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Hanbazazh M, Morlote D, Mackinnon AC, Harada S. Utility of Single-Gene Testing in Cancer Specimens. Clin Lab Med 2022; 42:385-394. [DOI: 10.1016/j.cll.2022.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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2
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Quindipan C, Cotter JA, Ji J, Mitchell WG, Moke DJ, Navid F, Thomas SM, VanHirtum-Das M, Wang L, Saitta SC, Biegel JA, Hiemenz MC. Custom Pediatric Oncology Next-Generation Sequencing Panel Identifies Somatic Mosaicism in Archival Tissue and Enhances Targeted Clinical Care. Pediatr Neurol 2021; 114:55-59. [PMID: 33221597 DOI: 10.1016/j.pediatrneurol.2020.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/06/2020] [Accepted: 09/27/2020] [Indexed: 11/16/2022]
Abstract
BACKGROUND Disorders in the PIK3CA-related overgrowth spectrum because of somatic mosaicism are associated with segmental overgrowth of the body in conjunction with vascular, skeletal, and brain malformations such as hemimegalencephaly. A pathogenic variant may only be detectable in affected tissue and not in peripheral blood or saliva samples; therefore archival tissue may be the only relevant available specimen for testing. Although this is a common approach for cancer testing, it is not typically used for constitutional genetic disorders. METHODS PIK3CA mosaicism was assessed with a custom pediatric oncology next-generation sequencing panel (OncoKids) designed to capture somatic mutations in pediatric malignancies. The panel covers a wide range of targets including PIK3CA and AKT1 hotspots. We used OncoKids on archival formalin-fixed, paraffin-embedded or frozen samples from seven patients with facial hemihypertrophy and lipomas, hemimegalencephaly, or hemihypertrophy with a lymphovascular malformation. The age of the archival tissue examined by next-generation sequencing ranged from two to 13 years (median 5 years). Every patient had clinical manifestations within the PIK3CA-related overgrowth spectrum and had a sample of an affected tissue available for testing from a prior surgical intervention. RESULTS PIK3CA mosaicism was detected in all seven patients and the mutant allele fraction was lower in the lymphovascular malformation tissues (8% to 11%) than in brain (20% to 32%) and lipomatous (16% to 23%) tissues. CONCLUSIONS Our study highlights the clinical utility of using a robust, oncology-focused next-generation sequencing assay to identify PIK3CA mosaicism in noncancer cases. It is feasible to use archival samples that are more than a decade old to obtain a molecular diagnosis, which can then be used to improve health care management.
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Affiliation(s)
- Catherine Quindipan
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California.
| | - Jennifer A Cotter
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine at the University of Southern California, Los Angeles, California
| | - Jianling Ji
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine at the University of Southern California, Los Angeles, California
| | - Wendy G Mitchell
- Division of Pediatric Neurology, Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California; Department of Pediatrics, Keck School of Medicine at the University of Southern California, Los Angeles, California
| | - Diana J Moke
- Department of Pediatrics, Keck School of Medicine at the University of Southern California, Los Angeles, California; Division of Hematology and Oncology, Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California
| | - Fariba Navid
- Department of Pediatrics, Keck School of Medicine at the University of Southern California, Los Angeles, California; Division of Hematology and Oncology, Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California
| | - Stefanie M Thomas
- Department of Pediatrics, Keck School of Medicine at the University of Southern California, Los Angeles, California; Division of Hematology and Oncology, Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California
| | - Michele VanHirtum-Das
- Division of Pediatric Neurology, Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California; Department of Pediatrics, Keck School of Medicine at the University of Southern California, Los Angeles, California
| | - Larry Wang
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine at the University of Southern California, Los Angeles, California
| | - Sulagna C Saitta
- Division of Medical Genets, Department of Obstetrics and Gynecology, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, California
| | - Jaclyn A Biegel
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine at the University of Southern California, Los Angeles, California
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Aggarwal C, Davis CW, Mick R, Thompson JC, Ahmed S, Jeffries S, Bagley S, Gabriel P, Evans TL, Bauml JM, Ciunci C, Alley E, Morrissette JJD, Cohen RB, Carpenter EL, Langer CJ. Influence of TP53 Mutation on Survival in Patients With Advanced EGFR-Mutant Non-Small-Cell Lung Cancer. JCO Precis Oncol 2018; 2018. [PMID: 30766968 DOI: 10.1200/po.18.00107] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Purpose TP53 mutation (MT) in epidermal growth factor receptor (EGFR) -MT non-small cell lung cancer (NSCLC) is associated with poor response to targeted therapy; however, its impact on survival is not clearly established. Patients and Methods We performed an analysis of patients with stage IV EGFR MT NSCLC with available gene sequencing data. Associations between baseline characteristics; molecular profile, including TP53 MT; and survival outcomes were assessed. Results We identified 131 consecutive patients with EGFR MT; 81 (62%) had a TP53 MT, and 55 (42%) had other coexisting oncogenic MTs. Emergent EGFR T790M MT was observed in 42 patients (32%). Overall survival (OS) was longer for younger patients (P = .003), never smokers (P = .002), those with Eastern Cooperative Oncology Group performance status 0 to 1 (P = .004), and emergent T790M MT (P = .018). TP53 MT (P = .021) and other coexisting oncogenic MTs (P = 0.011) were associated with inferior OS. In a multivariable regression analysis adjusted for age, smoking, Eastern Cooperative Oncology Group performance status, and the presence of TP53 MT (P = .063) and other coexisting MTs (P = .064) did not achieve statistical significance. Patients with EGFR T790M/TP53 double MT had worse OS compared with patients with T790M MT alone (46.4 months v 82.9 months). In our series, five patients transformed to small-cell lung cancer (5.6%). All had TP53 MT. In four patients, allelic fraction of TP53 MT increased at the time of transformation. Conclusion The presence of TP53 and other coexisting MTs in EGFR MT NSCLC were associated with inferior OS, including patients with emergent T790M MT. An increase in TP53 mutation allelic fraction may potentially be a useful clinical predictor of small-cell transformation.
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Affiliation(s)
| | | | | | | | - Saman Ahmed
- State University of New York at Buffalo, Buffalo, NY
| | | | | | | | | | | | | | - Evan Alley
- University of Pennsylvania, Philadelphia, PA
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4
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Akbari H, Bakas S, Pisapia JM, Nasrallah MP, Rozycki M, Martinez-Lage M, Morrissette JJD, Dahmane N, O’Rourke DM, Davatzikos C. In vivo evaluation of EGFRvIII mutation in primary glioblastoma patients via complex multiparametric MRI signature. Neuro Oncol 2018; 20:1068-1079. [PMID: 29617843 PMCID: PMC6280148 DOI: 10.1093/neuonc/noy033] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Background Epidermal growth factor receptor variant III (EGFRvIII) is a driver mutation and potential therapeutic target in glioblastoma. Non-invasive in vivo EGFRvIII determination, using clinically acquired multiparametric MRI sequences, could assist in assessing spatial heterogeneity related to EGFRvIII, currently not captured via single-specimen analyses. We hypothesize that integration of subtle, yet distinctive, quantitative imaging/radiomic patterns using machine learning may lead to non-invasively determining molecular characteristics, and particularly the EGFRvIII mutation. Methods We integrated diverse imaging features, including the tumor's spatial distribution pattern, via support vector machines, to construct an imaging signature of EGFRvIII. This signature was evaluated in independent discovery (n = 75) and replication (n = 54) cohorts of de novo glioblastoma, and compared with the EGFRvIII status obtained through an assay based on next-generation sequencing. Results The cross-validated accuracy of the EGFRvIII signature in classifying the mutation status in individual patients of the independent discovery and replication cohorts was 85.3% (specificity = 86.3%, sensitivity = 83.3%, area under the curve [AUC] = 0.85) and 87% (specificity = 90%, sensitivity = 78.6%, AUC = 0.86), respectively. The signature was consistent with EGFRvIII+ tumors having increased neovascularization and cell density, as well as a distinctive spatial pattern involving relatively more frontal and parietal regions compared with EGFRvIII- tumors. Conclusions An imaging signature of EGFRvIII was found, revealing a complex, yet distinct macroscopic glioblastoma phenotype. By non-invasively capturing the tumor in its entirety, the proposed methodology can assist in evaluating the tumor's spatial heterogeneity, hence overcoming common spatial sampling limitations of tissue-based analyses. This signature can preoperatively stratify patients for EGFRvIII-targeted therapies, and potentially monitor dynamic mutational changes during treatment.
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Affiliation(s)
- Hamed Akbari
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadephia, Pennsylvania
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadephia, Pennsylvania
| | - Spyridon Bakas
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadephia, Pennsylvania
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadephia, Pennsylvania
| | - Jared M Pisapia
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadephia, Pennsylvania
| | - MacLean P Nasrallah
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadephia, Pennsylvania
| | - Martin Rozycki
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadephia, Pennsylvania
| | - Maria Martinez-Lage
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadephia, Pennsylvania
| | - Jennifer J D Morrissette
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadephia, Pennsylvania
| | - Nadia Dahmane
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadephia, Pennsylvania
| | - Donald M O’Rourke
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadephia, Pennsylvania
| | - Christos Davatzikos
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadephia, Pennsylvania
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadephia, Pennsylvania
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5
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Gangadhar TC, Savitch SL, Yee SS, Xu W, Huang AC, Harmon S, Lieberman DB, Soucier D, Fan R, Black TA, Morrissette JJD, Salathia N, Waters J, Zhang S, Toung J, van Hummelen P, Fan JB, Xu X, Amaravadi RK, Schuchter LM, Karakousis GC, Hwang WT, Carpenter EL. Feasibility of monitoring advanced melanoma patients using cell-free DNA from plasma. Pigment Cell Melanoma Res 2018; 31:73-81. [PMID: 28786531 PMCID: PMC5742050 DOI: 10.1111/pcmr.12623] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 07/31/2017] [Indexed: 12/24/2022]
Abstract
To determine the feasibility of liquid biopsy for monitoring of patients with advanced melanoma, cell-free DNA was extracted from plasma for 25 Stage III/IV patients, most (84.0%) having received previous therapy. DNA concentrations ranged from 0.6 to 390.0 ng/ml (median = 7.8 ng/ml) and were positively correlated with tumor burden as measured by imaging (Spearman rho = 0.5435, p = .0363). Using ultra-deep sequencing for a 61-gene panel, one or more mutations were detected in 12 of 25 samples (48.0%), and this proportion did not vary significantly for patients on or off therapy at the time of blood draw (52.9% and 37.5% respectively; p = .673). Sixteen mutations were detected in eight different genes, with the most frequent mutations detected in BRAF, NRAS, and KIT. Allele fractions ranged from 1.1% to 63.2% (median = 29.1%). Among patients with tissue next-generation sequencing, nine of 11 plasma mutations were also detected in matched tissue, for a concordance of 81.8%.
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Affiliation(s)
- Tara C. Gangadhar
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Samantha L. Savitch
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Stephanie S. Yee
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Wei Xu
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Alexander C. Huang
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Institue for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Parker Institute of Immunotherapy at the University of Pennsylvania
| | - Shannon Harmon
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - David B. Lieberman
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Devon Soucier
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Ryan Fan
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Taylor A. Black
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Jennifer J. D. Morrissette
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA
| | | | | | | | | | | | | | - Xiaowei Xu
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Ravi K. Amaravadi
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Lynn M. Schuchter
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | | | - Wei-Ting Hwang
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Department of Biostatistics & Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Erica L. Carpenter
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
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6
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Garman B, Anastopoulos IN, Krepler C, Brafford P, Sproesser K, Jiang Y, Wubbenhorst B, Amaravadi R, Bennett J, Beqiri M, Elder D, Flaherty KT, Frederick DT, Gangadhar TC, Guarino M, Hoon D, Karakousis G, Liu Q, Mitra N, Petrelli NJ, Schuchter L, Shannan B, Shields CL, Wargo J, Wenz B, Wilson MA, Xiao M, Xu W, Xu X, Yin X, Zhang NR, Davies MA, Herlyn M, Nathanson KL. Genetic and Genomic Characterization of 462 Melanoma Patient-Derived Xenografts, Tumor Biopsies, and Cell Lines. Cell Rep 2017; 21:1936-1952. [PMID: 29141224 PMCID: PMC5709812 DOI: 10.1016/j.celrep.2017.10.052] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 08/17/2017] [Accepted: 10/13/2017] [Indexed: 12/30/2022] Open
Abstract
Tumor-sequencing studies have revealed the widespread genetic diversity of melanoma. Sequencing of 108 genes previously implicated in melanomagenesis was performed on 462 patient-derived xenografts (PDXs), cell lines, and tumors to identify mutational and copy number aberrations. Samples came from 371 unique individuals: 263 were naive to treatment, and 108 were previously treated with targeted therapy (34), immunotherapy (54), or both (20). Models of all previously reported major melanoma subtypes (BRAF, NRAS, NF1, KIT, and WT/WT/WT) were identified. Multiple minor melanoma subtypes were also recapitulated, including melanomas with multiple activating mutations in the MAPK-signaling pathway and chromatin-remodeling gene mutations. These well-characterized melanoma PDXs and cell lines can be used not only as reagents for a large array of biological studies but also as pre-clinical models to facilitate drug development.
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Affiliation(s)
- Bradley Garman
- Department of Medicine, Division of Translational Medicine and Human Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Ioannis N Anastopoulos
- Department of Medicine, Division of Translational Medicine and Human Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Clemens Krepler
- The Wistar Institute, Molecular and Cellular Oncogenesis Program, Tumor Microenvironment and Metastasis Program, and Melanoma Research Center, Philadelphia, PA, USA
| | - Patricia Brafford
- The Wistar Institute, Molecular and Cellular Oncogenesis Program, Tumor Microenvironment and Metastasis Program, and Melanoma Research Center, Philadelphia, PA, USA
| | - Katrin Sproesser
- The Wistar Institute, Molecular and Cellular Oncogenesis Program, Tumor Microenvironment and Metastasis Program, and Melanoma Research Center, Philadelphia, PA, USA
| | - Yuchao Jiang
- Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - Bradley Wubbenhorst
- Department of Medicine, Division of Translational Medicine and Human Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Ravi Amaravadi
- Department of Medicine, Division of Hematology/Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph Bennett
- Helen F. Graham Cancer Center at Christiana Care Health System, Newark, DE, USA
| | - Marilda Beqiri
- The Wistar Institute, Molecular and Cellular Oncogenesis Program, Tumor Microenvironment and Metastasis Program, and Melanoma Research Center, Philadelphia, PA, USA
| | - David Elder
- Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Keith T Flaherty
- Department of Medicine, Division of Hematology & Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Dennie T Frederick
- Department of Medicine, Division of Hematology & Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Tara C Gangadhar
- Department of Medicine, Division of Hematology/Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Michael Guarino
- Helen F. Graham Cancer Center at Christiana Care Health System, Newark, DE, USA
| | - David Hoon
- Department of Translational Molecular Medicine, John Wayne Cancer Institute, Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Giorgos Karakousis
- Department of Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Qin Liu
- The Wistar Institute, Molecular and Cellular Oncogenesis Program, Tumor Microenvironment and Metastasis Program, and Melanoma Research Center, Philadelphia, PA, USA
| | - Nandita Mitra
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Nicholas J Petrelli
- Helen F. Graham Cancer Center at Christiana Care Health System, Newark, DE, USA
| | - Lynn Schuchter
- Department of Medicine, Division of Hematology/Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Batool Shannan
- The Wistar Institute, Molecular and Cellular Oncogenesis Program, Tumor Microenvironment and Metastasis Program, and Melanoma Research Center, Philadelphia, PA, USA
| | - Carol L Shields
- Ocular Oncology Service, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, PA, USA
| | - Jennifer Wargo
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Brandon Wenz
- Department of Medicine, Division of Translational Medicine and Human Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Melissa A Wilson
- Perlmutter Cancer Center, NYU School of Medicine, NYU Langone Medical Center, New York, NY, USA
| | - Min Xiao
- The Wistar Institute, Molecular and Cellular Oncogenesis Program, Tumor Microenvironment and Metastasis Program, and Melanoma Research Center, Philadelphia, PA, USA
| | - Wei Xu
- Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Xaiowei Xu
- Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Xiangfan Yin
- The Wistar Institute, Molecular and Cellular Oncogenesis Program, Tumor Microenvironment and Metastasis Program, and Melanoma Research Center, Philadelphia, PA, USA
| | - Nancy R Zhang
- Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael A Davies
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Meenhard Herlyn
- The Wistar Institute, Molecular and Cellular Oncogenesis Program, Tumor Microenvironment and Metastasis Program, and Melanoma Research Center, Philadelphia, PA, USA
| | - Katherine L Nathanson
- Department of Medicine, Division of Translational Medicine and Human Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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7
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Goh F, Duhig EE, Clarke BE, McCaul E, Passmore L, Courtney D, Windsor M, Naidoo R, Franz L, Parsonson K, Yang IA, Bowman RV, Fong KM. Low tumour cell content in a lung tumour bank: implications for molecular characterisation. Pathology 2017; 49:611-617. [PMID: 28811084 DOI: 10.1016/j.pathol.2017.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 07/08/2017] [Indexed: 12/23/2022]
Abstract
Lung cancer encompasses multiple malignant epithelial tumour types, each with specific targetable, potentially actionable mutations, such that precision management mandates accurate tumour typing. Molecular characterisation studies require high tumour cell content and low necrosis content, yet lung cancers are frequently a heterogeneous mixture of tumour and stromal cells. We hypothesised that there may be systematic differences in tumour cell content according to histological subtype, and that this may have implications for tumour banks as a resource for comprehensive molecular characterisation studies in lung cancer. To investigate this, we estimated tumour cell and necrosis content of 4267 samples resected from 752 primary lung tumour specimens contributed to a lung tissue bank. We found that banked lung cancer samples had low tumour cell content (33%) generally, although it was higher in carcinoids (77.5%) than other lung cancer subtypes. Tumour cells comprise a variable and often small component of banked resected tumour samples, and are accompanied by stromal reaction, inflammation, fibrosis, and normal structures. This has implications for the adequacy of unselected tumour bank samples for diagnostic and molecular investigations, and further research is needed to determine whether tumour cell content has a significant impact on analytical results in studies using tissue from tumour bank resources.
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Affiliation(s)
- Felicia Goh
- University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, Qld, Australia.
| | - Edwina E Duhig
- Sullivan Nicolaides Pathology, The John Flynn Hospital, Tugun, Qld, Australia
| | - Belinda E Clarke
- Pathology Queensland, The Prince Charles Hospital, Brisbane, Qld, Australia
| | - Elizabeth McCaul
- University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, Qld, Australia
| | - Linda Passmore
- University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, Qld, Australia
| | - Deborah Courtney
- University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, Qld, Australia
| | - Morgan Windsor
- Cardiothoracic Surgery, The Prince Charles Hospital, Brisbane, Qld, Australia
| | - Rishendren Naidoo
- Cardiothoracic Surgery, The Prince Charles Hospital, Brisbane, Qld, Australia
| | - Louise Franz
- University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, Qld, Australia
| | - Kylie Parsonson
- University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, Qld, Australia
| | - Ian A Yang
- University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, Qld, Australia
| | - Rayleen V Bowman
- University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, Qld, Australia
| | - Kwun M Fong
- University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, Qld, Australia
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8
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Bakas S, Akbari H, Pisapia J, Martinez-Lage M, Rozycki M, Rathore S, Dahmane N, O'Rourke DM, Davatzikos C. In Vivo Detection of EGFRvIII in Glioblastoma via Perfusion Magnetic Resonance Imaging Signature Consistent with Deep Peritumoral Infiltration: The φ-Index. Clin Cancer Res 2017; 23:4724-4734. [PMID: 28428190 DOI: 10.1158/1078-0432.ccr-16-1871] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 11/30/2016] [Accepted: 04/17/2017] [Indexed: 12/24/2022]
Abstract
Purpose: The epidermal growth factor receptor variant III (EGFRvIII) mutation has been considered a driver mutation and therapeutic target in glioblastoma, the most common and aggressive brain cancer. Currently, detecting EGFRvIII requires postoperative tissue analyses, which are ex vivo and unable to capture the tumor's spatial heterogeneity. Considering the increasing evidence of in vivo imaging signatures capturing molecular characteristics of cancer, this study aims to detect EGFRvIII in primary glioblastoma noninvasively, using routine clinically acquired imaging.Experimental Design: We found peritumoral infiltration and vascularization patterns being related to EGFRvIII status. We therefore constructed a quantitative within-patient peritumoral heterogeneity index (PHI/φ-index), by contrasting perfusion patterns of immediate and distant peritumoral edema. Application of φ-index in preoperative perfusion scans of independent discovery (n = 64) and validation (n = 78) cohorts, revealed the generalizability of this EGFRvIII imaging signature.Results: Analysis in both cohorts demonstrated that the obtained signature is highly accurate (89.92%), specific (92.35%), and sensitive (83.77%), with significantly distinctive ability (P = 4.0033 × 10-10, AUC = 0.8869). Findings indicated a highly infiltrative-migratory phenotype for EGFRvIII+ tumors, which displayed similar perfusion patterns throughout peritumoral edema. Contrarily, EGFRvIII- tumors displayed perfusion dynamics consistent with peritumorally confined vascularization, suggesting potential benefit from extensive peritumoral resection/radiation.Conclusions: This EGFRvIII signature is potentially suitable for clinical translation, since obtained from analysis of clinically acquired images. Use of within-patient heterogeneity measures, rather than population-based associations, renders φ-index potentially resistant to inter-scanner variations. Overall, our findings enable noninvasive evaluation of EGFRvIII for patient selection for targeted therapy, stratification into clinical trials, personalized treatment planning, and potentially treatment-response evaluation. Clin Cancer Res; 23(16); 4724-34. ©2017 AACR.
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Affiliation(s)
- Spyridon Bakas
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Hamed Akbari
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jared Pisapia
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Maria Martinez-Lage
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Martin Rozycki
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Saima Rathore
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Nadia Dahmane
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Donald M O'Rourke
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Christos Davatzikos
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania. .,Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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9
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Thompson JC, Yee SS, Troxel AB, Savitch SL, Fan R, Balli D, Lieberman DB, Morrissette JD, Evans TL, Bauml J, Aggarwal C, Kosteva JA, Alley E, Ciunci C, Cohen RB, Bagley S, Stonehouse-Lee S, Sherry VE, Gilbert E, Langer C, Vachani A, Carpenter EL. Detection of Therapeutically Targetable Driver and Resistance Mutations in Lung Cancer Patients by Next-Generation Sequencing of Cell-Free Circulating Tumor DNA. Clin Cancer Res 2016; 22:5772-5782. [PMID: 27601595 DOI: 10.1158/1078-0432.ccr-16-1231] [Citation(s) in RCA: 241] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/26/2016] [Accepted: 08/29/2016] [Indexed: 12/23/2022]
Abstract
PURPOSE The expanding number of targeted therapeutics for non-small cell lung cancer (NSCLC) necessitates real-time tumor genotyping, yet tissue biopsies are difficult to perform serially and often yield inadequate DNA for next-generation sequencing (NGS). We evaluated the feasibility of using cell-free circulating tumor DNA (ctDNA) NGS as a complement or alternative to tissue NGS. EXPERIMENTAL DESIGN A total of 112 plasma samples obtained from a consecutive study of 102 prospectively enrolled patients with advanced NSCLC were subjected to ultra-deep sequencing of up to 70 genes and matched with tissue samples, when possible. RESULTS We detected 275 alterations in 45 genes, and at least one alteration in the ctDNA for 86 of 102 patients (84%), with EGFR variants being most common. ctDNA NGS detected 50 driver and 12 resistance mutations, and mutations in 22 additional genes for which experimental therapies, including clinical trials, are available. Although ctDNA NGS was completed for 102 consecutive patients, tissue sequencing was only successful for 50 patients (49%). Actionable EGFR mutations were detected in 24 tissue and 19 ctDNA samples, yielding concordance of 79%, with a shorter time interval between tissue and blood collection associated with increased concordance (P = 0.038). ctDNA sequencing identified eight patients harboring a resistance mutation who developed progressive disease while on targeted therapy, and for whom tissue sequencing was not possible. CONCLUSIONS Therapeutically targetable driver and resistance mutations can be detected by ctDNA NGS, even when tissue is unavailable, thus allowing more accurate diagnosis, improved patient management, and serial sampling to monitor disease progression and clonal evolution. Clin Cancer Res; 22(23); 5772-82. ©2016 AACR.
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Affiliation(s)
- Jeffrey C Thompson
- Division of Pulmonary, Allergy and Critical Care Medicine, Thoracic Oncology Group, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Stephanie S Yee
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Andrea B Troxel
- Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Samantha L Savitch
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Ryan Fan
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - David Balli
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - David B Lieberman
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jennifer D Morrissette
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Tracey L Evans
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Joshua Bauml
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Charu Aggarwal
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - John A Kosteva
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Evan Alley
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Christine Ciunci
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Roger B Cohen
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Stephen Bagley
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Susan Stonehouse-Lee
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Victoria E Sherry
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Elizabeth Gilbert
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Corey Langer
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Anil Vachani
- Division of Pulmonary, Allergy and Critical Care Medicine, Thoracic Oncology Group, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Erica L Carpenter
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania. .,Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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