1
|
Ahting S, Nährlich L, Held I, Henn C, Krill A, Landwehr K, Meister J, Nährig S, Nolde A, Remke K, Ruppel R, Sauer-Heilborn A, Schebek M, Schopper G, Schulte-Hubbert B, Schwarz C, Smaczny C, Wege S, Hentschel J. Every CFTR variant counts - Target-capture based next-generation-sequencing for molecular diagnosis in the German CF Registry. J Cyst Fibros 2024; 23:774-781. [PMID: 37867076 DOI: 10.1016/j.jcf.2023.10.009] [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: 07/13/2023] [Revised: 10/01/2023] [Accepted: 10/09/2023] [Indexed: 10/24/2023]
Abstract
BACKGROUND In times of genotype guided therapy options, a total of 3.2 % of people with CF (pwCF) in the German CF Registry[1] only have one or no CFTR-variant detected after genetic analysis. Additionally, genetic data in the Registry can be documented as free text and can therefore be prone to error. In order to allow the greatest possible amount of pwCF access to modern therapies, we conducted a re-evaluation of free text entries and established a custom-whole-CFTR-locus NGS-approach for all pwCF who remained without genetic confirmation afterwards. METHODS To this end, we assembled 731 free text variants of 655 pwCF in the German CF Registry. All variants were evaluated using ClinVar, HGMD and CFTR1/2, corrected in the Registries' database and uploaded to ClinVar. PwCF whose diagnosis remained uncertain as well as additional pwCF or pwCFTR-RD that were assembled through a nationwide call for testing of unclear cases were offered genetic analysis. Samples were analysed using a target-capture based NGS-custom-design-panel covering the entire CFTR-locus. RESULTS Evaluation of free text variants led to the discovery of 43 variants not formerly reported in the context of CF. The Registries' dropdown list was extended by 497 variants and over 500 pwCF were provided with their most up-to-date genotype. Samples of 47 pwCF/pwCFTR-RD were sequenced via NGS with an overall success rate of 61.7 %, resulting in implementation of entire CFTR-genotyping into routine diagnostics. CONCLUSION Entire CFTR-genotyping can greatly increase the genetic diagnostic rate of pwCF/pwCFTR-RD and should be considered after inconspicuous CFTR screening panels in CFTR-diagnostics.
Collapse
Affiliation(s)
- Simone Ahting
- Institute of Human Genetics, University Medical Center Leipzig, Leipzig, Germany.
| | - Lutz Nährlich
- Department of Pediatrics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Inka Held
- Pediatric Practice Friesenweg, Cystic Fibrosis Center Altona, Hamburg, Germany
| | - Constance Henn
- Division of pediatric Pulmonology and Allergology, Hospital for children and adolescents, University Medical Center Leipzig, Leipzig, Germany
| | - Angelika Krill
- Division of Pneumology, University Medical Center Homburg, Homburg/Saar, Germany
| | - Kerstin Landwehr
- Division of Allergology and Pediatric Pneumology, University Children's Hospital Bethel, University Medical Center Ostwestfalen-Lippe, Bielefeld, Germany
| | - Jochen Meister
- Division of Pneumology, Allergology and Psychotherapy, Children's Hospital, Helios Hospital Aue, Aue, Germany
| | - Susanne Nährig
- Cystic Fibrosis Center for Adults, Med. Klinik V, University Hospital LMU, Munich, Germany
| | - Anna Nolde
- Division of Pneumology, II. Department of Medicine and University Transplant Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katharina Remke
- Department for General Paediatrics, Neonatology and Paediatric Cardiology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Renate Ruppel
- University Children's Hospital, University Medical Center Erlangen, Erlangen, Germany
| | | | - Martin Schebek
- Division of Pediatric Pneumology, Center for Pediatric and Women's Medicine Kassel, Kassel, Germany
| | - Gudrun Schopper
- University Children's Hospital Schwabing, Technical University of Munich, Munich, Germany
| | - Bernhard Schulte-Hubbert
- Department of medical clinic I, Medical Center Carl Gustav Carus, Technical University of Dresden, Dresden, Germany
| | - Carsten Schwarz
- Department Medicine, HMU-Health and Medical University Potsdam and Director CF Center Westbrandenburg, Division Cystic Fibrosis, Clinic Westbrandenburg, Potsdam, Germany
| | - Christina Smaczny
- Christiane Herzog CF-centre Frankfurt/Main, University Medical Center Frankfurt, Goethe-University Frankfurt, Frankfurt/Main, Germany
| | - Sabine Wege
- Cystic Fibrosis Center, Thoraxklinik Heidelberg, University Medical Center Heidelberg, Heidelberg, Germany
| | - Julia Hentschel
- Institute of Human Genetics, University Medical Center Leipzig, Leipzig, Germany
| |
Collapse
|
2
|
Popova L, Carabetta VJ. The use of next-generation sequencing in personalized medicine. ARXIV 2024:arXiv:2403.03688v1. [PMID: 38495572 PMCID: PMC10942477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The revolutionary progress in development of next-generation sequencing (NGS) technologies has made it possible to deliver accurate genomic information in a timely manner. Over the past several years, NGS has transformed biomedical and clinical research and found its application in the field of personalized medicine. Here we discuss the rise of personalized medicine and the history of NGS. We discuss current applications and uses of NGS in medicine, including infectious diseases, oncology, genomic medicine, and dermatology. We provide a brief discussion of selected studies where NGS was used to respond to wide variety of questions in biomedical research and clinical medicine. Finally, we discuss the challenges of implementing NGS into routine clinical use.
Collapse
Affiliation(s)
- Liya Popova
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden NJ, 08103
| | - Valerie J. Carabetta
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden NJ, 08103
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
Kim SM, Noh ES, Park JH, Park HD, Lee SY, Jang JH, Cho SY. A novel splicing variant in GALNS in mucopolysaccharidosis IVA and the necessity of re-evaluating primer sequences. Ann Hum Genet 2022; 86:361-368. [PMID: 36000290 DOI: 10.1111/ahg.12483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/21/2022] [Accepted: 07/25/2022] [Indexed: 11/27/2022]
Abstract
Mucopolysaccharidosis type IVA (MPS IVA; Morquio syndrome type A) is an autosomal recessive disorder caused by defects in the lysosomal hydrolase N-acetylgalactosamine-6-sulfatase (GALNS) gene, leading to progressive systemic skeletal dysplasia. Early diagnosis and early intervention with enzyme replacement therapy are crucial for improving outcomes in these patients. However, a relatively high number of patients are genetically undiagnosed due to high allelic heterogeneity and the absence of robust functional evidence for most variants of the GALNS gene. Herein, we report a novel intronic variant identified with RNA analysis and an allele dropout (ADO) event caused by a common benign variant in the primer-binding site in a Korean boy with MPS IVA. A 28-month-old boy presented with pectus carinatum, kyphoscoliosis, and joint hypermobility with multiple skeletal dysplasia involving the vertebrae and hip joint. Total urinary glycosaminoglycans were elevated with a predominant keratan sulfate fraction, and GALNS (EC 3.1.6.4) activity was significantly decreased in leukocytes. Sanger sequencing was performed; however, only one heterozygous intronic variant with uncertain clinical significance, c.566+3A > T (p.(?)), was identified. As the patient exhibited clinical and biochemical features of MPS IVA, we conducted whole genome sequencing (WGS) of the patient and his family to clarify the molecular diagnosis. WGS revealed a compound heterozygous genotype, c.1019G > A (p.(Gly340Asp)) and c.566+3A > T (p.(?)), in the GALNS gene. On mRNA sequencing, c.566+3A > T, was confirmed to cause exon 5 skipping and a premature stop codon. With subsequent investigation, we discovered that the variant, c.1019G > A, was undetected on initial sequencing because of ADO due to a common benign variant (rs3859024:G > C) at the primer annealing location. We present a novel intronic variant with a splicing defect in the GALNS gene and suggest that clinicians review primer sequences in cases not diagnosed on Sanger sequencing before progressing to diagnostic steps such as WGS.
Collapse
Affiliation(s)
- Sang-Mi Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Eu Seon Noh
- Department of Pediatrics, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jong-Ho Park
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Korea.,Clinical Genomics Center, Samsung Medical Center, Seoul, Korea
| | - Hyung-Doo Park
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Soo-Youn Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sung Yoon Cho
- Department of Pediatrics, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| |
Collapse
|
5
|
Durães C, Pereira Gomes C, Costa JL, Quagliata L. Demystifying the Discussion of Sequencing Panel Size in Oncology Genetic Testing. EUROPEAN MEDICAL JOURNAL 2022. [DOI: 10.33590/emj/22c9259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Clinical laboratories worldwide are implementing next-generation sequencing (NGS) to identify cancer genomic variants and ultimately improve patient outcomes. The ability to massively sequence the entire genome or exome of tumour cells has been critical to elucidating many complex biological questions. However, the depth of information obtained by these methods is strenuous to process in the clinical setting, making them currently unfeasible for broader adoption. Instead, targeted sequencing, usually on a selection of clinically relevant genes, represents the predominant approach that best balances accurate identification of genomic variants with high sensitivity and a good cost-effectiveness ratio. The information obtained from targeted sequencing can support diagnostic classification, guide therapeutic decisions, and provide prognostic insights. The use of targeted gene panels expedites sample processing, including data analysis, results interpretation, and medical reports generation, directly affecting patient management. The key decision factors for selecting sequencing methods and panel size in routine testing should include diagnostic yield and clinical utility, sample availability, and processing turnaround time.
Profiling by default all patients with late-stage cancer with large panels is not affordable for most healthcare systems and does not provide substantial clinical benefit at present. Balancing between understanding cancer biology, including patients in clinical trials, maximising testing, and ensuring a sustainable financial burden for society requires thorough consideration. This review provides an overview of the advantages and drawbacks of different sizes NGS panels for tumour molecular profiling and their clinical applicability.
Collapse
Affiliation(s)
- Cecília Durães
- Clinical Next-Generation Sequencing Division, Genetic Sciences Group, Thermo Fisher Scientific, Carlsbad, California, USA
| | | | - Jose Luis Costa
- Clinical Next-Generation Sequencing Division, Genetic Sciences Group, Thermo Fisher Scientific, Carlsbad, California, USA
| | - Luca Quagliata
- Clinical Next-Generation Sequencing Division, Genetic Sciences Group, Thermo Fisher Scientific, Carlsbad, California, USA
| |
Collapse
|
6
|
Circulating tumor cells and cell-free tumor DNA analyses in urothelial cancer using the LiquidBiopsy platform. Curr Urol 2022; 16:99-106. [PMID: 36570364 PMCID: PMC9782328 DOI: 10.1097/cu9.0000000000000091] [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: 03/15/2020] [Accepted: 04/15/2020] [Indexed: 12/27/2022] Open
Abstract
Background Emerging data suggested that liquid biopsy such as detection of circulating tumor cells (CTCs) and cell-free tumor DNA analysis augments the management of patients with urothelial cancer (UC). We presented our pilot experience of liquid biopsy using the Ion Torrent platform to detect CTCs and genomic alterations in UC. Materials and methods Blood or urine samples from 16 patients were subjected to CTC and plasma/urine cell-free tumor DNA isolation for next generation sequencing (NGS) using the Ion S5 system to detect mutations among 50 oncogenes on the Ion AmpliSeq Cancer Hotspot Panel. Results The Ion Torrent platform detected a higher number of CTCs than those in previous studies using the CellSearchTM system. Overall, mutations were detected in 13/16 (81.3%) patients with a median number of 18 (range 12-25). NGS isolated 17 hotspot mutations from 11 genes and 41 novel genomic alterations from 24 genes, some of which are supposed to be clinically actionable. Conclusions The Ion Torrent platform efficiently detected CTCs compared with previous reports. NGS with the present system also allowed for detection of gene alterations which are likely to be therapeutic targets and provided an attractive tool to guide personalized therapy for patients with advanced UC.
Collapse
|
7
|
Milbury CA, Creeden J, Yip WK, Smith DL, Pattani V, Maxwell K, Sawchyn B, Gjoerup O, Meng W, Skoletsky J, Concepcion AD, Tang Y, Bai X, Dewal N, Ma P, Bailey ST, Thornton J, Pavlick DC, Frampton GM, Lieber D, White J, Burns C, Vietz C. Clinical and analytical validation of FoundationOne®CDx, a comprehensive genomic profiling assay for solid tumors. PLoS One 2022; 17:e0264138. [PMID: 35294956 PMCID: PMC8926248 DOI: 10.1371/journal.pone.0264138] [Citation(s) in RCA: 122] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 02/03/2022] [Indexed: 12/14/2022] Open
Abstract
FoundationOne®CDx (F1CDx) is a United States (US) Food and Drug Administration (FDA)-approved companion diagnostic test to identify patients who may benefit from treatment in accordance with the approved therapeutic product labeling for 28 drug therapies. F1CDx utilizes next-generation sequencing (NGS)-based comprehensive genomic profiling (CGP) technology to examine 324 cancer genes in solid tumors. F1CDx reports known and likely pathogenic short variants (SVs), copy number alterations (CNAs), and select rearrangements, as well as complex biomarkers including tumor mutational burden (TMB) and microsatellite instability (MSI), in addition to genomic loss of heterozygosity (gLOH) in ovarian cancer. CGP services can reduce the complexity of biomarker testing, enabling precision medicine to improve treatment decision-making and outcomes for cancer patients, but only if test results are reliable, accurate, and validated clinically and analytically to the highest standard available. The analyses presented herein demonstrate the extensive analytical and clinical validation supporting the F1CDx initial and subsequent FDA approvals to ensure high sensitivity, specificity, and reliability of the data reported. The analytical validation included several in-depth evaluations of F1CDx assay performance including limit of detection (LoD), limit of blank (LoB), precision, and orthogonal concordance for SVs (including base substitutions [SUBs] and insertions/deletions [INDELs]), CNAs (including amplifications and homozygous deletions), genomic rearrangements, and select complex biomarkers. The assay validation of >30,000 test results comprises a considerable and increasing body of evidence that supports the clinical utility of F1CDx to match patients with solid tumors to targeted therapies or immunotherapies based on their tumor's genomic alterations and biomarkers. F1CDx meets the clinical needs of providers and patients to receive guideline-based biomarker testing, helping them keep pace with a rapidly evolving field of medicine.
Collapse
Affiliation(s)
- Coren A. Milbury
- Department Product Development, Cambridge, MA, United States of America
| | - James Creeden
- Global Medical Affairs, Basel, MA, United States of America
| | - Wai-Ki Yip
- Department Product Development, Cambridge, MA, United States of America
| | - David L. Smith
- Department of Franchise Development, Cambridge, MA, United States of America
| | - Varun Pattani
- Department Product Development, Cambridge, MA, United States of America
| | - Kristi Maxwell
- Department of Health Economic and Outcomes Research & Payer Policy, Reimbursement, Cambridge, MA, United States of America
| | - Bethany Sawchyn
- Department of Scientific and Medical Publications, Clinical Operations, Cambridge, MA, United States of America
| | - Ole Gjoerup
- Department of Scientific and Medical Publications, Clinical Operations, Cambridge, MA, United States of America
| | - Wei Meng
- Department Product Development, Cambridge, MA, United States of America
| | - Joel Skoletsky
- Department Product Development, Cambridge, MA, United States of America
| | | | - Yanhua Tang
- Department Product Development, Cambridge, MA, United States of America
| | - Xiaobo Bai
- Department Product Development, Cambridge, MA, United States of America
| | - Ninad Dewal
- Department Product Development, Cambridge, MA, United States of America
| | - Pei Ma
- Department Product Development, Cambridge, MA, United States of America
| | - Shannon T. Bailey
- Department Product Development, Cambridge, MA, United States of America
| | - James Thornton
- Department Product Development, Cambridge, MA, United States of America
| | - Dean C. Pavlick
- Department of Cancer Genomics, Cambridge, MA, United States of America
| | | | - Daniel Lieber
- Department of Computational Biology, Cambridge, MA, United States of America
| | - Jared White
- Department of Computational Biology, Cambridge, MA, United States of America
| | - Christine Burns
- Department Product Development, Cambridge, MA, United States of America
| | - Christine Vietz
- Department Product Development, Cambridge, MA, United States of America
| |
Collapse
|
8
|
Barbirou M, Miller A, Manjunath Y, Ramirez AB, Ericson NG, Staveley-O’Carroll KF, Mitchem JB, Warren WC, Chaudhuri AA, Huang Y, Li G, Tonellato PJ, Kaifi JT. Single Circulating-Tumor-Cell-Targeted Sequencing to Identify Somatic Variants in Liquid Biopsies in Non-Small-Cell Lung Cancer Patients. Curr Issues Mol Biol 2022; 44:750-763. [PMID: 35723337 PMCID: PMC8928994 DOI: 10.3390/cimb44020052] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 01/30/2022] [Accepted: 01/31/2022] [Indexed: 12/12/2022] Open
Abstract
Non-small-cell lung cancer (NSCLC) accounts for most cancer-related deaths worldwide. Liquid biopsy by a blood draw to detect circulating tumor cells (CTCs) is a tool for molecular profiling of cancer using single-cell and next-generation sequencing (NGS) technologies. The aim of the study was to identify somatic variants in single CTCs isolated from NSCLC patients by targeted NGS. Thirty-one subjects (20 NSCLC patients, 11 smokers without cancer) were enrolled for blood draws (7.5 mL). CTCs were identified by immunofluorescence, individually retrieved, and DNA-extracted. Targeted NGS was performed to detect somatic variants (single-nucleotide variants (SNVs) and insertions/deletions (Indels)) across 65 oncogenes and tumor suppressor genes. Cancer-associated variants were classified using OncoKB database. NSCLC patients had significantly higher CTC counts than control smokers (p = 0.0132; Mann–Whitney test). Analyzing 23 CTCs and 13 white blood cells across seven patients revealed a total of 644 somatic variants that occurred in all CTCs within the same subject, ranging from 1 to 137 per patient. The highest number of variants detected in ≥1 CTC within a patient was 441. A total of 18/65 (27.7%) genes were highly mutated. Mutations with oncogenic impact were identified in functional domains of seven oncogenes/tumor suppressor genes (NF1, PTCH1, TP53, SMARCB1, SMAD4, KRAS, and ERBB2). Single CTC-targeted NGS detects heterogeneous and shared mutational signatures within and between NSCLC patients. CTC single-cell genomics have potential for integration in NSCLC precision oncology.
Collapse
Affiliation(s)
- Mouadh Barbirou
- Center for Biomedical Informatics, Department of Health Management and Informatics, School of Medicine, University of Missouri, Columbia, MO 65212, USA; (M.B.); (A.M.); (P.J.T.)
| | - Amanda Miller
- Center for Biomedical Informatics, Department of Health Management and Informatics, School of Medicine, University of Missouri, Columbia, MO 65212, USA; (M.B.); (A.M.); (P.J.T.)
| | - Yariswamy Manjunath
- Department of Surgery, University of Missouri School of Medicine, Columbia, MO 65212, USA; (Y.M.); (K.F.S.-O.); (J.B.M.); (G.L.)
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65201, USA
| | | | | | - Kevin F. Staveley-O’Carroll
- Department of Surgery, University of Missouri School of Medicine, Columbia, MO 65212, USA; (Y.M.); (K.F.S.-O.); (J.B.M.); (G.L.)
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65201, USA
- Siteman Cancer Center, St. Louis, MO 63110, USA; (W.C.W.); (A.A.C.); (Y.H.)
| | - Jonathan B. Mitchem
- Department of Surgery, University of Missouri School of Medicine, Columbia, MO 65212, USA; (Y.M.); (K.F.S.-O.); (J.B.M.); (G.L.)
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65201, USA
- Siteman Cancer Center, St. Louis, MO 63110, USA; (W.C.W.); (A.A.C.); (Y.H.)
| | - Wesley C. Warren
- Siteman Cancer Center, St. Louis, MO 63110, USA; (W.C.W.); (A.A.C.); (Y.H.)
- Department of Animal Sciences and Surgery, Informatics and Data Sciences Institute, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Aadel A. Chaudhuri
- Siteman Cancer Center, St. Louis, MO 63110, USA; (W.C.W.); (A.A.C.); (Y.H.)
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yi Huang
- Siteman Cancer Center, St. Louis, MO 63110, USA; (W.C.W.); (A.A.C.); (Y.H.)
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Guangfu Li
- Department of Surgery, University of Missouri School of Medicine, Columbia, MO 65212, USA; (Y.M.); (K.F.S.-O.); (J.B.M.); (G.L.)
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65201, USA
- Siteman Cancer Center, St. Louis, MO 63110, USA; (W.C.W.); (A.A.C.); (Y.H.)
| | - Peter J. Tonellato
- Center for Biomedical Informatics, Department of Health Management and Informatics, School of Medicine, University of Missouri, Columbia, MO 65212, USA; (M.B.); (A.M.); (P.J.T.)
| | - Jussuf T. Kaifi
- Center for Biomedical Informatics, Department of Health Management and Informatics, School of Medicine, University of Missouri, Columbia, MO 65212, USA; (M.B.); (A.M.); (P.J.T.)
- Department of Surgery, University of Missouri School of Medicine, Columbia, MO 65212, USA; (Y.M.); (K.F.S.-O.); (J.B.M.); (G.L.)
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65201, USA
- Siteman Cancer Center, St. Louis, MO 63110, USA; (W.C.W.); (A.A.C.); (Y.H.)
- Correspondence:
| |
Collapse
|
9
|
Fernandes MGO, Cruz-Martins N, Machado JC, Costa JL, Hespanhol V. The value of cell-free circulating tumour DNA profiling in advanced non-small cell lung cancer (NSCLC) management. Cancer Cell Int 2021; 21:675. [PMID: 34915883 PMCID: PMC8680243 DOI: 10.1186/s12935-021-02382-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/30/2021] [Indexed: 01/04/2023] Open
Abstract
AbstractLiquid biopsy (LB) has boosted a remarkable change in the management of cancer patients by contributing to tumour genomic profiling. Plasma circulating cell-free tumour DNA (ctDNA) is the most widely searched tumour-related element for clinical application. Specifically, for patients with lung cancer, LB has revealed valuable to detect the diversity of targetable genomic alterations and to detect and monitor the emergence of resistance mechanisms. Furthermore, its non-invasive nature helps to overcome the difficulty in obtaining tissue samples, offering a comprehensive view about tumour diversity. However, the use of the LB to support diagnostic and therapeutic decisions still needs further clarification. In this sense, this review aims to provide a critical view of the clinical importance of plasma ctDNA analysis, the most widely applied LB, and its limitations while anticipating concepts that will intersect the present and future of LB in non-small cell lung cancer patients.
Graphical Abstract
Collapse
|
10
|
Dalurzo ML, Avilés-Salas A, Soares FA, Hou Y, Li Y, Stroganova A, Öz B, Abdillah A, Wan H, Choi YL. Testing for EGFR Mutations and ALK Rearrangements in Advanced Non-Small-Cell Lung Cancer: Considerations for Countries in Emerging Markets. Onco Targets Ther 2021; 14:4671-4692. [PMID: 34511936 PMCID: PMC8420791 DOI: 10.2147/ott.s313669] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/08/2021] [Indexed: 12/24/2022] Open
Abstract
The treatment of patients with advanced non-small-cell lung cancer (NSCLC) in recent years has been increasingly guided by biomarker testing. Testing has centered on driver genetic alterations involving the epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase (ALK) rearrangements. The presence of these mutations is predictive of response to targeted therapies such as EGFR tyrosine kinase inhibitors (TKIs) and ALK TKIs. However, there are substantial challenges for the implementation of biomarker testing, particularly in emerging countries. Understanding the barriers to testing in NSCLC will be key to improving molecular testing rates worldwide and patient outcomes as a result. In this article, we review EGFR mutations and ALK rearrangements as predictive biomarkers for NSCLC, discuss a selection of appropriate tests and review the literature with respect to the global uptake of EGFR and ALK testing. To help improve testing rates and unify procedures, we review our experiences with biomarker testing in China, South Korea, Russia, Turkey, Brazil, Argentina and Mexico, and propose a set of recommendations that pathologists from emerging countries can apply to assist with the diagnosis of NSCLC.
Collapse
Affiliation(s)
- Mercedes L Dalurzo
- Department of Pathology, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | | | | | - Yingyong Hou
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, People’s Republic of China
| | - Yuan Li
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, People’s Republic of China
| | - Anna Stroganova
- N.N. Blokhin National Medical Research Centre of Oncology, Russian Academy of Medical Sciences, Moscow, Russia
| | - Büge Öz
- Cerrahpaşa School of Medicine, Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | - Arif Abdillah
- Takeda Pharmaceuticals International AG – Singapore Branch, Singapore, Singapore
| | - Hui Wan
- Takeda Pharmaceuticals International AG – Singapore Branch, Singapore, Singapore
| | - Yoon-La Choi
- Department of Pathology and Translational Genomics, Samsung Medical Centre, Sungkyunkwan University School of Medicine, Seoul, South Korea
| |
Collapse
|
11
|
Zhu Y, Allard GM, Ericson NG, George TC, Kunder CA, Lowe AC. Identification and characterization of effusion tumor cells (ETCs) from remnant pleural effusion specimens. Cancer Cytopathol 2021; 129:893-906. [PMID: 34171181 DOI: 10.1002/cncy.22483] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/24/2021] [Accepted: 05/25/2021] [Indexed: 12/25/2022]
Abstract
BACKGROUND Cancer is a leading cause of death worldwide, and patients may have advanced disease when diagnosed. Targeted therapies guided by molecular subtyping of cancer can benefit patients significantly. Pleural effusions are frequently observed in patients with metastatic cancer and are routinely removed for therapeutic purposes; however, effusion specimens have not been recognized as typical substrates for clinical molecular testing because of frequent low tumor cellularity. METHODS Excess remnant pleural effusion samples (N = 25) from 21 patients with and without suspected malignancy were collected at Stanford Health Care between December 2019 and November 2020. Samples were processed into ThinPrep slides and underwent novel effusion tumor cell (ETC) analysis. The ETC results were compared with the original clinical diagnoses for accuracy. A subset of confirmed ETCs was further isolated and processed for molecular profiling to identify cancer driver mutations. All samples were obtained with Institutional Review Board approval. RESULTS The authors established novel quantitative standards to identify ETCs and detected epithelial malignancy with 89.5% sensitivity and 100% specificity in the pleural effusion samples. Molecular profiling of confirmed ETCs (pools of 5 cells evaluated) revealed key pathogenic mutations consistent with clinical molecular findings. CONCLUSIONS In this study, the authors developed a novel ETC-testing assay that detected epithelial malignancies in pleural effusions with high sensitivity and specificity. Molecular profiling of 5 ETCs showed promising concordance with the clinical molecular findings. To promote cancer subtyping and guide treatment, this ETC-testing assay will need to be validated in larger patient cohorts to facilitate integration into cytologic workflow.
Collapse
Affiliation(s)
- Yili Zhu
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California
| | - Grace M Allard
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California
| | | | | | - Christian A Kunder
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California
| | - Alarice C Lowe
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California
| |
Collapse
|
12
|
Belkadi A, Thareja G, Dadhania D, Lee JR, Muthukumar T, Snopkowski C, Li C, Halama A, Abdelkader S, Abdulla S, Mahmoud Y, Malek J, Suthanthiran M, Suhre K. Deep sequencing of DNA from urine of kidney allograft recipients to estimate donor/recipient-specific DNA fractions. PLoS One 2021; 16:e0249930. [PMID: 33857204 PMCID: PMC8049329 DOI: 10.1371/journal.pone.0249930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 03/27/2021] [Indexed: 11/19/2022] Open
Abstract
Kidney transplantation is the treatment of choice for patients with end-stage kidney failure, but transplanted allograft could be affected by viral and bacterial infections and by immune rejection. The standard test for the diagnosis of acute pathologies in kidney transplants is kidney biopsy. However, noninvasive tests would be desirable. Various methods using different techniques have been developed by the transplantation community. But these methods require improvements. We present here a cost-effective method for kidney rejection diagnosis that estimates donor/recipient-specific DNA fraction in recipient urine by sequencing urinary cell DNA. We hypothesized that in the no-pathology stage, the largest tissue types present in recipient urine are donor kidney cells, and in case of rejection, a larger number of recipient immune cells would be observed. Extensive in-silico simulation was used to tune the sequencing parameters: number of variants and depth of coverage. Sequencing of DNA mixture from 2 healthy individuals showed the method is highly predictive (maximum error < 0.04). We then demonstrated the insignificant impact of familial relationship and ethnicity using an in-house and public database. Lastly, we performed deep DNA sequencing of urinary cell pellets from 32 biopsy-matched samples representing two pathology groups: acute rejection (AR, 11 samples) and acute tubular injury (ATI, 12 samples) and 9 samples with no pathology. We found a significant association between the donor/recipient-specific DNA fraction in the two pathology groups compared to no pathology (P = 0.0064 for AR and P = 0.026 for ATI). We conclude that deep DNA sequencing of urinary cells from kidney allograft recipients offers a noninvasive means of diagnosing acute pathologies in the human kidney allograft.
Collapse
Affiliation(s)
- Aziz Belkadi
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| | - Gaurav Thareja
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| | - Darshana Dadhania
- Department of Transplantation Medicine, New-York Presbyterian Hospital-Weill Cornell Medicine, New York, United States of America
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, United States of America
| | - John R. Lee
- Department of Transplantation Medicine, New-York Presbyterian Hospital-Weill Cornell Medicine, New York, United States of America
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, United States of America
| | - Thangamani Muthukumar
- Department of Transplantation Medicine, New-York Presbyterian Hospital-Weill Cornell Medicine, New York, United States of America
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, United States of America
| | - Catherine Snopkowski
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, United States of America
| | - Carol Li
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, United States of America
| | - Anna Halama
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| | - Sara Abdelkader
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| | - Silvana Abdulla
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| | - Yasmin Mahmoud
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| | - Joel Malek
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| | - Manikkam Suthanthiran
- Department of Transplantation Medicine, New-York Presbyterian Hospital-Weill Cornell Medicine, New York, United States of America
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, United States of America
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| |
Collapse
|
13
|
Steele JL, Stevens RC, Cabrera OA, Bassill GJ, Cramer SM, Guzman F, Shuber AP. Novel CRISPR-based sequence specific enrichment methods for target loci and single base mutations. PLoS One 2020; 15:e0243781. [PMID: 33362267 PMCID: PMC7757808 DOI: 10.1371/journal.pone.0243781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/25/2020] [Indexed: 01/10/2023] Open
Abstract
The programmable sequence specificity of CRISPR has found uses in gene editing and diagnostics. This manuscript describes an additional application of CRISPR through a family of novel DNA enrichment technologies. CAMP (CRISPR Associated Multiplexed PCR) and cCAMP (chimeric CRISPR Associated Multiplexed PCR) utilize the sequence specificity of the Cas9/sgRNA complex to target loci for the ligation of a universal adapter that is used for subsequent amplification. cTRACE (chimeric Targeting Rare Alleles with CRISPR-based Enrichment) also applies this method to use Cas9/sgRNA to target loci for the addition of universal adapters, however it has an additional selection for specific mutations through the use of an allele-specific primer. These three methods can produce multiplex PCR that significantly reduces the optimization required for every target. The methods are also not specific to any downstream analytical platform. We additionally will present a mutation specific enrichment technology that is non-amplification based and leaves the DNA in its native state: TRACE (Targeting Rare Alleles with CRISPR-based Enrichment). TRACE utilizes the Cas9/sgRNA complex to sterically protect the ends of targeted sequences from exonuclease activity which digests both the normal variant as well as any off-target sequences.
Collapse
Affiliation(s)
| | | | - Oscar A. Cabrera
- Genetics Research LLC, Waltham, Massachusetts, United States of America
| | - Gary J. Bassill
- Genetics Research LLC, Waltham, Massachusetts, United States of America
| | - Sabrina M. Cramer
- Genetics Research LLC, Waltham, Massachusetts, United States of America
| | - Felipe Guzman
- Genetics Research LLC, Waltham, Massachusetts, United States of America
| | - Anthony P. Shuber
- Genetics Research LLC, Waltham, Massachusetts, United States of America
| |
Collapse
|
14
|
Jeong TD, Cho SY, Kim MW, Huh J. Significant allelic dropout phenomenon of Oncomine BRCA Research Assay on Ion Torrent S5. Clin Chem Lab Med 2020; 57:e124-e127. [PMID: 30367782 DOI: 10.1515/cclm-2018-0674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/02/2018] [Indexed: 11/15/2022]
Affiliation(s)
- Tae-Dong Jeong
- Department of Laboratory Medicine, College of Medicine, Ewha Womans University, Seoul, Republic of Korea
| | - Sung-Yup Cho
- Ewha Institute of Convergence Medicine, Ewha Womans University Mokdong Hospital, Seoul, Republic of Korea.,Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Mi-Wha Kim
- Department of Laboratory Medicine, College of Medicine, Ewha Womans University, Seoul, Republic of Korea
| | - Jungwon Huh
- Department of Laboratory Medicine, College of Medicine, Ewha Womans University, Seoul, Republic of Korea
| |
Collapse
|
15
|
Nasr Y, Bettoli M, El Demellawy D, Sekhon H, de Nanassy J. Sclerosing Pneumocytoma of the Lungs Arising in a Child With PTEN Mutation. Pediatr Dev Pathol 2019; 22:579-583. [PMID: 31166879 DOI: 10.1177/1093526619851423] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We report a rare case of sclerosing pneumocytoma occurring in a child with PTEN mutation. A 13-year-old female presented to the emergency department of an adult hospital following 2 to 3 days of upper respiratory tract infection symptoms. A primary lung lesion was discovered during her initial chest X-ray to rule out pneumonia. The patient underwent an uneventful thoracoscopic right upper lobe segmentectomy. The pathology demonstrated a sclerosing pneumocytoma of the lung. She tested positive for PTEN hamartoma tumor syndrome with a pathogenic variant at c.388 C > T. The PTEN mutation was also identified in the sclerosing pneumocytoma. Further study of PTEN mutation in sclerosing pneumocytoma is warranted.
Collapse
Affiliation(s)
- Youssef Nasr
- Biomedical Sciences Program, Faculty of Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Marcos Bettoli
- Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.,Department of Pediatric Surgery, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Dina El Demellawy
- Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.,Department of Pediatric Surgery, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Harman Sekhon
- Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.,Department of Pathology, The Ottawa Hospitals, Ottawa, Ontario, Canada
| | - Joseph de Nanassy
- Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.,Department of Pediatric Pathology, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| |
Collapse
|
16
|
Abstract
Since the discovery that DNA alterations initiate tumorigenesis, scientists and clinicians have been exploring ways to counter these changes with targeted therapeutics. The sequencing of tumor DNA was initially limited to highly actionable hot spots-areas of the genome that are frequently altered and have an approved matched therapy in a specific tumor type. Large-scale genome sequencing programs quickly developed technological improvements that enabled the deployment of whole-exome and whole-genome sequencing technologies at scale for pristine sample materials in research environments. However, the turning point for precision medicine in oncology was the innovations in clinical laboratories that improved turnaround time, depth of coverage, and the ability to reliably sequence archived, clinically available samples. Today, tumor genome sequencing no longer suffers from significant technical or financial hurdles, and the next opportunity for improvement lies in the optimal utilization of the technologies and data for many different tumor types.
Collapse
Affiliation(s)
- Kenna R Mills Shaw
- Khalifa Bin Zayed Institute for Personalized Cancer Therapy and Sheikh Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA;
| | - Anirban Maitra
- Khalifa Bin Zayed Institute for Personalized Cancer Therapy and Sheikh Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA;
| |
Collapse
|
17
|
Campbell WS, Carter AB, Cushman-Vokoun AM, Greiner TC, Dash RC, Routbort M, de Baca ME, Campbell JR. A Model Information Management Plan for Molecular Pathology Sequence Data Using Standards: From Sequencer to Electronic Health Record. J Mol Diagn 2019; 21:408-417. [PMID: 30797065 DOI: 10.1016/j.jmoldx.2018.12.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 11/10/2018] [Accepted: 12/04/2018] [Indexed: 10/27/2022] Open
Abstract
Incorporating genetic variant data into the electronic health record (EHR) in discrete computable fashion has vexed the informatics community for years. Genetic sequence test results are typically communicated by the molecular laboratory and stored in the EHR as textual documents. Although text documents are useful for human readability and initial use, they are not conducive for data retrieval and reuse. As a result, clinicians often struggle to find historical gene sequence results on a series of oncology patients within the EHR that might influence the care of the current patient. Second, identification of patients with specific mutation results in the EHR who are now eligible for new and/or changing therapy is not easily accomplished. Third, the molecular laboratory is challenged to monitor its sequencing processes for nonrandom process variation and other quality metrics. A novel approach to address each of these issues is presented and demonstrated. The authors use standard Health Level 7 laboratory result message formats in conjunction with international standards, Systematized Nomenclature of Medicine Clinical Terms and Human Genome Variant Society nomenclature, to represent, communicate, and store discrete gene sequence data within the EHR in a scalable fashion. This information management plan enables the support of the clinician at the point of care, enhances population management, and facilitates audits for maintaining laboratory quality.
Collapse
Affiliation(s)
- Walter S Campbell
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska.
| | - Alexis B Carter
- Department of Pathology, Children's Healthcare of Atlanta, Atlanta, Georgia
| | - Allison M Cushman-Vokoun
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Timothy C Greiner
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Rajesh C Dash
- Department of Pathology, Duke University Health System, Durham, North Carolina
| | - Mark Routbort
- Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - James R Campbell
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska
| |
Collapse
|
18
|
Reed EK, Steinmark L, Seibert DC, Edelman E. Somatic Testing: Implications for Targeted Treatment. Semin Oncol Nurs 2019; 35:22-33. [PMID: 30660356 DOI: 10.1016/j.soncn.2018.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
OBJECTIVE To provide an overview of key considerations for somatic testing for the purpose of targeting cancer treatment. DATA SOURCES Literature; research reports. CONCLUSION Genomic testing of cancer cells to identify variants that drive the carcinogenic process is becoming common in clinical settings. Providers and patients need to weigh the potential benefits of testing with technologic and logistic issues. IMPLICATIONS FOR NURSING PRACTICE Testing is available for thousands of genomic variants to identify one or more to guide targeted treatment. Oncology nurses need to understand the benefits and limitations of participating in patient-centered implementation of this testing.
Collapse
|
19
|
Pennell NA, Arcila ME, Gandara DR, West H. Biomarker Testing for Patients With Advanced Non-Small Cell Lung Cancer: Real-World Issues and Tough Choices. Am Soc Clin Oncol Educ Book 2019; 39:531-542. [PMID: 31099633 DOI: 10.1200/edbk_237863] [Citation(s) in RCA: 196] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Over the last decade, the treatment of patients with advanced non-small cell lung cancer (NSCLC) has become reliant on tissue and/or blood biomarkers to help guide treatment decisions. There are now multiple biomarker-defined patient subgroups, with evidence showing that treatment with targeted therapies has superior clinical outcomes when compared with traditional cytotoxic chemotherapy. However, rapid change in the field of precision oncology brings with it the challenge of translating recommendations into clinical practice. In this review, we discuss the major guidelines recommending biomarker testing in NSCLC, as well the logistical challenges to applying these guidelines to patients with NSCLC both in the United States and worldwide. The techniques commonly used for biomarker testing will be discussed, both for tissue- and blood-based biomarkers. Finally, we discuss the challenge of interpreting the results of biomarker testing and using these results to guide treatment decisions.
Collapse
Affiliation(s)
| | - Maria E Arcila
- 2 Memorial Sloan Kettering Cancer Institute, New York, NY
| | | | - Howard West
- 4 City of Hope Comprehensive Cancer Center, Duarte, CA
| |
Collapse
|
20
|
Gong J, Pan K, Fakih M, Pal S, Salgia R. Value-based genomics. Oncotarget 2018; 9:15792-15815. [PMID: 29644010 PMCID: PMC5884665 DOI: 10.18632/oncotarget.24353] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 01/19/2018] [Indexed: 12/18/2022] Open
Abstract
Advancements in next-generation sequencing have greatly enhanced the development of biomarker-driven cancer therapies. The affordability and availability of next-generation sequencers have allowed for the commercialization of next-generation sequencing platforms that have found widespread use for clinical-decision making and research purposes. Despite the greater availability of tumor molecular profiling by next-generation sequencing at our doorsteps, the achievement of value-based care, or improving patient outcomes while reducing overall costs or risks, in the era of precision oncology remains a looming challenge. In this review, we highlight available data through a pre-established and conceptualized framework for evaluating value-based medicine to assess the cost (efficiency), clinical benefit (effectiveness), and toxicity (safety) of genomic profiling in cancer care. We also provide perspectives on future directions of next-generation sequencing from targeted panels to whole-exome or whole-genome sequencing and describe potential strategies needed to attain value-based genomics.
Collapse
Affiliation(s)
- Jun Gong
- Department of Medical Oncology, City of Hope National Medical Center, Duarte, CA, USA
| | - Kathy Pan
- Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Marwan Fakih
- Department of Medical Oncology, City of Hope National Medical Center, Duarte, CA, USA
| | - Sumanta Pal
- Department of Medical Oncology, City of Hope National Medical Center, Duarte, CA, USA
| | - Ravi Salgia
- Medical Oncology and Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| |
Collapse
|
21
|
Shin S, Kim Y, Chul Oh S, Yu N, Lee ST, Rak Choi J, Lee KA. Validation and optimization of the Ion Torrent S5 XL sequencer and Oncomine workflow for BRCA1 and BRCA2 genetic testing. Oncotarget 2018; 8:34858-34866. [PMID: 28422718 PMCID: PMC5471017 DOI: 10.18632/oncotarget.16799] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/24/2017] [Indexed: 01/09/2023] Open
Abstract
In this study, we validated the analytical performance of BRCA1/2 sequencing using Ion Torrent's new bench-top sequencer with amplicon panel with optimized bioinformatics pipelines. Using 43 samples that were previously validated by Illumina's MiSeq platform and/or by Sanger sequencing/multiplex ligation-dependent probe amplification, we amplified the target with the Oncomine™ BRCA Research Assay and sequenced on Ion Torrent S5 XL (Thermo Fisher Scientific, Waltham, MA, USA). We compared two bioinformatics pipelines for optimal processing of S5 XL sequence data: the Torrent Suite with a plug-in Torrent Variant Caller (Thermo Fisher Scientific), and commercial NextGENe software (Softgenetics, State College, PA, USA). All expected 681 single nucleotide variants, 15 small indels, and three copy number variants were correctly called, except one common variant adjacent to a rare variant on the primer-binding site. The sensitivity, specificity, false positive rate, and accuracy for detection of single nucleotide variant and small indels of S5 XL sequencing were 99.85%, 100%, 0%, and 99.99% for the Torrent Variant Caller and 99.85%, 99.99%, 0.14%, and 99.99% for NextGENe, respectively. The reproducibility of variant calling was 100%, and the precision of variant frequency also showed good performance with coefficients of variation between 0.32 and 5.29%. We obtained highly accurate data through uniform and sufficient coverage depth over all target regions and through optimization of the bioinformatics pipeline. We confirmed that our platform is accurate and practical for diagnostic BRCA1/2 testing in a clinical laboratory.
Collapse
Affiliation(s)
- Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea.,Department of Laboratory Medicine, Hallym University College of Medicine, Kangnam Sacred Heart Hospital, Seoul, Republic of Korea
| | - Yoonjung Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seoung Chul Oh
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Nae Yu
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Kyung-A Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| |
Collapse
|
22
|
Reinholt SJ, Craighead HG. Microfluidic Device for Aptamer-Based Cancer Cell Capture and Genetic Mutation Detection. Anal Chem 2018; 90:2601-2608. [PMID: 29323871 DOI: 10.1021/acs.analchem.7b04120] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a microfluidic device for specifically capturing cancer cells and isolating their genomic DNA (gDNA) for specific amplification and sequence analysis. To capture cancer cells within the device, nucleic acid aptamers that specifically bind to cancer cells were immobilized within a channel containing micropillars designed to increase capture efficiency. The captured cells were lysed in situ, and their gDNA was isolated by physical entanglement within a second smaller-dimensioned micropillar array. This type of isolation allows the gDNA to be retained and purified within the channel and enables amplification and analysis to be performed on the gDNA without the loss of the original template. We developed a technique for selectively amplifying genes from whole gDNA using multiple displacement amplification. The amplified gene samples were sequenced, and the resulting sequence information was compared against the known wild-type gene to identify any mutations. We have tested cervical and ovarian cancer cells for mutations in the TP53 gene using this technology. This approach offers a way to monitor multiple genetic mutations in the same small population of cells, which is beneficial given the wide diversity in cancer cells, and therefore it requires very few cells to be extracted from a patient sample.
Collapse
Affiliation(s)
- Sarah J Reinholt
- School of Applied and Engineering Physics, Cornell University , Ithaca, New York 14853, United States
| | - Harold G Craighead
- School of Applied and Engineering Physics, Cornell University , Ithaca, New York 14853, United States
| |
Collapse
|
23
|
Memon AA, Zhang H, Gu Y, Luo Q, Shi J, Deng Z, Ma J, Ma W. EGFR with TKI-sensitive mutations in exon 19 is highly expressed and frequently detected in Chinese patients with lung squamous carcinoma. Onco Targets Ther 2017; 10:4607-4613. [PMID: 29075127 PMCID: PMC5609803 DOI: 10.2147/ott.s130051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Recently, tyrosine kinase inhibitors (TKIs) have been recommended as a first-line treatment for advanced non-small cell lung cancer (NSCLC), significantly improving the treatment outcomes of lung adenocarcinoma patients with the EGFR mutation. However, the application of TKIs for lung squamous cell carcinoma (SCC), the second largest pathological subtype of NSCLC, remains controversial because available data for the EGFR mutation profile and frequency in SCC patients are limited. In this study, 89 bronchoscopic-biopsy specimens from Chinese SCC male patients were assayed for EGFR exon 19 mutation, using improved polymerase chain reaction-denature gel gradient electrophoresis. EGFR exon 19 mutations were detected in 77 of 89 (86.5%) patients, and included six kinds of point mutations (11.6%) and two deletions (Del_747-751 [64.9%] and Del_746-751 [23.3%]). We found that the proportion of mutated EGFR varied from 0.98% to 100% in positive specimens and increased with the development of the disease. The difference of proportion between Stage IV patients and Stage II patients or Stage III patients was significant (P<0.001). These results provided valuable clues to explain the reason why patients harboring the same mutation responded distinctly to TKI treatment. Del_747-751 and Del_746-751 were the dominant mutations in the assayed SCC patients (76.4%), and both belong to the EGFR-TKI-sensitive mutation. Recently research demonstrated that Del_746-751 patients have better response to EGFR-TKI than Del_L747-751 patients. However, our study indicated that majority of SCC patients (55.5%) carried Del_ L747-751. We suggest that the unique clinic features of SCC should be further studied to reveal the mechanism of poorer treatment outcome of EGFR-TKI therapy, and that a better treatment plan and more specific, potent targeted drugs for lung SCC need to be developed.
Collapse
Affiliation(s)
- Aadil Ahmed Memon
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University
| | | | - Ye Gu
- Endoscope Department, Shanghai Pulmonary Hospital, Tongji University School of Medicine
| | - Qian Luo
- Core Facility and Technical Service Center, School of Life Science and Biotechnology, Shanghai Jiao Tong University
| | - Jiajun Shi
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University
| | - Jian Ma
- Pneumology Department, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wei Ma
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University
| |
Collapse
|
24
|
Poirot B, Doucet L, Benhenda S, Champ J, Meignin V, Lehmann-Che J. MET Exon 14 Alterations and New Resistance Mutations to Tyrosine Kinase Inhibitors: Risk of Inadequate Detection with Current Amplicon-Based NGS Panels. J Thorac Oncol 2017; 12:1582-1587. [PMID: 28779874 DOI: 10.1016/j.jtho.2017.07.026] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 07/12/2017] [Accepted: 07/17/2017] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Targeted therapies such as tyrosine kinase inhibitors (TKIs) have dramatically improved the treatment of lung adenocarcinoma, and detection of activating mutations of genes such as EGFR or anaplastic lymphoma kinase gene (ALK) is now mandatory in the clinical setting. However, additional targetable alterations are continuously being described and forcing us to adapt our detection methods. Here we have evaluated the ability of eight amplicon-based next-generation sequencing (NGS) panels to detect the recently described mesenchymal epithelial transition factor (MET) exon 14 (METex14) alterations or new mutations conferring resistance to TKIs. METHODS A total of 191 tumor samples from patients with NSCLC were screened for METex14 mutations by Sanger sequencing, and 62 additional cases were screened by Sanger sequencing and two amplicon-based NGS panels. In silico comparison of eight commercially available targeted NGS panels was also performed for the detection of METex14 alterations or ALK, ROS1, or EGFR resistance mutations. RESULTS NGS analysis of the positive METex14 cases revealed a false-negative case because of amplicon design. Moreover, in silico analysis revealed that none of the eight panels considered would be able to detect more than 63% of literature-reported cases of METex14 mutations and similar limitations would be expected with new ALK, ROS1, or EGFR resistance mutations. CONCLUSIONS We have illustrated major limitations of commercially available amplicon-based DNA NGS panels for detection of METex14 and recently described resistance mutations to TKIs. Documented choice of available panels and their frequent reevaluation are mandatory to deliver the most accurate data to the clinician for therapeutic decisions.
Collapse
Affiliation(s)
- Brigitte Poirot
- Molecular Oncology Unit, Saint-Louis Hospital, Assistance Publique Hôpitaux de Paris, Paris, France; Paris Diderot University, Sorbonne Paris Cité Paris, France; INSERM U944, Saint-Louis Hospital Paris, France
| | - Ludovic Doucet
- Department of Medical Oncology, Saint-Louis Hospital, Assistance Publique Hôpitaux de Paris, Paris, France
| | | | - Jérôme Champ
- Molecular Oncology Unit, Saint-Louis Hospital, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Véronique Meignin
- Department of Pathology, Saint-Louis Hospital, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Jacqueline Lehmann-Che
- Molecular Oncology Unit, Saint-Louis Hospital, Assistance Publique Hôpitaux de Paris, Paris, France; Paris Diderot University, Sorbonne Paris Cité Paris, France; INSERM U944, Saint-Louis Hospital Paris, France.
| |
Collapse
|
25
|
Mehrotra M, Duose DY, Singh RR, Barkoh BA, Manekia J, Harmon MA, Patel KP, Routbort MJ, Medeiros LJ, Wistuba II, Luthra R. Versatile ion S5XL sequencer for targeted next generation sequencing of solid tumors in a clinical laboratory. PLoS One 2017; 12:e0181968. [PMID: 28767674 PMCID: PMC5540534 DOI: 10.1371/journal.pone.0181968] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 07/10/2017] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Next generation sequencing based tumor tissue genotyping involves complex workflow and a relatively longer turnaround time. Semiconductor based next generation platforms varied from low throughput Ion PGM to high throughput Ion Proton and Ion S5XL sequencer. In this study, we compared Ion PGM and Ion Proton, with a new Ion S5XL NGS system for workflow scalability, analytical sensitivity and specificity, turnaround time and sequencing performance in a clinical laboratory. METHODS Eighteen solid tumor samples positive for various mutations as detected previously by Ion PGM and Ion Proton were selected for study. Libraries were prepared using DNA (range10-40ng) from micro-dissected formalin-fixed, paraffin-embedded (FFPE) specimens using the Ion Ampliseq Library Kit 2.0 for comprehensive cancer (CCP), oncomine comprehensive cancer (OCP) and cancer hotspot panel v2 (CHPv2) panel as per manufacturer's instructions. The CHPv2 were sequenced using Ion PGM whereas CCP and OCP were sequenced using Ion Proton respectively. All the three libraries were further sequenced individually (S540) or multiplexed (S530) using Ion S5XL. For S5XL, Ion chef was used to automate template preparation, enrichment of ion spheres and chip loading. Data analysis was performed using Torrent Suite 4.6 software on board S5XL and Ion Reporter. A limit of detection and reproducibility studies was performed using serially diluted DLD1 cell line. RESULTS A total of 241 variant calls (235 single nucleotide variants and 6 indels) expected in the studied cohort were successfully detected by S5XL with 100% and 97% concordance with Ion PGM and Proton, respectively. Sequencing run time was reduced from 4.5 to 2.5 hours with output range of 3-5 GB (S530) and 8-9.3Gb (S540). Data analysis time for the Ion S5XL is faster 1 h (S520), 2.5 h (S530) and 5 h (S540) chip, respectively as compared to the Ion PGM (3.5-5 h) and Ion Proton (8h). A limit detection of 5% allelic frequency was established along with high inter-run reproducibility. CONCLUSION Ion S5XL system simplified workflow in a clinical laboratory, was feasible for running smaller and larger panels on the same instrument, had a shorter turnaround time, and showed good concordance for variant calls with similar sensitivity and reproducibility as the Ion PGM and Proton.
Collapse
Affiliation(s)
- Meenakshi Mehrotra
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States of America.,Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States of America
| | - Dzifa Yawa Duose
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States of America
| | - Rajesh R Singh
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States of America
| | - Bedia A Barkoh
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States of America
| | - Jawad Manekia
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States of America
| | - Michael A Harmon
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States of America
| | - Keyur P Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States of America
| | - Mark J Routbort
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States of America
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States of America
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States of America
| | - Rajyalakshmi Luthra
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States of America.,Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States of America
| |
Collapse
|
26
|
Ozturk AR, Can T. A multiplex primer design algorithm for target amplification of continuous genomic regions. BMC Bioinformatics 2017. [PMID: 28629316 PMCID: PMC5477098 DOI: 10.1186/s12859-017-1716-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Background Targeted Next Generation Sequencing (NGS) assays are cost-efficient and reliable alternatives to Sanger sequencing. For sequencing of very large set of genes, the target enrichment approach is suitable. However, for smaller genomic regions, the target amplification method is more efficient than both the target enrichment method and Sanger sequencing. The major difficulty of the target amplification method is the preparation of amplicons, regarding required time, equipment, and labor. Multiplex PCR (MPCR) is a good solution for the mentioned problems. Results We propose a novel method to design MPCR primers for a continuous genomic region, following the best practices of clinically reliable PCR design processes. On an experimental setup with 48 different combinations of factors, we have shown that multiple parameters might effect finding the first feasible solution. Increasing the length of the initial primer candidate selection sequence gives better results whereas waiting for a longer time to find the first feasible solution does not have a significant impact. Conclusions We generated MPCR primer designs for the HBB whole gene, MEFV coding regions, and human exons between 2000 bp to 2100 bp-long. Our benchmarking experiments show that the proposed MPCR approach is able produce reliable NGS assay primers for a given sequence in a reasonable amount of time.
Collapse
Affiliation(s)
- Ahmet Rasit Ozturk
- Middle East Technical University, Informatics Institute, Ankara, Turkey.
| | - Tolga Can
- Department of Computer Engineering, Middle East Technical University, Ankara, Turkey
| |
Collapse
|
27
|
Silva FC, Torrezan GT, Brianese RC, Stabellini R, Carraro DM. Pitfalls in genetic testing: a case of a SNP in primer-annealing region leading to allele dropout in BRCA1. Mol Genet Genomic Med 2017; 5:443-447. [PMID: 28717669 PMCID: PMC5511807 DOI: 10.1002/mgg3.295] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 03/27/2017] [Accepted: 03/30/2017] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Hereditary breast and ovarian cancer is characterized by mutations in BRCA1 or BRCA2 genes and PCR-based screening techniques, such as capillary sequencing and next-generation sequencing (NGS), are considered gold standard methods for detection of pathogenic mutations in these genes. Single-nucleotide polymorphisms (SNPs) constitute a vast source of variation in the human genome and represent a risk for misdiagnosis in genetic testing, since the presence of a SNP in primer-annealing sites may cause false negative results due to allele dropout. However, few reports are available and the frequency of this phenomenon in diagnostic assays remains unknown. METHODS AND RESULTS In this article, we investigated the causes of a false negative capillary sequencing result in BRCA1 involving a mother-daughter dyad. Using several molecular strategies, including different DNA polymerases, primer redesign, allele-specific PCR and NGS, we established that the initial misdiagnosis was caused by a SNP located in the primer-annealing region, leading to allele dropout of the mutated allele. CONCLUSION Assuming that this problem can also occur in any PCR-based method that are widely used in diagnostic settings, the clinical report presented here draws attention for one of the limitations of genetic testing in general, for which medical and laboratory communities need to be aware.
Collapse
Affiliation(s)
- Felipe Carneiro Silva
- Laboratory of Genomics and Molecular BiologyInternational Research CenterAC Camargo Cancer CenterSão PauloBrazil
| | - Giovana Tardin Torrezan
- Laboratory of Genomics and Molecular BiologyInternational Research CenterAC Camargo Cancer CenterSão PauloBrazil
| | - Rafael Canfield Brianese
- Laboratory of Genomics and Molecular BiologyInternational Research CenterAC Camargo Cancer CenterSão PauloBrazil
| | - Raquel Stabellini
- Genomic Diagnostics LaboratoryAnatomic Pathologic DepartmentAC Camargo Cancer CenterSão PauloBrazil
| | - Dirce Maria Carraro
- Laboratory of Genomics and Molecular BiologyInternational Research CenterAC Camargo Cancer CenterSão PauloBrazil.,Genomic Diagnostics LaboratoryAnatomic Pathologic DepartmentAC Camargo Cancer CenterSão PauloBrazil
| |
Collapse
|
28
|
Cabanillas R, Diñeiro M, Castillo D, Pruneda PC, Penas C, Cifuentes GA, de Vicente Á, Durán NS, Álvarez R, Ordóñez GR, Cadiñanos J. A novel molecular diagnostics platform for somatic and germline precision oncology. Mol Genet Genomic Med 2017; 5:336-359. [PMID: 28717660 PMCID: PMC5511795 DOI: 10.1002/mgg3.291] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 03/13/2017] [Accepted: 03/15/2017] [Indexed: 12/28/2022] Open
Abstract
Background Next‐generation sequencing (NGS) opens new options in clinical oncology, from therapy selection to genetic counseling. However, realization of this potential not only requires succeeding in the bioinformatics and interpretation of the results, but also in their integration into the clinical practice. We have developed a novel NGS diagnostic platform aimed at detecting (1) somatic genomic alterations associated with the response to approved targeted cancer therapies and (2) germline mutations predisposing to hereditary malignancies. Methods Next‐generation sequencing libraries enriched in the exons of 215 cancer genes (97 for therapy selection and 148 for predisposition, with 30 informative for both applications), as well as selected introns from 17 genes involved in drug‐related rearrangements, were prepared from 39 tumors (paraffin‐embedded tissues/cytologies), 36 germline samples (blood) and 10 cell lines using hybrid capture. Analysis of NGS results was performed with specifically developed bioinformatics pipelines. Results The platform detects single‐nucleotide variants (SNVs) and insertions/deletions (indels) with sensitivity and specificity >99.5% (allelic frequency ≥0.1), as well as copy‐number variants (CNVs) and rearrangements. Somatic testing identified tailored approved targeted drugs in 35/39 tumors (89.74%), showing a diagnostic yield comparable to that of leading commercial platforms. A somatic EGFR p.E746_S752delinsA mutation in a mediastinal metastasis from a breast cancer prompted its anatomopathologic reassessment, its definite reclassification as a lung cancer and its treatment with gefitinib (partial response sustained for 15 months). Testing of 36 germline samples identified two pathogenic mutations (in CDKN2A and BRCA2). We propose a strategy for interpretation and reporting of results adaptable to the aim of the request, the availability of tumor and/or normal samples and the scope of the informed consent. Conclusion With an adequate methodology, it is possible to translate to the clinical practice the latest advances in precision oncology, integrating under the same platform the identification of somatic and germline genomic alterations.
Collapse
Affiliation(s)
- Rubén Cabanillas
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.Avda. Richard Grandío s/n33193OviedoSpain
| | - Marta Diñeiro
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.Avda. Richard Grandío s/n33193OviedoSpain
| | - David Castillo
- Disease Research And Medicine (DREAMgenics) S. L.Vivero Empresarial de Ciencias de la SaludC/Colegio Santo Domingo de Guzmán s/n33011OviedoSpain
| | - Patricia C Pruneda
- Disease Research And Medicine (DREAMgenics) S. L.Vivero Empresarial de Ciencias de la SaludC/Colegio Santo Domingo de Guzmán s/n33011OviedoSpain
| | - Cristina Penas
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.Avda. Richard Grandío s/n33193OviedoSpain
| | - Guadalupe A Cifuentes
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.Avda. Richard Grandío s/n33193OviedoSpain
| | - Álvaro de Vicente
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.Avda. Richard Grandío s/n33193OviedoSpain
| | - Noelia S Durán
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.Avda. Richard Grandío s/n33193OviedoSpain
| | - Rebeca Álvarez
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.Avda. Richard Grandío s/n33193OviedoSpain
| | - Gonzalo R Ordóñez
- Disease Research And Medicine (DREAMgenics) S. L.Vivero Empresarial de Ciencias de la SaludC/Colegio Santo Domingo de Guzmán s/n33011OviedoSpain
| | - Juan Cadiñanos
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.Avda. Richard Grandío s/n33193OviedoSpain
| |
Collapse
|
29
|
Albitar AZ, Ma W, Albitar M. Wild-type Blocking PCR Combined with Direct Sequencing as a Highly Sensitive Method for Detection of Low-Frequency Somatic Mutations. J Vis Exp 2017. [PMID: 28447972 DOI: 10.3791/55130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Accurate detection and identification of low frequency mutations can be problematic when assessing residual disease after therapy, screening for emerging resistance mutations during therapy, or when patients have few circulating tumor cells. Wild-type blocking PCR followed by sequencing analysis offers high sensitivity, flexibility, and simplicity as a methodology for detecting these low frequency mutations. By adding a custom designed locked nucleic acid oligonucleotide to a new or previously established conventional PCR based sequencing assay, sensitivities of approximately 1 mutant allele in a background of 1,000 WT alleles can be achieved (1:1,000). Sequencing artifacts associated with deamination events commonly found in formalin fixed paraffin embedded tissues can be partially remedied by the use of uracil DNA glycosylase during extraction steps. The optimized protocol here is specific for detecting MYD88 mutation, but can serve as a template to design any WTB-PCR assay. Advantages of the WTB-PCR assay over other commonly utilized assays for the detection of low frequency mutations including allele specific PCR and real-time quantitative PCR include fewer occurrences of false positives, greater flexibility and ease of implementation, and the ability to detect both known and unknown mutations.
Collapse
|
30
|
Stroncek DF, Butterfield LH, Cannarile MA, Dhodapkar MV, Greten TF, Grivel JC, Kaufman DR, Kong HH, Korangy F, Lee PP, Marincola F, Rutella S, Siebert JC, Trinchieri G, Seliger B. Systematic evaluation of immune regulation and modulation. J Immunother Cancer 2017; 5:21. [PMID: 28331613 PMCID: PMC5359947 DOI: 10.1186/s40425-017-0223-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 02/10/2017] [Indexed: 02/06/2023] Open
Abstract
Cancer immunotherapies are showing promising clinical results in a variety of malignancies. Monitoring the immune as well as the tumor response following these therapies has led to significant advancements in the field. Moreover, the identification and assessment of both predictive and prognostic biomarkers has become a key component to advancing these therapies. Thus, it is critical to develop systematic approaches to monitor the immune response and to interpret the data obtained from these assays. In order to address these issues and make recommendations to the field, the Society for Immunotherapy of Cancer reconvened the Immune Biomarkers Task Force. As a part of this Task Force, Working Group 3 (WG3) consisting of multidisciplinary experts from industry, academia, and government focused on the systematic assessment of immune regulation and modulation. In this review, the tumor microenvironment, microbiome, bone marrow, and adoptively transferred T cells will be used as examples to discuss the type and timing of sample collection. In addition, potential types of measurements, assays, and analyses will be discussed for each sample. Specifically, these recommendations will focus on the unique collection and assay requirements for the analysis of various samples as well as the high-throughput assays to evaluate potential biomarkers.
Collapse
Affiliation(s)
- David F Stroncek
- Department of Transfusion Medicine, National Institutes of Health, 10 Center Drive, Building 10, Room 3C720, Bethesda, MD 20892 USA
| | - Lisa H Butterfield
- Department of Medicine, Surgery and Immunology, University of Pittsburgh Cancer Institute, 5117 Centre Avenue, Pittsburgh, PA 15213 USA
| | - Michael A Cannarile
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Munich, Nonnenwald 2, 82377 Penzberg, Germany
| | - Madhav V Dhodapkar
- Department of Hematology & Immunobiology, Yale University, 333 Cedar Street, Box 208021, New Haven, CT 06510 USA
| | - Tim F Greten
- GI-Malignancy Section, Thoracic and GI Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 10 Room 12 N226, 9000 Rockville, Bethesda, MD 20892 USA
| | - Jean Charles Grivel
- Division of Translational Medicine, Sidra Medical and Research Center, PO Box 26999, Al Luqta Street, Doha, Qatar
| | - David R Kaufman
- Merck Research Laboratories, PO Box 1000, UG 3CD28, North Wales, PA 19454 USA
| | - Heidi H Kong
- Dermatology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 10, MSC 1908, Bethesda, MD 20892-1908 USA
| | - Firouzeh Korangy
- GI-Malignancy Section, Thoracic and GI Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 10 Room 12 N226, 9000 Rockville, Bethesda, MD 20892 USA
| | - Peter P Lee
- Department of Immuno-Oncology, City of Hope, 1500 East Duarte Road, Duarte, CA 91010 USA
| | - Francesco Marincola
- Division of Translational Medicine, Sidra Medical and Research Center, PO Box 26999, Al Luqta Street, Doha, Qatar
| | - Sergio Rutella
- The John van Geest Cancer Research Centre, Nottingham Trent University, Clifton Campus, Nottingham, NG11 8NS UK
| | - Janet C Siebert
- CytoAnalytics, 3500 South Albion Street, Cherry Hills Village, CO 80113 USA
| | - Giorgio Trinchieri
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 37/Room 4146, Bethesda, MD 20892 USA
| | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, Halle, Germany
| |
Collapse
|
31
|
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.
Collapse
|
32
|
A Targeted High-Throughput Next-Generation Sequencing Panel for Clinical Screening of Mutations, Gene Amplifications, and Fusions in Solid Tumors. J Mol Diagn 2017; 19:255-264. [DOI: 10.1016/j.jmoldx.2016.09.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 09/20/2016] [Accepted: 09/29/2016] [Indexed: 11/22/2022] Open
|
33
|
Sheikine Y, Kuo FC, Lindeman NI. Clinical and Technical Aspects of Genomic Diagnostics for Precision Oncology. J Clin Oncol 2017; 35:929-933. [PMID: 28297627 DOI: 10.1200/jco.2016.70.7539] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The emergence of precision medicine has been predicated on significant recent advances in diagnostic technology, particularly the advent of next-generation sequencing (NGS). Although the chemical technology underlying NGS is complex, and the computational biology expertise required to build systems to facilely interpret the results is highly specialized, the variables involved in designing and deploying a genomic testing program for cancer can be readily understood and applied by understanding several basic considerations. In this review, we present key strategic decisions required to optimize a genomic testing program and summarize the technical aspects of different technologies that render those methods more or less suitable for different types of programs.
Collapse
Affiliation(s)
- Yuri Sheikine
- Yuri Sheikine, Beth Israel Deaconess Medical Center, Harvard Medical School; and Frank C. Kuo and Neal I. Lindeman, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Frank C Kuo
- Yuri Sheikine, Beth Israel Deaconess Medical Center, Harvard Medical School; and Frank C. Kuo and Neal I. Lindeman, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Neal I Lindeman
- Yuri Sheikine, Beth Israel Deaconess Medical Center, Harvard Medical School; and Frank C. Kuo and Neal I. Lindeman, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| |
Collapse
|
34
|
Shimoda Y, Nagashima T, Urakami K, Tanabe T, Saito J, Naruoka A, Serizawa M, Mochizuki T, Ohshima K, Ohnami S, Ohnami S, Kusuhara M, Yamaguchi K. Integrated next-generation sequencing analysis of whole exome and 409 cancer-related genes. Biomed Res 2017; 37:367-379. [PMID: 28003584 DOI: 10.2220/biomedres.37.367] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The use of next-generation sequencing (NGS) techniques to analyze the genomes of cancer cells has identified numerous genomic alterations, including single-base substitutions, small insertions and deletions, amplification, recombination, and epigenetic modifications. NGS contributes to the clinical management of patients as well as new discoveries that identify the mechanisms of tumorigenesis. Moreover, analysis of gene panels targeting actionable mutations enhances efforts to optimize the selection of chemotherapeutic regimens. However, whole genome sequencing takes several days and costs at least $10,000, depending on sequence coverage. Therefore, laboratories with relatively limited resources must employ a more economical approach. For this purpose, we conducted an integrated nucleotide sequence analysis of a panel of 409-cancer related genes (409-CRG) combined with whole exome sequencing (WES). Analysis of the 409-CRG panel detected low-frequency variants with high sensitivity, and WES identified moderate and high frequency somatic variants as well as germline variants.
Collapse
Affiliation(s)
- Yuji Shimoda
- Cancer Diagnostics Reseach Division, Shizuoka Cancer Center Research Institute
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Jung HS, Lefferts JA, Tsongalis GJ. Utilization of the oncoscan microarray assay in cancer diagnostics. ACTA ACUST UNITED AC 2017. [DOI: 10.1186/s41241-016-0007-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
36
|
High-density array-CGH with targeted NGS unmask multiple noncontiguous minute deletions on chromosome 3p21 in mesothelioma. Proc Natl Acad Sci U S A 2016; 113:13432-13437. [PMID: 27834213 DOI: 10.1073/pnas.1612074113] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We used a custom-made comparative genomic hybridization array (aCGH; average probe interval 254 bp) to screen 33 malignant mesothelioma (MM) biopsies for somatic copy number loss throughout the 3p21 region (10.7 Mb) that harbors 251 genes, including BRCA1 (breast cancer 1)-associated protein 1 (BAP1), the most commonly mutated gene in MM. We identified frequent minute biallelic deletions (<3 kb) in 46 of 251 genes: four were cancer-associated genes: SETD2 (SET domain-containing protein 2) (7 of 33), BAP1 (8 of 33), PBRM1 (polybromo 1) (3 of 33), and SMARCC1 (switch/sucrose nonfermentable- SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily c, member 1) (2 of 33). These four genes were further investigated by targeted next-generation sequencing (tNGS), which revealed sequence-level mutations causing biallelic inactivation. Combined high-density aCGH and tNGS revealed biallelic gene inactivation in SETD2 (9 of 33, 27%), BAP1 (16 of 33, 48%), PBRM1 (5 of 33, 15%), and SMARCC1 (2 of 33, 6%). The incidence of genetic alterations detected is much higher than reported in the literature because minute deletions are not detected by NGS or commercial aCGH. Many of these minute deletions were not contiguous, but rather alternated with segments showing oscillating copy number changes along the 3p21 region. In summary, we found that in MM: (i) multiple minute simultaneous biallelic deletions are frequent in chromosome 3p21, where they occur as distinct events involving multiple genes; (ii) in addition to BAP1, mutations of SETD2, PBRM1, and SMARCC1 are frequent in MM; and (iii) our results suggest that high-density aCGH combined with tNGS provides a more precise estimate of the frequency and types of genes inactivated in human cancer than approaches based exclusively on NGS strategy.
Collapse
|
37
|
Khotskaya YB, Mills GB, Mills Shaw KR. Next-Generation Sequencing and Result Interpretation in Clinical Oncology: Challenges of Personalized Cancer Therapy. Annu Rev Med 2016; 68:113-125. [PMID: 27813876 DOI: 10.1146/annurev-med-102115-021556] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The tools of next-generation sequencing (NGS) technology, such as targeted sequencing of candidate cancer genes and whole-exome and -genome sequencing, coupled with encouraging clinical results based on the use of targeted therapeutics and biomarker-guided clinical trials, are fueling further technological advancements of NGS technology. However, NGS data interpretation is associated with challenges that must be overcome to promote the techniques' effective integration into clinical oncology practice. Specifically, sequencing of a patient's tumor often yields 30-65 somatic variants, but most of these variants are "passenger" mutations that are phenotypically neutral and thus not targetable. Therefore, NGS data must be interpreted by multidisciplinary decision-support teams to determine mutation actionability and identify potential "drivers," so that the treating physician can prioritize what clinical decisions can be pursued in order to provide cancer therapy that is personalized to the patient and his or her unique genome.
Collapse
Affiliation(s)
| | - Gordon B Mills
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy.,Department of Systems Biology, University of Texas, MD Anderson Cancer Center, Houston, Texas 77030;
| | - Kenna R Mills Shaw
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy
| |
Collapse
|
38
|
Eijkelenboom A, Kamping EJ, Kastner-van Raaij AW, Hendriks-Cornelissen SJ, Neveling K, Kuiper RP, Hoischen A, Nelen MR, Ligtenberg MJ, Tops BB. Reliable Next-Generation Sequencing of Formalin-Fixed, Paraffin-Embedded Tissue Using Single Molecule Tags. J Mol Diagn 2016; 18:851-863. [DOI: 10.1016/j.jmoldx.2016.06.010] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 05/04/2016] [Accepted: 06/08/2016] [Indexed: 10/21/2022] Open
|
39
|
Masumura K, Toyoda-Hokaiwado N, Ukai A, Gondo Y, Honma M, Nohmi T. Dose-dependent de novo germline mutations detected by whole-exome sequencing in progeny of ENU-treated male gpt delta mice. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2016; 810:30-39. [DOI: 10.1016/j.mrgentox.2016.09.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 09/20/2016] [Accepted: 09/27/2016] [Indexed: 01/06/2023]
|
40
|
Abstract
The rise of genomically targeted therapies and immunotherapy has revolutionized the practice of oncology in the last 10–15 years. At the same time, new technologies and the electronic health record (EHR) in particular have permeated the oncology clinic. Initially designed as billing and clinical documentation systems, EHR systems have not anticipated the complexity and variety of genomic information that needs to be reviewed, interpreted, and acted upon on a daily basis. Improved integration of cancer genomic data with EHR systems will help guide clinician decision making, support secondary uses, and ultimately improve patient care within oncology clinics. Some of the key factors relating to the challenge of integrating cancer genomic data into EHRs include: the bioinformatics pipelines that translate raw genomic data into meaningful, actionable results; the role of human curation in the interpretation of variant calls; and the need for consistent standards with regard to genomic and clinical data. Several emerging paradigms for integration are discussed in this review, including: non-standardized efforts between individual institutions and genomic testing laboratories; “middleware” products that portray genomic information, albeit outside of the clinical workflow; and application programming interfaces that have the potential to work within clinical workflow. The critical need for clinical-genomic knowledge bases, which can be independent or integrated into the aforementioned solutions, is also discussed.
Collapse
Affiliation(s)
- Jeremy L Warner
- Department of Medicine, Division of Hematology/Oncology, Vanderbilt University, Nashville, TN, USA. .,Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, 37232, USA. .,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
| | - Sandeep K Jain
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, 37232, USA.,Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Mia A Levy
- Department of Medicine, Division of Hematology/Oncology, Vanderbilt University, Nashville, TN, USA.,Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, 37232, USA.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| |
Collapse
|
41
|
Biomarkers of genome instability and cancer epigenetics. Tumour Biol 2016; 37:13029-13038. [DOI: 10.1007/s13277-016-5278-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 07/15/2016] [Indexed: 02/06/2023] Open
|
42
|
Evaluation of an amplicon-based next-generation sequencing panel for detection of BRCA1 and BRCA2 genetic variants. Breast Cancer Res Treat 2016; 158:433-40. [PMID: 27383479 DOI: 10.1007/s10549-016-3891-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 06/27/2016] [Indexed: 01/15/2023]
Abstract
The recent advances in the next-generation sequencing (NGS) technology have enabled fast, accurate, and cost-effective genetic testing. Here, we evaluated the performance of a targeted NGS panel for BRCA1/2 sequencing and confirmed its applicability in routine clinical diagnostics. We tested samples from 88 patients using the TruSeq custom panel (Illumina Inc, USA) and a MiSeq sequencer (Illumina) and compared the results to the outcomes of conventional Sanger sequencing. All 1015 sequence variations identified by Sanger sequencing were detected by NGS, except for one missense variant that might have been missed due to a rare mutation on a primer-binding site. One deletion variation, c.1909 + 12delT of BRCA2, was falsely called in all samples due to a homopolymer error. In addition, seven different single-nucleotide substitutions with low variant frequencies (range: 16.2-33.3 %) were falsely called by NGS. In a separate batch, 10 different false-positive variations were found in five samples. The overall sensitivity and positive predictive value of NGS were estimated to be 99.9 and 87.5 %, respectively. The false-positive results could be excluded by setting quality and alternative allele ratio filters and/or by visual inspection using the IGV software. Targeted NGS panel for BRCA1 and BRCA2 showed an excellent agreement with Sanger sequencing results. We therefore conclude that this NGS panel can be used for routine diagnostic method in a clinical genetic laboratory.
Collapse
|
43
|
Abstract
Next-generation sequencing (NGS) has been rapidly integrated into molecular pathology, dramatically increasing the breadth genomic of information available to oncologists and their patients. This review will explore the ways in which this new technology is currently applied to bolster care for patients with solid tumors and hematological malignancies, focusing on practices and guidelines for assessing the technical validity and clinical utility of DNA variants identified during clinical NGS oncology testing.
Collapse
Affiliation(s)
- Samuel P Strom
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| |
Collapse
|