Genomic Alterations in Metastatic Non–Small-Cell Lung Cancer Using a Decision Analytic Model. JCO Precis Oncol 2019; 3:1-9. [DOI: 10.1200/po.18.00356] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE The aim of the current study was to assess the economic impact of using next-generation sequencing (NGS) versus single-gene testing strategies among patients with metastatic non–small-cell lung cancer (mNSCLC) from the perspective of the Centers for Medicare & Medicaid Services (CMS) and US commercial payers. METHODS A decision analytic model considered patients who were newly diagnosed with mNSCLC who received programmed death ligand 1 and genomic alteration tests— EGFR, ALK, ROS1, BRAF, MET, HER2, RET, and NTRK1—using upfront NGS (all alterations tested simultaneously plus KRAS), sequential testing (sequence of single-gene tests), exclusionary testing ( KRAS plus sequential testing), and hotspot panels ( EGFR, ALK, ROS1, and BRAF tested simultaneously plus single-gene tests or NGS for MET, HER2, RET, and NTRK1). Model outcomes for each strategy were time-to-test results, the proportion of patients identified harboring alterations with or without US Food and Drug Administration–approved therapies, and total testing costs. A budget impact analysis assessed the economic effects of increasing the proportion of NGS-tested patients. RESULTS In a hypothetical 1,000,000-member health plan, 2,066 Medicare-insured patients and 156 commercially insured patients were estimated to have mNSCLC and to be eligible for testing. Time-to-test results were 2.0 weeks for NGS and the hotspot panel, faster than exclusionary and sequential testing by 2.7 and 2.8 weeks, respectively. NGS was associated with cost savings for both CMS ($1,393,678; $1,530,869; and $2,140,795 less than exclusionary, sequential testing, and hotspot panels, respectively) and commercial payers ($3,809; $127,402; and $250,842 less than exclusionary, sequential testing, and hotspot panels, respectively). Increasing the proportion of NGS-tested patients translated into substantial cost savings for both CMS and commercial payers. CONCLUSION Use of upfront NGS testing in patients with mNSCLC was associated with substantial cost savings and shorter time-to-test results for both CMS and commercial payers.
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Dehghani M, Rosenblatt KP, Li L, Rakhade M, Amato RJ. Validation and Clinical Applications of a Comprehensive Next Generation Sequencing System for Molecular Characterization of Solid Cancer Tissues. Front Mol Biosci 2019; 6:82. [PMID: 31681791 PMCID: PMC6798036 DOI: 10.3389/fmolb.2019.00082] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 08/23/2019] [Indexed: 12/18/2022] Open
Abstract
Identification of somatic molecular alterations in primary and metastatic solid tumor specimens can provide critical information regarding tumor biology and its heterogeneity, and enables the detection of molecular markers for clinical personalized treatment assignment. However, the optimal methods and target genes for clinical use are still being in development. Toward this end, we validated a targeted amplification-based NGS panel (Oncomine comprehensive assay v1) on a personal genome machine sequencer for molecular profiling of solid tumors. This panel covers 143 genes, and requires low amounts of DNA (20 ng) and RNA (10 ng). We used 27 FFPE tissue specimens, 10 cell lines, and 24 commercial reference materials to evaluate the performance characteristics of this assay. We also evaluated the performance of the assay on 26 OCT-embedded fresh frozen specimens (OEFF). The assay was found to be highly specific (>99%) and sensitive (>99%), with low false-positive and false-negative rates for single-nucleotide variants, indels, copy number alterations, and gene fusions. Our results indicate that this is a reliable method to determine molecular alterations in both fixed and fresh frozen solid tumor samples, including core needle biopsies.
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Affiliation(s)
- Mehdi Dehghani
- Division of Oncology, Department of Internal Medicine, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, United States
| | - Kevin P Rosenblatt
- Division of Oncology, Department of Internal Medicine, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, United States.,NX Prenatal, Inc., Bellaire, TX, United States.,Consultative Genomics, PLLC, Bellaire, TX, United States
| | - Lei Li
- Principle Health Systems, Houston, TX, United States
| | - Mrudula Rakhade
- Division of Oncology, Department of Internal Medicine, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, United States
| | - Robert J Amato
- Division of Oncology, Department of Internal Medicine, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, United States
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Mordechai O, Weyl-Ben-Arush M. Precision Medicine in Relapsed and Refractory Childhood Cancers: Single-center Experience, Literature Review, and Meta-analysis. Rambam Maimonides Med J 2018; 9:RMMJ.10342. [PMID: 30089094 PMCID: PMC6115480 DOI: 10.5041/rmmj.10342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
OBJECTIVE To date, the understanding of pediatric tumor genomics and how these genetic aberrations correlate with clinical outcome is lacking. Here, we report our experience with the next-generation sequencing (NGS) test program and discuss implications for the inclusion of molecular profiling into clinical pediatric oncology trials. We also aimed to explore studies on NGS in pediatric cancers and to quantify the variability of finding actionable mutations and the clinical implications. METHODS We present a retrospective case series of all patients whose tumor tissue underwent NGS tests during treatment in our department. We also reviewed the literature and carried out a meta-analysis to explore studies on NGS in pediatric cancers. RESULTS In 35/37 (94%) patients, we found at least one genomic alteration (GA); mean number of GAs per patient was 2 (range, 0-67), while 164 GAs were detected. Only 3 (8%) patients received precision medicine due to their GAs for a mean of 9 months (range, 5-14 months). Four studies were included in the meta-analysis. The pooled positive actionable mutation rate was 52% (95% CI 39%-66%), and the pooled rate of children who received precision medicine was 10% (95% CI 3%-20%). CONCLUSIONS In children and young adults with high-risk, recurrent, or refractory malignancies, tumor profiling results have clinical implications, despite barriers to the use of matched precision therapy.
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Affiliation(s)
- Oz Mordechai
- Department of Pediatric Hematology Oncology, Ruth Rappaport Children’s Hospital, Rambam Health Care Campus, Haifa, Israel
- To whom correspondence should be addressed. E-mail:
| | - Myriam Weyl-Ben-Arush
- Department of Pediatric Hematology Oncology, Ruth Rappaport Children’s Hospital, Rambam Health Care Campus, Haifa, Israel
- Rappaport Faculty of Medicine, Technion–Israel Institute of Technology, Haifa, Israel
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Dalal AA, Guerin A, Mutebi A, Culver KW. Economic analysis of BRAF gene mutation testing in real world practice using claims data: costs of single gene versus panel tests in patients with lung cancer. J Med Econ 2018. [PMID: 29516752 DOI: 10.1080/13696998.2018.1450261] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
AIMS To assess the time to BRAF testing, compare the characteristics of tested vs not-tested patients, and describe the costs for sequential vs next-generation sequencing (NGS) BRAF testing. METHODS Patients diagnosed with lung cancer after December 1, 2013 were identified from two US claims databases; their characteristics were assessed during the 12 months before diagnosis (index date). Testing modalities were analyzed from the index date to end of continuous health plan enrollment or data availability (December 2015), based on combinations of Current Procedural Terminology (CPT) procedure codes. Time to BRAF testing was assessed using Kaplan-Meier analysis. Costs were analyzed from a payer's perspective. RESULTS A total of 28,011 patients newly-diagnosed with lung cancer were identified. Of them, 1,260 (4.5%) were tested for BRAF: 3.2% and 4.2% were tested at 6 and 12 months, respectively, after the index date. Compared to non-tested patients, tested patients were younger (58.3 vs 65.3 years; p < .001), had a lower Charlson Comorbidity Index (2.8 vs 2.9; p = .005), and a higher proportion had metastases (70.9% vs 43.4%; p < .001). In 76.0% of cases, BRAF was tested along with KRAS. BRAF was tested using NGS in 6.6% of cases. The average reimbursed amounts for the 10 most common CPT code combinations were $207-$2,074. Using the average costs of individual mutation tests, the total cost of sequential testing comprising KRAS, EGFR, ALK, ROS1, and BRAF tests was $3,763 ($464, $696, $1,070, $1,127, and $406, respectively), that of NGS was $2,860. LIMITATIONS Claims data did not include BRAF test results. CONCLUSIONS Among patients newly-diagnosed with lung cancer, 4.5% were tested for BRAF. Tested patients were younger and had a lower comorbidity burden, but more advanced disease. While reimbursed amounts varied greatly based on combinations of testing procedures, NGS testing was associated with cost savings compared to sequential testing of individual mutations.
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Affiliation(s)
- Anand A Dalal
- a Novartis Pharmaceuticals Corporation , East Hanover , NJ , USA
| | - Annie Guerin
- b Analysis Group, Inc. , Montréal , Québec , Canada
| | - Alex Mutebi
- a Novartis Pharmaceuticals Corporation , East Hanover , NJ , USA
| | - Kenneth W Culver
- a Novartis Pharmaceuticals Corporation , East Hanover , NJ , USA
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Luo Z, Fan X, Su Y, Huang YS. Accurity: accurate tumor purity and ploidy inference from tumor-normal WGS data by jointly modelling somatic copy number alterations and heterozygous germline single-nucleotide-variants. Bioinformatics 2018; 34:2004-2011. [PMID: 29385401 PMCID: PMC9881684 DOI: 10.1093/bioinformatics/bty043] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 01/26/2018] [Indexed: 02/02/2023] Open
Abstract
Motivation Tumor purity and ploidy have a substantial impact on next-gen sequence analyses of tumor samples and may alter the biological and clinical interpretation of results. Despite the existence of several computational methods that are dedicated to estimate tumor purity and/or ploidy from The Cancer Genome Atlas (TCGA) tumor-normal whole-genome-sequencing (WGS) data, an accurate, fast and fully-automated method that works in a wide range of sequencing coverage, level of tumor purity and level of intra-tumor heterogeneity, is still missing. Results We describe a computational method called Accurity that infers tumor purity, tumor cell ploidy and absolute allelic copy numbers for somatic copy number alterations (SCNAs) from tumor-normal WGS data by jointly modelling SCNAs and heterozygous germline single-nucleotide-variants (HGSNVs). Results from both in silico and real sequencing data demonstrated that Accurity is highly accurate and robust, even in low-purity, high-ploidy and low-coverage settings in which several existing methods perform poorly. Accounting for tumor purity and ploidy, Accurity significantly increased signal/noise gaps between different copy numbers. We are hopeful that Accurity is of clinical use for identifying cancer diagnostic biomarkers. Availability and implementation Accurity is implemented in C++/Rust, available at http://www.yfish.org/software/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | - Yao Su
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yu S Huang
- To whom correspondence should be addressed.
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Abstract
The majority of cancer-related deaths result from metastasis, the process by which cancer cells escape the primary tumor site and enter into the blood circulation in order to disseminate to secondary locations throughout the body. Tumor cells found within the circulation are referred to as circulating tumor cells (CTCs), and their detection and enumeration correlate with poor prognosis. The epithelial-to-mesenchymal transition (EMT) is a dynamic process that imparts epithelial cells with mesenchymal-like properties, thus facilitating tumor cell dissemination and contributing to metastasis. However, EMT also results in the downregulation of various epithelial proteins typically utilized by CTC technologies for enrichment and detection of these rare cells, resulting in reduced detection of some CTCs, potentially those with a more metastatic phenotype. In addition to the current clinical role of CTCs as a prognostic biomarker, they also have potential as a predictive biomarker via CTC characterization. However, CTC characterization is complicated by the unknown biological significance of CTCs possessing an EMT-like phenotype, and the ability to capture and understand this CTC subpopulation is an essential step in the utilization of CTCs for patient management. This chapter will review the process of EMT and its contribution to metastasis; discusses current and future clinical applications of CTCs; and describes both traditional and novel methods for CTC enrichment, detection, and characterization with a specific focus on CTCs with an EMT phenotype.
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Gao P, Seebacher NA, Hornicek F, Guo Z, Duan Z. Advances in sarcoma gene mutations and therapeutic targets. Cancer Treat Rev 2017; 62:98-109. [PMID: 29190505 DOI: 10.1016/j.ctrv.2017.11.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 10/31/2017] [Accepted: 11/01/2017] [Indexed: 12/14/2022]
Abstract
Sarcomas are rare and complex malignancies that have been associated with a poor prognostic outcome. Over the last few decades, traditional treatment with surgery and/or chemotherapy has not significantly improved outcomes for most types of sarcomas. In recent years, there have been significant advances in the understanding of specific gene mutations that are important in driving the pathogenesis and progression of sarcomas. Identification of these new gene mutations, using next-generation sequencing and advanced molecular techniques, has revealed a range of potential therapeutic targets. This, in turn, may lead to the development of novel agents targeted to different sarcoma subtypes. In this review, we highlight the advances made in identifying sarcoma gene mutations, including those of p53, RB, PI3K and IDH genes, as well as novel therapeutic strategies aimed at utilizing these mutant genes. In addition, we discuss a number of preclinical studies and ongoing early clinical trials in sarcoma targeting therapies, as well as gene editing technology, which may provide a better choice for sarcoma patient management.
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Affiliation(s)
- Peng Gao
- Department of Orthopaedics, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China; UCLA Orthopaedic Surgery, Sarcoma Biology Laboratory, 615 Charles E Young Dr. South, Biomedical Sciences Research Building, Room 410, Los Angeles, CA 90095, USA
| | - Nicole A Seebacher
- UCLA Orthopaedic Surgery, Sarcoma Biology Laboratory, 615 Charles E Young Dr. South, Biomedical Sciences Research Building, Room 410, Los Angeles, CA 90095, USA
| | - Francis Hornicek
- UCLA Orthopaedic Surgery, Sarcoma Biology Laboratory, 615 Charles E Young Dr. South, Biomedical Sciences Research Building, Room 410, Los Angeles, CA 90095, USA
| | - Zheng Guo
- Department of Orthopaedics, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China.
| | - Zhenfeng Duan
- UCLA Orthopaedic Surgery, Sarcoma Biology Laboratory, 615 Charles E Young Dr. South, Biomedical Sciences Research Building, Room 410, Los Angeles, CA 90095, USA.
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Kumar G, Chaudhary KK, Misra K, Tripathi A. Next-Generation Sequencing for Drug Designing and Development: An Omics Approach for Cancer Treatment. INT J PHARMACOL 2017. [DOI: 10.3923/ijp.2017.709.723] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Validation of quantitative PCR-based assays for detection of gene copy number aberrations in formalin-fixed, paraffin embedded solid tumor samples. Cancer Genet 2017; 212-213:24-31. [PMID: 28449808 DOI: 10.1016/j.cancergen.2017.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 02/27/2017] [Accepted: 03/02/2017] [Indexed: 01/04/2023]
Abstract
Gene copy number changes are important somatic alterations in cancers. A number of high throughput methods, such as next generation sequencing, are capable of detecting copy number aberrations, but their use can be challenging and cost prohibitive for screening a small number of markers. Furthermore, detection of CNAs by high throughput platforms needs confirmation by an orthogonal technique, especially in cases with low level CNAs. Here, we have validated TaqMan based quantitative PCR (qPCR) assays to detect CNAs in genes of high clinical importance in formalin-fixed, paraffin-embedded (FFPE) samples. A cohort of 22 tumors of various types that harbor 67 CNAs in 13 genes was assessed. The abnormalities in these tumors were detected by using a NGS-based 50 gene hotspot panel on Ion Torrent PGM and molecular inversion probe (MIP) array. The CNAs included ERBB2 (n = 6), PDGFRA (n = 6), KIT (n = 7), NRAS (n = 3), PIK3CA (n = 6), MYC (n = 7), MET (n = 4), FLT3 (n = 6), FGFR3 (n = 3), FGFR2 (n = 3), EGFR (n = 7), KRAS (n = 6) and FGFR1 (n = 5). Different amounts of input DNA were tested and 5 ng FFPE DNA was found to be adequate without limiting detection sensitivity. All 22 (100%) positive tumor samples revealed by MIP array were confirmed by real time qPCR and 17 of 22 (77.2%) samples tested by NGS were confirmed. The limit of detection of the qPCR assay was determined by serial dilution of SKBR3 cell line DNA (with amplified ERBB2) and showed an ability to detect 3 copies consistently up to 0.75% dilution. The ability to use low input of FFPE DNA, high sensitivity, and short turnaround time makes qPCR a valuable and economically viable platform for detecting single gene CNAs as well as for confirmation of CNAs detected by high throughput screening assays.
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Luo Q, Shen J, Yang Y, Tang H, Shi M, Liu J, Liu Z, Shi X, Yi Y. CSF3R T618I, ASXL1 G942 fs and STAT5B N642H trimutation co-contribute to a rare chronic neutrophilic leukaemia manifested by rapidly progressive leucocytosis, severe infections, persistent fever and deep venous thrombosis. Br J Haematol 2016; 180:892-894. [PMID: 27984641 DOI: 10.1111/bjh.14456] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Qianhui Luo
- Department of Haematology, The Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Jiankai Shen
- Department of Haematology, The Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Yuan Yang
- Department of Medical Genetics, The Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Haiyan Tang
- Department of Medical Genetics, The Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Meng Shi
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Jun Liu
- Department of Radiology, The Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Zhonghua Liu
- National and Local Joint Engineering Laboratory for Animal Peptide Drug development, College of Life Sciences, Huan Normal University, Changsha, Hunan Province, China
| | - Xiaoliu Shi
- Department of Medical Genetics, The Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Yan Yi
- Department of Haematology, The Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
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16
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Clinical Applications of Next-Generation Sequencing in Cancer Diagnosis. Pathol Oncol Res 2016; 23:225-234. [PMID: 27722982 DOI: 10.1007/s12253-016-0124-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 10/04/2016] [Indexed: 12/22/2022]
Abstract
With the advancement and improvement of new sequencing technology, next-generation sequencing (NGS) has been applied increasingly in cancer genomics research fields. More recently, NGS has been adopted in clinical oncology to advance personalized treatment of cancer. NGS is utilized to novel diagnostic and rare cancer mutations, detection of translocations, inversions, insertions and deletions, detection of copy number variants, detect familial cancer mutation carriers, provide the molecular rationale for appropriate targeted, therapeutic and prognostic. NGS holds many advantages, such as the ability to fully sequence all types of mutations for a large number of genes (hundreds to thousands) and the sensitivity, speed in a single test at a relatively low cost compared to be other sequencing modalities. Here we described the technology, methods and applications that can be immediately considered and some of the challenges that lie ahead.
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Forte VA, Barrak DK, Elhodaky M, Tung L, Snow A, Lang JE. The potential for liquid biopsies in the precision medical treatment of breast cancer. Cancer Biol Med 2016; 13:19-40. [PMID: 27144060 PMCID: PMC4850125 DOI: 10.28092/j.issn.2095-3941.2016.0007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Currently the clinical management of breast cancer relies on relatively few prognostic/predictive clinical markers (estrogen receptor, progesterone receptor, HER2), based on primary tumor biology. Circulating biomarkers, such as circulating tumor DNA (ctDNA) or circulating tumor cells (CTCs) may enhance our treatment options by focusing on the very cells that are the direct precursors of distant metastatic disease, and probably inherently different than the primary tumor's biology. To shift the current clinical paradigm, assessing tumor biology in real time by molecularly profiling CTCs or ctDNA may serve to discover therapeutic targets, detect minimal residual disease and predict response to treatment. This review serves to elucidate the detection, characterization, and clinical application of CTCs and ctDNA with the goal of precision treatment of breast cancer.
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Affiliation(s)
- Victoria A Forte
- Department of Medicine, Division of Medical Oncology, University of Southern California (USC), Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | - Dany K Barrak
- USC Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA; Department of Surgery, Division of Breast, Endocrine and Soft Tissue Surgery, USC, Los Angeles, CA 90033, USA
| | - Mostafa Elhodaky
- USC Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA; Department of Stem Cell and Regenerative Medicine, USC, Los Angeles, CA 90033, USA
| | - Lily Tung
- USC Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA; Department of Surgery, Division of Breast, Endocrine and Soft Tissue Surgery, USC, Los Angeles, CA 90033, USA
| | - Anson Snow
- Department of Medicine, Division of Medical Oncology, University of Southern California (USC), Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | - Julie E Lang
- USC Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA; Department of Surgery, Division of Breast, Endocrine and Soft Tissue Surgery, USC, Los Angeles, CA 90033, USA
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Abstract
On December 18, 2014, a yellow female fly quietly emerged from her pupal case. What made her unique was that she had only one parent carrying a mutant allele of this classic recessive locus. Then, one generation later, after mating with a wild-type male, all her offspring displayed the same recessive yellow phenotype. Further analysis of other such yellow females revealed that the construct causing the mutation was converting the opposing chromosome with 95% efficiency. These simple results, seen also in mosquitoes and yeast, open the door to a new era of genetics wherein the laws of traditional Mendelian inheritance can be bypassed for a broad variety of purposes. Here, we consider the implications of this fundamentally new form of "active genetics," its applications for gene drives, reversal and amplification strategies, its potential for contributing to cell and gene therapy strategies, and ethical/biosafety considerations associated with such active genetic elements. Also watch the Video Abstract.
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Affiliation(s)
- Valentino M Gantz
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
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19
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Next-Generation Sequencing Workflow for NSCLC Critical Samples Using a Targeted Sequencing Approach by Ion Torrent PGM™ Platform. Int J Mol Sci 2015; 16:28765-82. [PMID: 26633390 PMCID: PMC4691076 DOI: 10.3390/ijms161226129] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 11/18/2015] [Accepted: 11/24/2015] [Indexed: 01/11/2023] Open
Abstract
Next-generation sequencing (NGS) is a cost-effective technology capable of screening several genes simultaneously; however, its application in a clinical context requires an established workflow to acquire reliable sequencing results. Here, we report an optimized NGS workflow analyzing 22 lung cancer-related genes to sequence critical samples such as DNA from formalin-fixed paraffin-embedded (FFPE) blocks and circulating free DNA (cfDNA). Snap frozen and matched FFPE gDNA from 12 non-small cell lung cancer (NSCLC) patients, whose gDNA fragmentation status was previously evaluated using a multiplex PCR-based quality control, were successfully sequenced with Ion Torrent PGM™. The robust bioinformatic pipeline allowed us to correctly call both Single Nucleotide Variants (SNVs) and indels with a detection limit of 5%, achieving 100% specificity and 96% sensitivity. This workflow was also validated in 13 FFPE NSCLC biopsies. Furthermore, a specific protocol for low input gDNA capable of producing good sequencing data with high coverage, high uniformity, and a low error rate was also optimized. In conclusion, we demonstrate the feasibility of obtaining gDNA from FFPE samples suitable for NGS by performing appropriate quality controls. The optimized workflow, capable of screening low input gDNA, highlights NGS as a potential tool in the detection, disease monitoring, and treatment of NSCLC.
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20
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21
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Harwood JL, Alexander JH, Mayerson JL, Scharschmidt TJ. Targeted Chemotherapy in Bone and Soft-Tissue Sarcoma. Orthop Clin North Am 2015; 46:587-608. [PMID: 26410647 DOI: 10.1016/j.ocl.2015.06.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Historically surgical intervention has been the mainstay of therapy for bone and soft-tissue sarcomas, augmented with adjuvant radiation for local control. Although cytotoxic chemotherapy revolutionized the treatment of many sarcomas, classic treatment regimens are fraught with side effects while outcomes have plateaued. However, since the approval of imatinib in 2002, research into targeted chemotherapy has increased exponentially. With targeted therapies comes the potential for decreased side effects and more potent, personalized treatment options. This article reviews the evolution of medical knowledge regarding sarcoma, the basic science of sarcomatogenesis, and the major targets and pathways now being studied.
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Affiliation(s)
- Jared L Harwood
- Department of Orthopaedics, The Ohio State University, 725 Prior Hall, 376 West 10 Avenue, Columbus, OH 43210, USA
| | - John H Alexander
- Department of Orthopaedics, The Ohio State University, 725 Prior Hall, 376 West 10 Avenue, Columbus, OH 43210, USA
| | - Joel L Mayerson
- Department of Orthopaedics, The Ohio State University, 725 Prior Hall, 376 West 10 Avenue, Columbus, OH 43210, USA.
| | - Thomas J Scharschmidt
- Department of Orthopaedics, The Ohio State University, 725 Prior Hall, 376 West 10 Avenue, Columbus, OH 43210, USA
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22
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Reinhold WC, Varma S, Rajapakse VN, Luna A, Sousa FG, Kohn KW, Pommier YG. Using drug response data to identify molecular effectors, and molecular "omic" data to identify candidate drugs in cancer. Hum Genet 2015; 134:3-11. [PMID: 25213708 PMCID: PMC4282979 DOI: 10.1007/s00439-014-1482-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 08/19/2014] [Indexed: 12/31/2022]
Abstract
The current convergence of molecular and pharmacological data provides unprecedented opportunities to gain insights into the relationships between the two types of data. Multiple forms of large-scale molecular data, including but not limited to gene and microRNA transcript expression, DNA somatic and germline variations from next-generation DNA and RNA sequencing, and DNA copy number from array comparative genomic hybridization are all potentially informative when one attempts to recognize the panoply of potentially influential events both for cancer progression and therapeutic outcome. Concurrently, there has also been a substantial expansion of the pharmacological data being accrued in a systematic fashion. For cancer cell lines, the National Cancer Institute cell line panel (NCI-60), the Cancer Cell Line Encyclopedia (CCLE), and the collaborative Genomics of Drug Sensitivity in Cancer (GDSC) databases all provide subsets of these forms of data. For the patient-derived data, The Cancer Genome Atlas (TCGA) provides analogous forms of genomic information along with treatment histories. Integration of these data in turn relies on the fields of statistics and statistical learning. Multiple algorithmic approaches may be chosen, depending on the data being considered, and the nature of the question being asked. Combining these algorithms with prior biological knowledge, the results of molecular biological studies, and the consideration of genes as pathways or functional groups provides both the challenge and the potential of the field. The ultimate goal is to provide a paradigm shift in the way that drugs are selected to provide a more targeted and efficacious outcome for the patient.
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Affiliation(s)
- William C Reinhold
- Developmental Therapeutic Branch, Center for Cancer Research, NCI, NIH, 9000 Rockville Pike, Building 37, room 5041, Bethesda, MD, 20892, USA,
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23
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NCI-60 whole exome sequencing and pharmacological CellMiner analyses. PLoS One 2014; 9:e101670. [PMID: 25032700 PMCID: PMC4102467 DOI: 10.1371/journal.pone.0101670] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 06/05/2014] [Indexed: 01/01/2023] Open
Abstract
Exome sequencing provides unprecedented insights into cancer biology and pharmacological response. Here we assess these two parameters for the NCI-60, which is among the richest genomic and pharmacological publicly available cancer cell line databases. Homozygous genetic variants that putatively affect protein function were identified in 1,199 genes (approximately 6% of all genes). Variants that are either enriched or depleted compared to non-cancerous genomes, and thus may be influential in cancer progression and differential drug response were identified for 2,546 genes. Potential gene knockouts are made available. Assessment of cell line response to 19,940 compounds, including 110 FDA-approved drugs, reveals ≈80-fold range in resistance versus sensitivity response across cell lines. 103,422 gene variants were significantly correlated with at least one compound (at p<0.0002). These include genes of known pharmacological importance such as IGF1R, BRAF, RAD52, MTOR, STAT2 and TSC2 as well as a large number of candidate genes such as NOM1, TLL2, and XDH. We introduce two new web-based CellMiner applications that enable exploration of variant-to-compound relationships for a broad range of researchers, especially those without bioinformatics support. The first tool, “Genetic variant versus drug visualization”, provides a visualization of significant correlations between drug activity-gene variant combinations. Examples are given for the known vemurafenib-BRAF, and novel ifosfamide-RAD52 pairings. The second, “Genetic variant summation” allows an assessment of cumulative genetic variations for up to 150 combined genes together; and is designed to identify the variant burden for molecular pathways or functional grouping of genes. An example of its use is provided for the EGFR-ERBB2 pathway gene variant data and the identification of correlated EGFR, ERBB2, MTOR, BRAF, MEK and ERK inhibitors. The new tools are implemented as an updated web-based CellMiner version, for which the present publication serves as a compendium.
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24
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Boland GM, Meric-Bernstam F. The role of surgeons in building a personalized medicine program. J Surg Oncol 2014; 111:3-8. [PMID: 24964977 DOI: 10.1002/jso.23684] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 04/17/2014] [Indexed: 12/30/2022]
Abstract
Changes in technology, with decreases in the cost of molecular profiling, has expanded the interest in creating institution-wide personalized medicine platforms to allow selective assessment of a given patient's tumor in real time, with the ability to utilize that information for patient-care decisions. In order for this approach to function adequately, a multidisciplinary team must be created in an environment with dedicated support at an institutional level.
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Affiliation(s)
- Genevieve M Boland
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
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25
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Pant S, Weiner R, Marton MJ. Navigating the rapids: the development of regulated next-generation sequencing-based clinical trial assays and companion diagnostics. Front Oncol 2014; 4:78. [PMID: 24860780 PMCID: PMC4029014 DOI: 10.3389/fonc.2014.00078] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 03/28/2014] [Indexed: 12/11/2022] Open
Abstract
Over the past decade, next-generation sequencing (NGS) technology has experienced meteoric growth in the aspects of platform, technology, and supporting bioinformatics development allowing its widespread and rapid uptake in research settings. More recently, NGS-based genomic data have been exploited to better understand disease development and patient characteristics that influence response to a given therapeutic intervention. Cancer, as a disease characterized by and driven by the tumor genetic landscape, is particularly amenable to NGS-based diagnostic (Dx) approaches. NGS-based technologies are particularly well suited to studying cancer disease development, progression and emergence of resistance, all key factors in the development of next-generation cancer Dxs. Yet, to achieve the promise of NGS-based patient treatment, drug developers will need to overcome a number of operational, technical, regulatory, and strategic challenges. Here, we provide a succinct overview of the state of the clinical NGS field in terms of the available clinically targeted platforms and sequencing technologies. We discuss the various operational and practical aspects of clinical NGS testing that will facilitate or limit the uptake of such assays in routine clinical care. We examine the current strategies for analytical validation and Food and Drug Administration (FDA)-approval of NGS-based assays and ongoing efforts to standardize clinical NGS and build quality control standards for the same. The rapidly evolving companion diagnostic (CDx) landscape for NGS-based assays will be reviewed, highlighting the key areas of concern and suggesting strategies to mitigate risk. The review will conclude with a series of strategic questions that face drug developers and a discussion of the likely future course of NGS-based CDx development efforts.
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Affiliation(s)
- Saumya Pant
- Merck Research Laboratories, Molecular Biomarkers and Diagnostics , Rahway, NJ , USA
| | - Russell Weiner
- Merck Research Laboratories, Molecular Biomarkers and Diagnostics , Rahway, NJ , USA
| | - Matthew J Marton
- Merck Research Laboratories, Molecular Biomarkers and Diagnostics , Rahway, NJ , USA
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26
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Lowes LE, Allan AL. Recent advances in the molecular characterization of circulating tumor cells. Cancers (Basel) 2014; 6:595-624. [PMID: 24633084 PMCID: PMC3980613 DOI: 10.3390/cancers6010595] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 01/28/2014] [Accepted: 02/20/2014] [Indexed: 12/16/2022] Open
Abstract
Although circulating tumor cells (CTCs) were first observed over a century ago, lack of sensitive methodology precluded detailed study of these cells until recently. However, technological advances have now facilitated the identification, enumeration, and characterization of CTCs using a variety of methods. The majority of evidence supporting the use of CTCs in clinical decision-making has been related to enumeration using the CellSearch® system and correlation with prognosis. Growing evidence also suggests that CTC monitoring can provide an early indication of patient treatment response based on comparison of CTC levels before and after therapy. However, perhaps the greatest potential that CTCs hold for oncology lies at the level of molecular characterization. Clinical treatment decisions may be more effective if they are based on molecular characteristics of metastatic cells rather than on those of the primary tumor alone. Molecular characterization of CTCs (which can be repeatedly isolated in a minimally invasive fashion) provides the opportunity for a "real-time liquid biopsy" that allows assessment of genetic drift, investigation of molecular disease evolution, and identification of actionable genomic characteristics. This review focuses on recent advances in this area, including approaches involving immunophenotyping, fluorescence in situ hybridization (FISH), multiplex RT-PCR, microarray, and genomic sequencing.
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Affiliation(s)
- Lori E Lowes
- London Regional Cancer Program, London Health Sciences Centre, London, ON N6A 4L6, Canada.
| | - Alison L Allan
- London Regional Cancer Program, London Health Sciences Centre, London, ON N6A 4L6, Canada.
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27
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Abi-Jaoudeh N, Duffy AG, Greten TF, Kohn EC, Clark TWI, Wood BJ. Personalized oncology in interventional radiology. J Vasc Interv Radiol 2014; 24:1083-92; quiz 1093. [PMID: 23885909 DOI: 10.1016/j.jvir.2013.04.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 04/15/2013] [Accepted: 04/15/2013] [Indexed: 12/31/2022] Open
Abstract
As personalized medicine becomes more applicable to oncologic practice, image-guided biopsies will be integral for enabling predictive and pharmacodynamic molecular pathology. Interventional radiology has a key role in defining patient-specific management. Advances in diagnostic techniques, genomics, and proteomics enable a window into subcellular mechanisms driving hyperproliferation, metastatic capabilities, and tumor angiogenesis. A new era of personalized medicine has evolved whereby clinical decisions are adjusted according to a patient's molecular profile. Several mutations and key markers already have been introduced into standard oncologic practice. A broader understanding of personalized oncology will help interventionalists play a greater role in therapy selection and discovery.
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Affiliation(s)
- Nadine Abi-Jaoudeh
- Radiology and Imaging Sciences, National Institutes of Health, Rockville Pike, Bethesda, MD 20892, USA.
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28
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Jia S, Zocco D, Samuels ML, Chou MF, Chammas R, Skog J, Zarovni N, Momen-Heravi F, Kuo WP. Emerging technologies in extracellular vesicle-based molecular diagnostics. Expert Rev Mol Diagn 2014; 14:307-21. [PMID: 24575799 DOI: 10.1586/14737159.2014.893828] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Extracellular vesicles (EVs), including exosomes and microvesicles, have been shown to carry a variety of biomacromolecules including mRNA, microRNA and other non-coding RNAs. Within the past 5 years, EVs have emerged as a promising minimally invasive novel source of material for molecular diagnostics. Although EVs can be easily identified and collected from biological fluids, further research and proper validation is needed in order for them to be useful in the clinical setting. In addition, innovative and more efficient means of nucleic acid profiling are needed to facilitate investigations into the cellular and molecular mechanisms of EV function and to establish their potential as useful clinical biomarkers and therapeutic tools. In this article, we provide an overview of recent technological improvements in both upstream EV isolation and downstream analytical technologies, including digital PCR and next generation sequencing, highlighting future prospects for EV-based molecular diagnostics.
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Affiliation(s)
- Shidong Jia
- Oncology Biomarker Development, Genentech Inc., South San Francisco, CA 94080, USA
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29
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Vollbrecht C, König K, Heukamp L, Büttner R, Odenthal M. [Molecular pathology of the lungs. New perspectives by next generation sequencing]. DER PATHOLOGE 2013; 34:16-24. [PMID: 23389825 DOI: 10.1007/s00292-012-1704-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Lung cancer is one of the most frequent malignancies in the western world. Its frequent association with a wide spectrum of mutations in genes encoding various signal transducers that are often linked to therapy response, emphasizes the obvious need for improved, fast and highly efficient approaches in molecular pathology. Comprehensive analyses of the mutation status of progression and therapy relevant genes can be performed by the novel sequencing forms named next generation sequencing (NGS) providing extremely high capacities for ultra-deep sequence analyses. The 454 pyrosequencing method, the sequencing by synthesis and the semiconductor sequencing platform are now available for parallel sequencing approaches of multitudinous target genes linked to multiple tumor DNA applications. The "one molecule, one clone, one read" principle by the NGS approaches supplies not only information on allele frequencies and mutation rates but also has the advantage of a very sensitive detection of low frequency variants.
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Affiliation(s)
- C Vollbrecht
- Institut für Pathologie, Universitätsklinik zu Köln, Kerpener Str. 62, 50924, Köln, Deutschland
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30
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Monks NR, Cherba DM, Kamerling SG, Simpson H, Rusk AW, Carter D, Eugster E, Mooney M, Sigler R, Steensma M, Grabinski T, Marotti KR, Webb CP. A multi-site feasibility study for personalized medicine in canines with osteosarcoma. J Transl Med 2013; 11:158. [PMID: 23815880 PMCID: PMC3702405 DOI: 10.1186/1479-5876-11-158] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 06/28/2013] [Indexed: 01/06/2023] Open
Abstract
Background A successful therapeutic strategy, specifically tailored to the molecular constitution of an individual and their disease, is an ambitious objective of modern medicine. In this report, we highlight a feasibility study in canine osteosarcoma focused on refining the infrastructure and processes required for prospective clinical trials using a series of gene expression-based Personalized Medicine (PMed) algorithms to predict suitable therapies within 5 days of sample receipt. Methods Tumor tissue samples were collected immediately following limb amputation and shipped overnight from veterinary practices. Upon receipt (day 1), RNA was extracted from snap-frozen tissue, with an adjacent H&E section for pathological diagnosis. Samples passing RNA and pathology QC were shipped to a CLIA-certified laboratory for genomic profiling. After mapping of canine probe sets to human genes and normalization against a (normal) reference set, gene level Z-scores were submitted to the PMed algorithms. The resulting PMed report was immediately forwarded to the veterinarians. Upon receipt and review of the PMed report, feedback from the practicing veterinarians was captured. Results 20 subjects were enrolled over a 5 month period. Tissue from 13 subjects passed both histological and RNA QC and were submitted for genomic analysis and subsequent PMed analysis and report generation. 11 of the 13 samples for which PMed reports were produced were communicated to the veterinarian within the target 5 business days. Of the 7 samples that failed QC, 4 were due to poor RNA quality, whereas 2 were failed following pathological review. Comments from the practicing veterinarians were generally positive and constructive, highlighting a number of areas for improvement, including enhanced education regarding PMed report interpretation, drug availability, affordable pricing and suitable canine dosing. Conclusions This feasibility trial demonstrated that with the appropriate infrastructure and processes it is possible to perform an in-depth molecular analysis of a patient’s tumor in support of real time therapeutic decision making within 5 days of sample receipt. A number of areas for improvement have been identified that should reduce the level of sample attrition and support clinical decision making.
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31
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Grumbt B, Eck SH, Hinrichsen T, Hirv K. Diagnostic applications of next generation sequencing in immunogenetics and molecular oncology. ACTA ACUST UNITED AC 2013; 40:196-206. [PMID: 23922545 DOI: 10.1159/000351267] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 03/19/2013] [Indexed: 12/23/2022]
Abstract
SUMMARY With the introduction of the next generation sequencing (NGS) technologies, remarkable new diagnostic applications have been established in daily routine. Implementation of NGS is challenging in clinical diagnostics, but definite advantages and new diagnostic possibilities make the switch to the technology inevitable. In addition to the higher sequencing capacity, clonal sequencing of single molecules, multiplexing of samples, higher diagnostic sensitivity, workflow miniaturization, and cost benefits are some of the valuable features of the technology. After the recent advances, NGS emerged as a proven alternative for classical Sanger sequencing in the typing of human leukocyte antigens (HLA). By virtue of the clonal amplification of single DNA molecules ambiguous typing results can be avoided. Simultaneously, a higher sample throughput can be achieved by tagging of DNA molecules with multiplex identifiers and pooling of PCR products before sequencing. In our experience, up to 380 samples can be typed for HLA-A, -B, and -DRB1 in high-resolution during every sequencing run. In molecular oncology, NGS shows a markedly increased sensitivity in comparison to the conventional Sanger sequencing and is developing to the standard diagnostic tool in detection of somatic mutations in cancer cells with great impact on personalized treatment of patients.
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Affiliation(s)
- Barbara Grumbt
- Center for Human Genetics and Laboratory Medicine, Martinsried, Germany
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32
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Long É, Hofman V, Ilie M, Washetine K, Lespinet V, Bonnetaud C, Bordone O, Gavric-Tanga V, Gaziello MC, Lassalle S, Selva É, Zahaf K, Lamy A, Sabourin JC, Hofman P. Accréditation de l’activité de pathologie moléculaire selon la norme ISO 15189. Principales étapes à respecter et principaux écueils possibles. Ann Pathol 2013; 33:12-23. [DOI: 10.1016/j.annpat.2012.11.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 10/30/2012] [Accepted: 11/16/2012] [Indexed: 12/31/2022]
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33
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Mise en place d’un secteur de pathologie moléculaire en oncologie au sein d’un laboratoire d’anatomie pathologique (LPCE, CHU de Nice). Ann Pathol 2013; 33:24-37. [DOI: 10.1016/j.annpat.2012.12.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Revised: 12/06/2012] [Accepted: 12/16/2012] [Indexed: 12/12/2022]
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34
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Cagle PT, Allen TC. Lung cancer genotype-based therapy and predictive biomarkers: present and future. Arch Pathol Lab Med 2013. [PMID: 23194040 DOI: 10.5858/arpa.2012-0508-ra] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT The advent of genotype-based therapy and predictive biomarkers for lung cancer has thrust the pathologist into the front lines of precision medicine for this deadly disease. OBJECTIVE To provide the clinical background, current status, and future perspectives of molecular targeted therapy for lung cancer patients, including the pivotal participation of the pathologist. DATA SOURCES Data were obtained from review of the pertinent peer-reviewed literature. CONCLUSIONS First-generation tyrosine kinase inhibitors have produced clinical response in a limited number of non-small cell lung cancers demonstrated to have activating mutations of epidermal growth factor receptor or anaplastic lymphoma kinase rearrangements with fusion partners. Patients treated with first-generation tyrosine kinase inhibitors develop acquired resistance to their therapy. Ongoing investigations of second-generation tyrosine kinase inhibitors and new druggable targets as well as the development of next-generation genotyping and new antibodies for immunohistochemistry promise to significantly expand the pathologist's already crucial role in precision medicine of lung cancer.
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Affiliation(s)
- Philip T Cagle
- Department of Pathology & Genomic Medicine, The Methodist Hospital, Houston, Texas, USA.
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Li KK, Luo LF, Shen Y, Xu J, Chen Z, Chen SJ. DNA Methyltransferases in Hematologic Malignancies. Semin Hematol 2013; 50:48-60. [DOI: 10.1053/j.seminhematol.2013.01.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Patel R, Tsan A, Tam R, Desai R, Spoerke J, Schoenbrunner N, Myers TW, Bauer K, Smith E, Raja R. Mutation scanning using MUT-MAP, a high-throughput, microfluidic chip-based, multi-analyte panel. PLoS One 2012; 7:e51153. [PMID: 23284662 PMCID: PMC3524125 DOI: 10.1371/journal.pone.0051153] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 10/17/2012] [Indexed: 01/07/2023] Open
Abstract
Targeted anticancer therapies rely on the identification of patient subgroups most likely to respond to treatment. Predictive biomarkers play a key role in patient selection, while diagnostic and prognostic biomarkers expand our understanding of tumor biology, suggest treatment combinations, and facilitate discovery of novel drug targets. We have developed a high-throughput microfluidics method for mutation detection (MUT-MAP, mutation multi-analyte panel) based on TaqMan or allele-specific PCR (AS-PCR) assays. We analyzed a set of 71 mutations across six genes of therapeutic interest. The six-gene mutation panel was designed to detect the most common mutations in the EGFR, KRAS, PIK3CA, NRAS, BRAF, and AKT1 oncogenes. The DNA was preamplified using custom-designed primer sets before the TaqMan/AS-PCR assays were carried out using the Biomark microfluidics system (Fluidigm; South San Francisco, CA). A cross-reactivity analysis enabled the generation of a robust automated mutation-calling algorithm which was then validated in a series of 51 cell lines and 33 FFPE clinical samples. All detected mutations were confirmed by other means. Sample input titrations confirmed the assay sensitivity with as little as 2 ng gDNA, and demonstrated excellent inter- and intra-chip reproducibility. Parallel analysis of 92 clinical trial samples was carried out using 2-100 ng genomic DNA (gDNA), allowing the simultaneous detection of multiple mutations. DNA prepared from both fresh frozen and formalin-fixed, paraffin-embedded (FFPE) samples were used, and the analysis was routinely completed in 2-3 days: traditional assays require 0.5-1 µg high-quality DNA, and take significantly longer to analyze. This assay can detect a wide range of mutations in therapeutically relevant genes from very small amounts of sample DNA. As such, the mutation assay developed is a valuable tool for high-throughput biomarker discovery and validation in personalized medicine and cancer drug development.
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Affiliation(s)
- Rajesh Patel
- Oncology Biomarker Development, Genentech Inc., South San Francisco, California, United States of America.
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Guan YF, Li GR, Wang RJ, Yi YT, Yang L, Jiang D, Zhang XP, Peng Y. Application of next-generation sequencing in clinical oncology to advance personalized treatment of cancer. CHINESE JOURNAL OF CANCER 2012; 31:463-70. [PMID: 22980418 PMCID: PMC3777453 DOI: 10.5732/cjc.012.10216] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
With the development and improvement of new sequencing technology, next-generation sequencing (NGS) has been applied increasingly in cancer genomics research over the past decade. More recently, NGS has been adopted in clinical oncology to advance personalized treatment of cancer. NGS is used to identify novel and rare cancer mutations, detect familial cancer mutation carriers, and provide molecular rationale for appropriate targeted therapy. Compared to traditional sequencing, NGS holds many advantages, such as the ability to fully sequence all types of mutations for a large number of genes (hundreds to thousands) in a single test at a relatively low cost. However, significant challenges, particularly with respect to the requirement for simpler assays, more flexible throughput, shorter turnaround time, and most importantly, easier data analysis and interpretation, will have to be overcome to translate NGS to the bedside of cancer patients. Overall, continuous dedication to apply NGS in clinical oncology practice will enable us to be one step closer to personalized medicine.
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Affiliation(s)
- Yan-Fang Guan
- Shenzhen Clinical Molecular Diagnostic Engineering Laboratory, BGI-Shenzhen, Shenzhen, Guangdong, People's Republic of China
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Best practices for companion diagnostic and therapeutic development: translating between the stakeholders. N Biotechnol 2012; 29:689-94. [DOI: 10.1016/j.nbt.2012.06.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 06/10/2012] [Accepted: 06/10/2012] [Indexed: 11/21/2022]
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Leukemia gene atlas--a public platform for integrative exploration of genome-wide molecular data. PLoS One 2012; 7:e39148. [PMID: 22720055 PMCID: PMC3375295 DOI: 10.1371/journal.pone.0039148] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 05/16/2012] [Indexed: 11/19/2022] Open
Abstract
Leukemias are exceptionally well studied at the molecular level and a wealth of high-throughput data has been published. But further utilization of these data by researchers is severely hampered by the lack of accessible integrative tools for viewing and analysis. We developed the Leukemia Gene Atlas (LGA) as a public platform designed to support research and analysis of diverse genomic data published in the field of leukemia. With respect to leukemia research, the LGA is a unique resource with comprehensive search and browse functions. It provides extensive analysis and visualization tools for various types of molecular data. Currently, its database contains data from more than 5,800 leukemia and hematopoiesis samples generated by microarray gene expression, DNA methylation, SNP and next generation sequencing analyses. The LGA allows easy retrieval of large published data sets and thus helps to avoid redundant investigations. It is accessible at www.leukemia-gene-atlas.org.
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Wistuba II. Molecular testing of non-small cell lung carcinoma biopsy and cytology specimens. Am Soc Clin Oncol Educ Book 2012:459-64. [PMID: 24451780 DOI: 10.14694/edbook_am.2012.32.44] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
During the past decade, substantial progress has been made in the characterization of molecular abnormalities in non-small cell carcinoma (NSCLC) tumors that are being used as molecular targets and predictive biomarkers for selection of targeted therapy. These recent advances in NSCLC targeted therapy require the analysis of a panel of molecular abnormalities in tumor specimens, including gene mutations (e.g., EGFR, KRAS, BRAF, DDR2), gene amplifications (e.g., MET, FGFR1), and fusions (e.g., EML4-ALK) by applying different methods to tumor tissue (biopsy) and cell (cytology) samples. However, the biopsy and cytology samples available for molecular testing in advanced metastatic NSCLC tumors are likely to be small specimens, including core needle biopsies and/or fine needle aspiration, which may limit the molecular and genomic analysis with currently available methods and technologies. In this process, the role of the pathologist is becoming increasingly important to adequately integrate both routine histopathologic assessment and molecular testing into the clinical pathology for proper tumor diagnosis and subsequent selection of the most appropriate therapy.
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Affiliation(s)
- Ignacio I Wistuba
- From the Departments of Pathology and Thoracic/Head and Neck Medical Oncology, University of Texas M. D. Anderson Cancer Center, Houston, TX
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Translational research in infectious disease: current paradigms and challenges ahead. Transl Res 2012; 159:430-53. [PMID: 22633095 PMCID: PMC3361696 DOI: 10.1016/j.trsl.2011.12.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Revised: 12/23/2011] [Accepted: 12/24/2012] [Indexed: 12/25/2022]
Abstract
In recent years, the biomedical community has witnessed a rapid scientific and technologic evolution after the development and refinement of high-throughput methodologies. Concurrently and consequentially, the scientific perspective has changed from the reductionist approach of meticulously analyzing the fine details of a single component of biology to the "holistic" approach of broadmindedly examining the globally interacting elements of biological systems. The emergence of this new way of thinking has brought about a scientific revolution in which genomics, proteomics, metabolomics, and other "omics" have become the predominant tools by which large amounts of data are amassed, analyzed, and applied to complex questions of biology that were previously unsolvable. This enormous transformation of basic science research and the ensuing plethora of promising data, especially in the realm of human health and disease, have unfortunately not been followed by a parallel increase in the clinical application of this information. On the contrary, the number of new potential drugs in development has been decreasing steadily, suggesting the existence of roadblocks that prevent the translation of promising research into medically relevant therapeutic or diagnostic application. In this article, we will review, in a noninclusive fashion, several recent scientific advancements in the field of translational research, with a specific focus on how they relate to infectious disease. We will also present a current picture of the limitations and challenges that exist for translational research, as well as ways that have been proposed by the National Institutes of Health to improve the state of this field.
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Key Words
- 2-de, 2-dimensional electrophoresis
- 2-d dige, 2-dimensional differential in-gel electrophoresis
- cf, cystic fibrosis
- ctsa, clinical and translational science awards program
- ebv, epstein-barr virus
- fda, u.s. food and drug administration
- gwas, genome-wide association studies
- hcv, hepatitis c virus
- hmp, human microbiome project
- hplc, high-pressure liquid chromatography
- lc, liquid chromatography
- lsb, laboratory of systems biology
- mab, monoclonal antibody
- mrm/srm, multiple reaction monitoring/selective reaction monitoring
- ms, mass spectrometry
- ms/ms, tandem mass spectrometry
- ncats, national center for advancing translational sciences
- ncrr, national center of research resources
- niaid, national institute of allergy and infectious disease
- nih, national institutes of health
- nme, new molecular entity
- nmr, nuclear magnetic resonance
- pbmc, peripheral blood mononuclear cell
- pcr, polymerase chain reaction
- prr, pathogen recognition receptor
- qqq, triple quadrupole mass spectrometry
- sars-cov, coronavirus associated with severe acute respiratory syndrome
- snp, single nucleotide polymorphism
- tb, tuberculosis
- uti, urinary tract infection
- yfv, yellow fever virus
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Milbury CA, Correll M, Quackenbush J, Rubio R, Makrigiorgos GM. COLD-PCR enrichment of rare cancer mutations prior to targeted amplicon resequencing. Clin Chem 2011; 58:580-9. [PMID: 22194627 DOI: 10.1373/clinchem.2011.176198] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
BACKGROUND Despite widespread interest in next-generation sequencing (NGS), the adoption of personalized clinical genomics and mutation profiling of cancer specimens is lagging, in part because of technical limitations. Tumors are genetically heterogeneous and often contain normal/stromal cells, features that lead to low-abundance somatic mutations that generate ambiguous results or reside below NGS detection limits, thus hindering the clinical sensitivity/specificity standards of mutation calling. We applied COLD-PCR (coamplification at lower denaturation temperature PCR), a PCR methodology that selectively enriches variants, to improve the detection of unknown mutations before NGS-based amplicon resequencing. METHODS We used both COLD-PCR and conventional PCR (for comparison) to amplify serially diluted mutation-containing cell-line DNA diluted into wild-type DNA, as well as DNA from lung adenocarcinoma and colorectal cancer samples. After amplification of TP53 (tumor protein p53), KRAS (v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog), IDH1 [isocitrate dehydrogenase 1 (NADP(+)), soluble], and EGFR (epidermal growth factor receptor) gene regions, PCR products were pooled for library preparation, bar-coded, and sequenced on the Illumina HiSeq 2000. RESULTS In agreement with recent findings, sequencing errors by conventional targeted-amplicon approaches dictated a mutation-detection limit of approximately 1%-2%. Conversely, COLD-PCR amplicons enriched mutations above the error-related noise, enabling reliable identification of mutation abundances of approximately 0.04%. Sequencing depth was not a large factor in the identification of COLD-PCR-enriched mutations. For the clinical samples, several missense mutations were not called with conventional amplicons, yet they were clearly detectable with COLD-PCR amplicons. Tumor heterogeneity for the TP53 gene was apparent. CONCLUSIONS As cancer care shifts toward personalized intervention based on each patient's unique genetic abnormalities and tumor genome, we anticipate that COLD-PCR combined with NGS will elucidate the role of mutations in tumor progression, enabling NGS-based analysis of diverse clinical specimens within clinical practice.
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Affiliation(s)
- Coren A Milbury
- Division of DNA Repair and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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Zhao X, Liu Q, Cai Q, Li Y, Xu C, Li Y, Li Z, Zhang X. Dr.VIS: a database of human disease-related viral integration sites. Nucleic Acids Res 2011; 40:D1041-6. [PMID: 22135288 PMCID: PMC3245036 DOI: 10.1093/nar/gkr1142] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Viral integration plays an important role in the development of malignant diseases. Viruses differ in preferred integration site and flanking sequence. Viral integration sites (VIS) have been found next to oncogenes and common fragile sites. Understanding the typical DNA features near VIS is useful for the identification of potential oncogenes, prediction of malignant disease development and assessing the probability of malignant transformation in gene therapy. Therefore, we have built a database of human disease-related VIS (Dr.VIS, http://www.scbit.org/dbmi/drvis) to collect and maintain human disease-related VIS data, including characteristics of the malignant disease, chromosome region, genomic position and viral–host junction sequence. The current build of Dr.VIS covers about 600 natural VIS of 5 oncogenic viruses representing 11 diseases. Among them, about 200 VIS have viral–host junction sequence.
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Affiliation(s)
- Xin Zhao
- School of Life Sciences and Technology, Tongji University, 1239 Siping Road, Shanghai, China
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