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Xiao X, Sun Z, Liang S, Li W, Guo H, Zhao H, Zhao L, Ma H, Sun Y, Wang C, Chang X, Zhang Z. Liquid-based cytology specimens for next-generation sequencing in lung adenocarcinoma: challenges and evaluation of targeted therapy. BMC Cancer 2024; 24:749. [PMID: 38902688 DOI: 10.1186/s12885-024-12520-2] [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: 04/07/2024] [Accepted: 06/14/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND To explore challenges of liquid-based cytology (LBC) specimens for next-generation sequencing (NGS) in lung adenocarcinoma and evaluate the efficacy of targeted therapy. METHODS A retrospective analysis was conducted on the NGS test of 357 cases of advanced lung adenocarcinoma LBC specimens and compared with results of histological specimens to assess the consistency. The impact of tumor cellularity on NGS test results was evaluated. The utility of epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs) was collected. Clinical efficacy evaluation was performed and survival curve analysis was conducted using the Kaplan-Meier method. RESULTS There were 275 TKI-naive and 82 TKI-treated specimens, the mutation rates of cancer-related genes detected in both groups were similar (86.2% vs. 86.6%). The EGFR mutation rate in the TKI treated group was higher than that in the TKI-naive group (69.5% > 54.9%, P = 0.019). There was no significant difference in the EGFR mutation frequency among different tumor cellularity in the TKI-naive group. However, in the TKI treated group, the frequency of EGFR sensitizing mutation and T790M resistance mutation in specimens with < 20% tumor cellularity was significantly lower than that in specimens with ≥ 20% tumor cellularity. Among 22 cases with matched histological specimens, 72.7% (16/22) of LBC specimens were completely consistent with results of histological specimens. Among 92 patients with EGFR-mutant lung adenocarcinoma treated with EGFR-TKIs in the two cohorts, 88 cases experienced progression, and the median progression-free survival (PFS) was 12.1 months. CONCLUSIONS Cytological specimens are important sources for gene detection of advanced lung adenocarcinoma. When using LBC specimens for molecular testing, it is recommended to fully evaluate the tumor cellularity of the specimens.
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Affiliation(s)
- Xiaoyue Xiao
- Cytopathology Section, Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - ZiHan Sun
- Cytopathology Section, Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Shuo Liang
- Cytopathology Section, Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Weihua Li
- Cytopathology Section, Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - HuiQin Guo
- Cytopathology Section, Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Huan Zhao
- Cytopathology Section, Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - LinLin Zhao
- Cytopathology Section, Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - HaiYue Ma
- Cytopathology Section, Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yue Sun
- Cytopathology Section, Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Cong Wang
- Cytopathology Section, Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - XinXiang Chang
- Cytopathology Section, Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - ZhiHui Zhang
- Cytopathology Section, Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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Washimi K, Hiroshima Y, Sato S, Ueno M, Kobayashi S, Yamamoto N, Hasegawa C, Yoshioka E, Ono K, Okubo Y, Yokose T, Miyagi Y. Evaluation of pancreatic cancer specimens for comprehensive genomic profiling. Pathol Int 2024; 74:252-261. [PMID: 38477638 DOI: 10.1111/pin.13416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/30/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024]
Abstract
Inadequate specimen quality or quantity hinders comprehensive genomic profiling in identifying actionable mutations and guiding treatment strategies. We investigated the optimal conditions for pancreatic cancer specimen selection for comprehensive genomic profiling. We retrospectively analyzed 213 pancreatic cancer cases ordered for comprehensive genomic profiling and compared results from pancreatic biopsy, liver biopsy of pancreatic cancer metastases, pancreatectomy, liquid, and nonliver metastatic organ specimens. We examined preanalytical conditions, including cellularity (tumor cell count/size). The successfully tested cases were those that underwent comprehensive genomic profiling tests without any issues. The successfully tested case ratio was 72.8%. Pancreatic biopsy had the highest successfully tested case ratio (87%), with a high tumor cell percentage, despite the small number of cells (median, 3425). Pancreatic biopsy, liver biopsy of pancreatic cancer metastases, and non-liver metastatic organ had higher successfully tested case ratios than that for pancreatectomy. Liver biopsy of pancreatic cancer metastases and pancreatectomy cases with tumor size (mm2) × tumor ratio (%) > 150 and >3000, respectively, had high successfully tested case ratios. The success of comprehensive genomic profiling is significantly influenced by the tumor cell ratio, and pancreatic biopsy is a potentially suitable specimen for comprehensive genomic profiling.
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Affiliation(s)
- Kota Washimi
- Department of Pathology, Kanagawa Cancer Center, Yokohama, Kanagawa, Japan
| | - Yukihiko Hiroshima
- Division of Advanced Cancer Therapeutics, Kanagawa Cancer Center Research Institute, Yokohama, Kanagawa, Japan
- Center for Cancer Genome Medicine, Kanagawa Cancer Center, Yokohama, Kanagawa, Japan
| | - Shinya Sato
- Department of Pathology, Kanagawa Cancer Center, Yokohama, Kanagawa, Japan
- Division of Molecular Pathology and Genetics, Kanagawa Cancer Center Research Institute, Yokohama, Kanagawa, Japan
| | - Makoto Ueno
- Department of Gastoroenterology, Kanagawa Cancer Center, Yokohama, Kanagawa, Japan
| | - Satoshi Kobayashi
- Department of Gastoroenterology, Kanagawa Cancer Center, Yokohama, Kanagawa, Japan
| | - Naoto Yamamoto
- Department of Gastrointestinal Surgery, Kanagawa Cancer Center, Yokohama, Kanagawa, Japan
| | - Chie Hasegawa
- Department of Pathology, Kanagawa Cancer Center, Yokohama, Kanagawa, Japan
| | - Emi Yoshioka
- Department of Pathology, Kanagawa Cancer Center, Yokohama, Kanagawa, Japan
| | - Kyoko Ono
- Department of Pathology, Kanagawa Cancer Center, Yokohama, Kanagawa, Japan
| | - Yoichiro Okubo
- Department of Pathology, Kanagawa Cancer Center, Yokohama, Kanagawa, Japan
| | - Tomoyuki Yokose
- Department of Pathology, Kanagawa Cancer Center, Yokohama, Kanagawa, Japan
| | - Yohei Miyagi
- Center for Cancer Genome Medicine, Kanagawa Cancer Center, Yokohama, Kanagawa, Japan
- Division of Molecular Pathology and Genetics, Kanagawa Cancer Center Research Institute, Yokohama, Kanagawa, Japan
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Goh LY, Limbachia K, Moonim M, Morley AMS. Primary lacrimal sac melanoma: a case report describing the novel use of fine needle aspiration cytology (FNAC) for diagnosis, together with literature review and immunotherapy treatment update. Orbit 2024; 43:270-279. [PMID: 36069101 DOI: 10.1080/01676830.2022.2119264] [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: 07/24/2022] [Accepted: 08/25/2022] [Indexed: 10/14/2022]
Abstract
Primary lacrimal sac melanoma (PLSM) is exceedingly rare and associated with high morbidity and mortality. Unfortunately, PLSM often presents insidiously resulting in delayed detection and poor prognosis. A 69-year-old Black man was suspected of having a lacrimal sac tumour following presentation with a left sided watery eye, bloody tears, and a lacrimal mass. Due to the patient's implantable pacemaker, defibrillator, and high anticoagulation, an ultrasound-guided FNAC was performed instead of incisional biopsy, revealing a PLSM. Diagnosis was confirmed following complete tumour resection with free flap reconstruction and neck dissection. Unfortunately, disease progression ensued despite further neck dissection and three cycles of both pembrolizumab and iplimumab. This is the first description of FNAC to accurately diagnose PLSM and highlights its use as an accurate, rapid, and minimally invasive technique that may allow an earlier screening diagnosis of lacrimal sac tumours. We also discuss the outcome of immunotherapy in recent similar cases.
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Affiliation(s)
- Li Yen Goh
- Department of Ophthalmology, Guy's and St Thomas' Hospital NHS Trust, London, UK
| | - Ketan Limbachia
- Department of Ophthalmology, Guy's and St Thomas' Hospital NHS Trust, London, UK
| | - Mufaddal Moonim
- Department of Histopathology, Guy's and St Thomas' Hospital NHS Trust, London, UK
| | - Ana M S Morley
- Department of Ophthalmology, Guy's and St Thomas' Hospital NHS Trust, London, UK
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4
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Meireles SI, Cruz MV, de Godoy CD, de Testagrossa L. Performance of non-formalin fixed paraffin embedded samples in hybrid capture and amplicon next-generation sequencing panels. Diagn Cytopathol 2024; 52:171-182. [PMID: 38124281 DOI: 10.1002/dc.25267] [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: 09/06/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Genomic profiling using next-generation sequencing (NGS) is fundamental for driving prognostic and therapy in cancer. Formalin-fixed paraffin embedded (FFPE) tissue is the widely used material, whereas non-FFPE may represent an alternative. However, studies comparing the NGS performance of non-FFPE materials to FFPE are still lacking in the literature. The objective of this study was to characterize in non-FFPE preparations the nucleic acid yield and NGS performance on both a capture-based and an amplicon-based NGS platform. NGS quality metrics obtained from non-FFPE preparations were compared to FFPE. METHODS We analyzed the cellularity and nucleic acid yield in 111 tumors from non-FFPE preparations. In addition, comprehensive hybrid capture panel sequencing metrics obtained from DNA and RNA libraries were compared between independent non-FFPE and FFPE samples. A paired comparison between non-FFPE and FFPE samples was performed to analyze concordance in mutant allele detection using an amplicon panel. RESULTS The mean target coverage from DNA libraries was 2× higher in non-FFPE samples than in FFPE. The detection of exogenous DNA was 2.5× higher in non-FFPE than in FFPE. Conversely, a lower performance was observed in non-FFPE RNA libraries in comparison to FFPE DNA libraries with no impact in minimum standard cutoffs. The variant allele detection in non-FFPE was found to be comparable to that of FFPE tumor samples in matched samples. CONCLUSIONS Non-FFPE was demonstrated to be a suitable material for DNA and RNA library preparations using a comprehensive NGS panel. This is the first study reporting library quality metrics according to the TSO500 analysis pipeline.
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Affiliation(s)
- Sibele Inácio Meireles
- Departamento de Anatomia Patológica e Molecular, Hospital Sírio Libanês, São Paulo, Brazil
| | - Mariana Vargas Cruz
- Departamento de Anatomia Patológica e Molecular, Hospital Sírio Libanês, São Paulo, Brazil
| | - Carla Daniele de Godoy
- Departamento de Anatomia Patológica e Molecular, Hospital Sírio Libanês, São Paulo, Brazil
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Chen YH, Cabanillas M, Sperling J, Xu L, Goswami M, Maniakas A, Williams MD, Lai SY, Busaidy N, Dadu R, Zafereo ME, Wang JR. Prior Thyroid and Nonthyroid Cancer History Do Not Significantly Alter Overall Survival in Patients Diagnosed with Anaplastic Thyroid Cancer. Thyroid 2023; 33:321-329. [PMID: 36511380 DOI: 10.1089/thy.2022.0350] [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] [Indexed: 12/15/2022]
Abstract
Background: A history of thyroid and nonthyroid malignancies has traditionally been an exclusion criterion in patients with anaplastic thyroid cancer (ATC) seeking to enroll in clinical trials. In this study, we examined the impact of prior malignancies on overall survival (OS) in patients diagnosed with ATC. Methods: In our retrospective cohort study, we identified 451 patients with ATC treated at MD Anderson between 2000 and 2019. Clinical and pathological information was obtained through chart review. Survival analyses were conducted using the Kaplan-Meier method and multivariable Cox proportional hazard models. Results: A history of clinically documented differentiated thyroid cancer (DTC) was reported in 14% of patients with ATC (n = 62), most commonly papillary thyroid cancer (81%, n = 50). The median time from diagnosis of prior DTC to ATC diagnosis was 3.5 years (range: 6 months to 35 years). Concomitant DTC was found on pathology in a higher proportion of patients (52%, n = 234). A history of nonthyroid cancer was reported in 23% of patients (n = 102), where 19% (n = 87) had one, 2% (n = 10) had two, and 1% (n = 5) had three prior cancers. The median time from diagnosis of prior nonthyroid cancer to ATC diagnosis was 8 years (range: 3 months to 53 years). The most common prior nonthyroid cancers were nonmelanoma skin (28.4%), prostate (19.6%), and breast cancers (16.7%). In a subgroup analysis performed in patients with available tumor mutation information (n = 183), the frequency of detected tumor driver mutations (BRAF, RAS, TP53) was not significantly different between patients with ATC with and without a history of nonthyroid cancer. On multivariate analysis after adjusting for age and overall stage, prior DTC, concomitant DTC, and prior nonthyroid cancers, all had no significant impact on OS. Conclusions: The presence of prior malignancy does not significantly impact OS in patients with ATC. Revision of eligibility criteria for enrollment of patients with ATC into clinical trials is warranted.
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Affiliation(s)
- Yu Han Chen
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Maria Cabanillas
- Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jared Sperling
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Li Xu
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Maitrayee Goswami
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Anastasios Maniakas
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Michelle D Williams
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Stephen Y Lai
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Naifa Busaidy
- Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ramona Dadu
- Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mark E Zafereo
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jennifer Rui Wang
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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6
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Morii E, Hatanaka Y, Motoi N, Kawahara A, Hamakawa S, Kuwata T, Nagatomo T, Oda Y, Okamoto A, Tanaka R, Iyoda A, Ichiro M, Matsuo Y, Nakamura N, Nakai T, Fukuhara M, Tokita K, Yamaguchi T, Takenaka M, Kawabata A, Hatanaka KC, Tsubame K, Satoh Y. Guidelines for Handling of Cytological Specimens in Cancer Genomic Medicine. Pathobiology 2023; 90:289-311. [PMID: 36754025 PMCID: PMC10627493 DOI: 10.1159/000528346] [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: 10/03/2022] [Accepted: 11/22/2022] [Indexed: 02/10/2023] Open
Abstract
Rapid advances are being made in cancer drug therapy. Since molecularly targeted therapy has been introduced, personalized medicine is being practiced, pathological tissue from malignant tumors obtained during routine practice is frequently used for genomic testing. Whereas cytological specimens fixed mainly in alcohol are considered to be more advantageous in terms of preservation of the nucleic acid quality and quantity. This article is aimed to share the information for the proper handling of cytological specimens in practice for genomic medicine based on the findings established in "Guidelines for Handling of Cytological Specimens in Cancer Genomic Medicine (in Japanese)" published by the Japanese Society of Clinical Cytology in 2021. The three-part practical guidelines are based on empirical data analyses; Part 1 describes general remarks on the use of cytological specimens in cancer genomic medicine, then Part 2 describes proper handling of cytological specimens, and Part 3 describes the empirical data related to handling of cytological specimens. The guidelines indicated proper handling of specimens in each fixation, preparation, and evaluation.
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Affiliation(s)
- Eiichi Morii
- Department of Pathology, Osaka University, Suita, Japan
| | - Yutaka Hatanaka
- Research Division of Genome Companion Diagnostics, Hokkaido University Hospital, Sapporo, Japan
| | - Noriko Motoi
- Department of Pathology, Saitama Cancer Center, Saitama, Japan
| | - Akihiko Kawahara
- Department of Diagnostic Pathology, Kurume University Hospital, Kurume, Japan
| | | | - Takeshi Kuwata
- Department of Genetic Medicine, National Cancer Center Hospital East, Kashiwa, Japan
| | | | - Yoshinao Oda
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Aikou Okamoto
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Tokyo, Japan
| | - Ryota Tanaka
- Department of Surgery, Kyorin University School of Medicine, Mitaka, Japan
| | - Akira Iyoda
- Division of Chest Surgery, Department of Surgery, Toho University School of Medicine, Tokyo, Japan
| | - Maeda Ichiro
- Department of Diagnostic Pathology, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Yukiko Matsuo
- Department of Thoracic Surgery, Kitasato University School of Medicine, Sagamihara, Japan
| | - Nobuyuki Nakamura
- Department of Clinical Laboratories, National Cancer Center Hospital East, Kashiwa, Japan
| | - Tokiko Nakai
- Department of Diagnostic Pathology, Harima-Himeji General Medical Center, Himeji, Japan
| | - Mei Fukuhara
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Kazuya Tokita
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Tomohiko Yamaguchi
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masataka Takenaka
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Tokyo, Japan
| | - Ayako Kawabata
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Tokyo, Japan
| | - Kanako C. Hatanaka
- Center for Development of Advanced Diagnostics, Hokkaido University Hospital, Sapporo, Japan
| | - Kaho Tsubame
- Center for Development of Advanced Diagnostics, Hokkaido University Hospital, Sapporo, Japan
| | - Yukitoshi Satoh
- Department of Thoracic Surgery, Kitasato University School of Medicine, Sagamihara, Japan
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7
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Fielding D, Dalley AJ, Singh M, Nandakumar L, Nones K, Lakis V, Chittoory H, Ferguson K, Bashirzadeh F, Bint M, Pahoff C, Son JH, Hodgson A, Sharma S, Godbolt D, Coleman K, Whitfield L, Waddell N, Lakhani SR, Hartel G, Simpson PT. Prospective Optimization of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration Lymph Node Assessment for Lung Cancer: Three Needle Agitations Are Noninferior to 10 Agitations for Adequate Tumor Cell and DNA Yield. JTO Clin Res Rep 2022; 3:100403. [PMID: 36147610 PMCID: PMC9486562 DOI: 10.1016/j.jtocrr.2022.100403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/03/2022] [Accepted: 08/22/2022] [Indexed: 10/30/2022] Open
Abstract
Introduction Methods Results Conclusions
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8
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Wang JR, Montierth M, Xu L, Goswami M, Zhao X, Cote G, Wang W, Iyer P, Dadu R, Busaidy NL, Lai SY, Gross ND, Ferrarotto R, Lu C, Gunn GB, Williams MD, Routbort M, Zafereo ME, Cabanillas ME. Impact of Somatic Mutations on Survival Outcomes in Patients With Anaplastic Thyroid Carcinoma. JCO Precis Oncol 2022; 6:e2100504. [PMID: 35977347 PMCID: PMC10530586 DOI: 10.1200/po.21.00504] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 03/02/2022] [Accepted: 06/23/2022] [Indexed: 12/15/2022] Open
Abstract
PURPOSE Anaplastic thyroid carcinoma (ATC) uniformly present with aggressive disease, but the mutational landscape of tumors varies. We aimed to determine whether tumor mutations affect survival outcomes in ATC. MATERIALS AND METHODS Patients who underwent mutation sequencing using targeted gene panels between 2005 and 2019 at a tertiary referral center were included. Associations between mutation status and survival outcomes were assessed using Cox proportional hazards models. RESULTS A total of 202 patients were included, where 122 died of ATC (60%). The median follow-up was 31 months (interquartile range, 18-45 months). The most common mutations were in TP53 (59%), BRAF (41%), TERT promoter (37%), and the RAS gene family (22%). Clinicopathologic characteristics and overall survival (OS) significantly correlated with mutations in BRAFV600E and RAS, which were mutually exclusive. The BRAFV600E mutation was associated with the presence of a papillary thyroid carcinoma precursor and significantly better OS (median OS: 24 months). RAS-mutated patients more commonly presented without cervical lymph node involvement but had the worst OS (median OS: 6 months). Tumors that were wild-type for both BRAF and RAS were enriched for NF1 mutations and harbored intermediate prognosis (median OS: 15 months). In multivariate analyses, RAS mutations were associated with a more than 2.5-fold higher risk of death (adjusted hazard ratio, 2.64; 95% CI, 1.66 to 4.20) compared with BRAFV600E. In patients treated with BRAF-directed therapy (n = 60), disease progression occurred in 48% of patients (n = 29). The median progression-free survival was 14 months. The presence of a TP53 mutation was independently associated with reduced progression-free survival in BRAFV600E-mutated patients treated with BRAF-directed therapy (adjusted hazard ratio, 2.89; 95% CI, 1.35 to 6.21). CONCLUSION Mutation analysis provides prognostic information in ATC and should be incorporated into routine clinical care.
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Affiliation(s)
- Jennifer Rui Wang
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center; Houston, TX
| | - Matthew Montierth
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center; Houston, TX
| | - Li Xu
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center; Houston, TX
| | - Maitrayee Goswami
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center; Houston, TX
| | - Xiao Zhao
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center; Houston, TX
| | - Gilbert Cote
- Department of Endocrine Neoplasia & Hormonal Disorders, The University of Texas MD Anderson Cancer Center; Houston, TX
| | - Wenyi Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center; Houston, TX
| | - Priyanka Iyer
- Department of Endocrine Neoplasia & Hormonal Disorders, The University of Texas MD Anderson Cancer Center; Houston, TX
| | - Ramona Dadu
- Department of Endocrine Neoplasia & Hormonal Disorders, The University of Texas MD Anderson Cancer Center; Houston, TX
| | - Naifa L Busaidy
- Department of Endocrine Neoplasia & Hormonal Disorders, The University of Texas MD Anderson Cancer Center; Houston, TX
| | - Stephen Y Lai
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center; Houston, TX
| | - Neil D Gross
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center; Houston, TX
| | - Renata Ferrarotto
- Department of Thoracic-Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center; Houston, TX
| | - Charles Lu
- Department of Thoracic-Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center; Houston, TX
| | - Gary Brandon Gunn
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center; Houston, TX
| | - Michelle D Williams
- Department of Pathology, The University of Texas MD Anderson Cancer Center; Houston, TX
| | - Mark Routbort
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center; Houston, TX
| | - Mark E Zafereo
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center; Houston, TX
| | - Maria E Cabanillas
- Department of Endocrine Neoplasia & Hormonal Disorders, The University of Texas MD Anderson Cancer Center; Houston, TX
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9
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Specimen Considerations in Molecular Oncology Testing. Clin Lab Med 2022; 42:367-383. [DOI: 10.1016/j.cll.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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10
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Penault-Llorca F, Kerr KM, Garrido P, Thunnissen E, Dequeker E, Normanno N, Patton SJ, Fairley J, Kapp J, de Ridder D, Ryška A, Moch H. Expert opinion on NSCLC small specimen biomarker testing - Part 1: Tissue collection and management. Virchows Arch 2022; 481:335-350. [PMID: 35857102 PMCID: PMC9485167 DOI: 10.1007/s00428-022-03343-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/16/2022] [Accepted: 05/18/2022] [Indexed: 12/11/2022]
Abstract
Biomarker testing is crucial for treatment selection in advanced non-small cell lung cancer (NSCLC). However, the quantity of available tissue often presents a key constraint for patients with advanced disease, where minimally invasive tissue biopsy typically returns small samples. In Part 1 of this two-part series, we summarise evidence-based recommendations relating to small sample processing for patients with NSCLC. Generally, tissue biopsy techniques that deliver the greatest quantity and quality of tissue with the least risk to the patient should be selected. Rapid on-site evaluation can help to ensure sufficient sample quality and quantity. Sample processing should be managed according to biomarker testing requirements, because tissue fixation methodology influences downstream nucleic acid, protein and morphological analyses. Accordingly, 10% neutral buffered formalin is recommended as an appropriate fixative, and the duration of fixation is recommended not to exceed 24–48 h. Tissue sparing techniques, including the ‘one biopsy per block’ approach and small sample cutting protocols, can help preserve tissue. Cytological material (formalin-fixed paraffin-embedded [FFPE] cytology blocks and non-FFPE samples such as smears and touch preparations) can be an excellent source of nucleic acid, providing either primary or supplementary patient material to complete morphological and molecular diagnoses. Considerations on biomarker testing, reporting and quality assessment are discussed in Part 2.
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Affiliation(s)
| | - Keith M Kerr
- Department of Pathology, Aberdeen University Medical School and Aberdeen Royal Infirmary, Aberdeen, UK
| | - Pilar Garrido
- Medical Oncology Department, Hospital Universitario Ramón Y Cajal, University of Alcalá, Madrid, Spain
| | - Erik Thunnissen
- Amsterdam University Medical Center, VU Medical Center, Amsterdam, the Netherlands
| | - Elisabeth Dequeker
- Department of Public Health, Biomedical Quality Assurance Research Unit, Campus Gasthuisberg, University Leuven, Leuven, Belgium
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione Giovanni Pascale" IRCCS, Naples, Italy
| | | | | | | | | | - Aleš Ryška
- Department of Pathology, Charles University Medical Faculty Hospital, Hradec Králové, Czech Republic
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich and University of Zurich, Zurich, Switzerland.
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11
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Ryan DJ, Toomey S, Smyth R, Madden SF, Workman J, Cummins R, Sheehan K, Fay J, Naidoo J, Breathnach OS, Morris PG, Grogan L, O'Brien ME, Sulaiman I, Hennessy BT, Morgan RK. Exhaled Breath Condensate (EBC) analysis of circulating tumour DNA (ctDNA) using a lung cancer specific UltraSEEK oncogene panel. Lung Cancer 2022; 168:67-73. [DOI: 10.1016/j.lungcan.2022.04.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/26/2022] [Accepted: 04/29/2022] [Indexed: 10/18/2022]
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12
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FFPE-Based NGS Approaches into Clinical Practice: The Limits of Glory from a Pathologist Viewpoint. J Pers Med 2022; 12:jpm12050750. [PMID: 35629172 PMCID: PMC9146170 DOI: 10.3390/jpm12050750] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 01/02/2023] Open
Abstract
The introduction of next-generation sequencing (NGS) in the molecular diagnostic armamentarium is deeply changing pathology practice and laboratory frameworks. NGS allows for the comprehensive molecular characterization of neoplasms, in order to provide the best treatment to oncologic patients. On the other hand, NGS raises technical issues and poses several challenges in terms of education, infrastructures and costs. The aim of this review is to give an overview of the main NGS sequencing platforms that can be used in current molecular diagnostics and gain insights into the clinical applications of NGS in precision oncology. Hence, we also focus on the preanalytical, analytical and interpretative issues raised by the incorporation of NGS in routine pathology diagnostics.
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13
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Ramani NS, Green LK. Metastatic hepatocellular carcinoma to the bone diagnosed by fine needle aspiration in a veteran population. Diagn Cytopathol 2022; 50:335-340. [PMID: 35403368 DOI: 10.1002/dc.24961] [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: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide and it may present initially with extrahepatic spread in 5%-15% cases. It most commonly metastasizes to lungs, lymph nodes and adrenal glands. Skeletal metastases from HCC are uncommon and carry a very poor prognosis. METHODS We retrospectively reviewed all fine needle aspiration (FNA) specimens of metastatic HCC at our institution from January 1994 to March 2021 using the SNOMED search computer option. Relevant clinical information was obtained from the review of patient's electronic medical records. RESULTS There were 36 FNAs of metastatic HCC over a period of 27 years. Six patients (16.7%) were found to have skeletal metastases. All six patients were males with a median age of 59 years (54-71 years) and their lesions were osteolytic. The most common site of metastases was vertebra (3/50%). Most patients (67%) had bone metastases as an initial presentation, without prior history of HCC. The mean survival after the diagnosis of skeletal metastases was only 8 months. CONCLUSION Detection of extrahepatic HCC to bone is important to avoid any unwanted surgical intervention. In our patient population, the most common site of skeletal metastases from HCC was vertebra, therefore in FNAs of vertebral lytic masses, metastatic HCC should be considered. On FNA, extrahepatic metastases of HCC can mimic other poorly differentiated tumors. They behave in an aggressive fashion, resulting in a grim prognosis. Cytological substrates can be used for future molecular testing, if needed.
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Affiliation(s)
- Nisha S Ramani
- Department of Pathology, Michael E. DeBakey VA Medical Center, Houston, Texas, USA.,Department of Pathology, Baylor College of Medicine, Houston, Texas, USA
| | - Linda K Green
- Department of Pathology, Michael E. DeBakey VA Medical Center, Houston, Texas, USA.,Department of Pathology, Baylor College of Medicine, Houston, Texas, USA
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14
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Dolinar A, Grubelnik G, Srebotnik-Kirbiš I, Strojan Fležar M, Žlajpah M. Optimization of pre-analytical and analytical steps for DNA and RNA analysis of fresh cytology samples. Cancer Med 2022; 11:4021-4032. [PMID: 35403378 DOI: 10.1002/cam4.4728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/16/2022] [Accepted: 03/16/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Different cytology preparations can be used for molecular diagnostics, however the influence of pre-analytical and analytical steps on the results are not yet well defined. We aimed to determine optimal steps for efficient extraction of DNA and RNA from fresh cells for molecular diagnostics. METHODS MCF7 and FaDu human cell lines, were used as a model to determine fresh cells storage conditions (temperature: 25°C, 4°C, -20°C, -80°C; duration: 0 h, 4 h, 12 h, 24 h, 48 h) and optimal nucleic acids extraction method. Besides, the minimal number of total cells and minimal percentage of mutated cells needed for successful extraction of nucleic acids and subsequent determination of present mutation were evaluated. RESULTS Extraction of nucleic acids using spin columns yielded the highest quantity and quality of nucleic acids. Isolation of nucleic acids was feasible in all storage conditions, however higher temperature and longer duration of fresh cells storage were associated with lower quality of isolated nucleic acids and similar quantification cycle of housekeeping genes. Successful molecular testing was feasible with least 104 cells, while specific mutation was detected in as low as 5% of mutated cells. CONCLUSIONS Our cell line model, mimicking fresh cytology samples, showed that quantity of extracted either DNA or RNA declined with higher temperatures and longer duration of storage but regardless of the storage conditions, we successfully detected both housekeeping genes and mutated gene using qPCR.
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Affiliation(s)
- Ana Dolinar
- Department of molecular genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Gašper Grubelnik
- Department of molecular genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Irena Srebotnik-Kirbiš
- Department of cytopathology, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Margareta Strojan Fležar
- Department of cytopathology, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Margareta Žlajpah
- Department of molecular genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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15
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DNA Sequencing from Subcritical Concentration of Cell-Free DNA Extracted from Electrowetting-on-Dielectric Platform. MICROMACHINES 2022; 13:mi13040507. [PMID: 35457812 PMCID: PMC9031944 DOI: 10.3390/mi13040507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/19/2022] [Accepted: 03/23/2022] [Indexed: 12/04/2022]
Abstract
Electro-Wetting-On-Dielectric (EWOD) based digital operations have demonstrated outstanding potential in actuating and manipulating liquid droplets. Here, we adapted the EWOD for extracting femtogram quantities of cell-free DNA (cf-DNA) from 1 μL of KSOM mouse embryo culture medium. Our group extracted the femtogram quantity of cf-DNA from 1 μL of mouse embryo culture medium in our previous work. Here, we initially explain a modification from our previous extraction protocol, which improves the extraction percentage to 36.74%. Though the modified extraction protocol improves the extraction percentage from our previously reported work, the quantity is still in the femtogram range. The cf-DNA in femtogram quantity is in subcritical/subthreshold concentration for any further analysis, such as sequencing. To the best of our knowledge, we need a minimum of picogram/nanogram DNA quantities for further analysis. We demonstrated a ground-breaking mechanism of this subcritical concentration of cf-DNA amplification to the nanogram range and performed DNA sequencing. Basic Local Alignment Search Tool (BLAST) is used as a sequence similarity search program to confirm the identity percentage between query and subject. More than 97% of nucleotide identities between query and subject sequences have been obtained from the sequencing result. Hence, we can use the methodology to amplify the subcritical concentration of extracted DNA for further analytics. Moreover, as we extract the cf-DNA from the embryo culture medium, the natural growth of the embryo has not been disrupted. This entire mechanism will pave a new path towards the lab-on-a-chip (LOC) concept.
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16
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Karadzovska-Kotevska M, Brunnström H, Kosieradzki J, Ek L, Estberg C, Staaf J, Barath S, Planck M. Feasibility of EBUS-TBNA for histopathological and molecular diagnostics of NSCLC-A retrospective single-center experience. PLoS One 2022; 17:e0263342. [PMID: 35108331 PMCID: PMC8809531 DOI: 10.1371/journal.pone.0263342] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 01/17/2022] [Indexed: 12/24/2022] Open
Abstract
Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is a minimally invasive bronchoscopic procedure, well established as a diagnostic modality of first choice for diagnosis and staging of non-small cell lung cancer (NSCLC). The therapeutic decisions for advanced NSCLC require comprehensive profiling of actionable mutations, which is currently considered to be an essential part of the diagnostic process. The purpose of this study was to evaluate the utility of EBUS-TBNA cytology specimen for histological subtyping, molecular profiling of NSCLC by massive parallel sequencing (MPS), as well as for PD-L1 analysis. A retrospective review of 806 EBUS bronchoscopies was performed, resulting in a cohort of 132 consecutive patients with EBUS-TBNA specimens showing NSCLC cells in lymph nodes. Data on patient demographics, radiology features of the suspected tumor and mediastinal engagement, lymph nodes sampled, the histopathological subtype of NSCLC, and performed molecular analysis were collected. The EBUS-TBNA specimen proved sufficient for subtyping NSCLC in 83% and analysis of treatment predictive biomarkers in 77% (MPS in 53%). The adequacy of the EBUS-TBNA specimen was 69% for EGFR gene mutation analysis, 49% for analysis of ALK rearrangement, 36% for ROS1 rearrangement, and 33% for analysis of PD-L1. The findings of our study confirm that EBUS-TBNA cytology aspirate is appropriate for diagnosis and subtyping of NSCLC and largely also for treatment predictive molecular testing, although more data is needed on the utility of EBUS cytology specimen for MPS and PD-L1 analysis.
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Affiliation(s)
- Marija Karadzovska-Kotevska
- Department of Respiratory Diseases and Allergology, Skåne University Hospital Lund, Lund, Sweden
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
- * E-mail:
| | - Hans Brunnström
- Division of Laboratory Medicine, Department of Genetics and Pathology, Region Skåne, Lund, Sweden
- Division of Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Jaroslaw Kosieradzki
- Department of Respiratory Diseases and Allergology, Skåne University Hospital Lund, Lund, Sweden
| | - Lars Ek
- Department of Respiratory Diseases and Allergology, Skåne University Hospital Lund, Lund, Sweden
| | - Christel Estberg
- Department of Respiratory Diseases and Allergology, Skåne University Hospital Lund, Lund, Sweden
| | - Johan Staaf
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Stefan Barath
- Department of Respiratory Diseases and Allergology, Skåne University Hospital Lund, Lund, Sweden
| | - Maria Planck
- Department of Respiratory Diseases and Allergology, Skåne University Hospital Lund, Lund, Sweden
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
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17
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Maddox A, Smart LM. Technical aspects of the use of cytopathological specimens for diagnosis and predictive testing in malignant epithelial neoplasms of the lung. Cytopathology 2021; 33:23-38. [PMID: 34717021 DOI: 10.1111/cyt.13072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/23/2021] [Accepted: 10/27/2021] [Indexed: 12/13/2022]
Abstract
Lung cancer is a leading cause of cancer mortality worldwide but recent years have seen a rapidly rising proportion of cases of advanced non-small cell carcinoma amenable to increasingly targeted therapy, initially based on the differential response to systemic treatment of tumours of squamous or glandular differentiation. In two-thirds of the cases, where patients present with advanced disease, both primary pathological diagnosis and biomarker testing is based on small biopsies and cytopathological specimens. The framework of this article is an overview of the technical aspect of each stage of the specimen pathway with emphasis on maximising potential for success when using small cytology samples. It brings together the current literature addressing pre-analytical and analytical aspects of specimen acquisition, performing rapid onsite evaluation, and undertaking diagnostic and predictive testing using immunocytochemistry and molecular platforms. The advantages and drawbacks of performing analysis on cell block and non-cell block specimen preparations is discussed.
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Affiliation(s)
- Anthony Maddox
- Department of Cellular Pathology, West Hertfordshire Hospitals NHS Trust, Hemel Hempstead Hospital, Hemel Hempstead, UK
| | - Louise M Smart
- Department of Pathology, Aberdeen Royal Infirmary, Aberdeen, UK
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18
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Kuijvenhoven JC, Kramer T, Korevaar DA, Ninaber MK, Trisolini R, Szlubowski A, Gnass M, von der Thüsen J, Cohen D, Bonta PI, Annema JT. Endobronchial ultrasound in diagnosing and staging of lung cancer by Acquire 22G TBNB versus regular 22G TBNA needles: study protocol of a randomised clinical trial. BMJ Open 2021; 11:e051820. [PMID: 34475187 PMCID: PMC8413963 DOI: 10.1136/bmjopen-2021-051820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
INTRODUCTION Accurate diagnosis and staging of lung cancer is crucial because it directs treatment and prognosis. Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) and endoscopic ultrasound with bronchoscope fine-needle aspiration (EUS-B-FNA) are important in this process by sampling hilar/mediastinal lymph nodes and centrally located lung tumours. With the upcoming of immunotherapy and targeted therapies, assessment of programmed death ligand 1 (PD-L1) expression and molecular profiling has become important but is often impossible in cytological samples obtained through standard 22G TBNA needles. Recently, a three-pronged cutting edge 22G needle was developed that allows for transbronchial needle biopsy (TBNB). Our objective is to determine if EBUS/EUS-B-guided nodal/lung tumour sampling with Acquire 22G TBNB needles results in an improved suitability rate for the assessment of PD-L1 expression in comparison to standard 22G TBNA needles in patients with a final diagnosis of lung cancer. METHODS AND ANALYSIS This is an investigator-initiated, parallel group randomised clinical trial. Patients are recruited at respiratory medicine outpatient clinics of participating university and general hospitals in the Netherlands, Poland and Italy. In total 158 adult patients with (suspected) lung cancer are included if they have an indication for mediastinal/hilar lymph node or lung tumour sampling by EBUS-TBNA and/or EUS-B-FNA based on current clinical guidelines. Web-based randomisation between the two needles will be performed. Samples obtained from mediastinal/hilar lymph nodes and/or primary tumour will be processed for cytology smears and cell block analysis and reviewed by blinded reference pathologists. An intention-to-treat analysis will be applied. Patients with missing data will be excluded from analysis for that specific variable but included in the analysis of other variables. This study is financially supported by Boston Scientific. ETHICS AND DISSEMINATION The study was approved by the local Ethics Committee (Medisch Ethische Toetsingscommissie Amsterdam Medical Center (AMC)). Dissemination will involve publication in a peer-reviewed biomedical journal. TRIAL REGISTRATION NUMBER NL7701; Pre-results.
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Affiliation(s)
- Jolanda C Kuijvenhoven
- Department of Respiratory Medicine, Amsterdam University Medical Centres, Amsterdam, The Netherlands
- Department of Respiratory Medicine, Medical Centre Leeuwarden, Leeuwarden, The Netherlands
| | - Tess Kramer
- Department of Respiratory Medicine, Amsterdam University Medical Centres, Amsterdam, The Netherlands
| | - Daniël A Korevaar
- Department of Respiratory Medicine, Amsterdam University Medical Centres, Amsterdam, The Netherlands
| | - Maarten K Ninaber
- Department of Respiratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Rocco Trisolini
- Department of Respiratory Medicine, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Roma, Italy
| | - Artur Szlubowski
- Department of Respiratory Medicine, Pulmonary Hospital, Zakopane, Poland
| | - Maciej Gnass
- Department of Respiratory Medicine, Pulmonary Hospital, Zakopane, Poland
| | | | - Danielle Cohen
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter I Bonta
- Department of Respiratory Medicine, Amsterdam University Medical Centres, Amsterdam, The Netherlands
| | - Jouke T Annema
- Department of Respiratory Medicine, Amsterdam University Medical Centres, Amsterdam, The Netherlands
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19
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Qin Y, Wang JR, Wang Y, Iyer P, Cote GJ, Busaidy NL, Dadu R, Zafereo M, Williams MD, Ferrarotto R, Gunn GB, Wei P, Patel K, Hofmann MC, Cabanillas ME. Clinical Utility of Circulating Cell-Free DNA Mutations in Anaplastic Thyroid Carcinoma. Thyroid 2021; 31:1235-1243. [PMID: 33599171 PMCID: PMC8420950 DOI: 10.1089/thy.2020.0296] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Background: Anaplastic thyroid carcinoma (ATC) is an aggressive thyroid cancer that requires a rapid diagnosis and treatment to achieve disease control. Gene mutation profiling of circulating cell-free DNA (cfDNA) in peripheral blood may help to facilitate early diagnosis and treatment selection. The relatively rapid turnaround time compared with conventional tumor mutation testing is a major advantage. The objectives of this study were to examine the concordance of ATC-related mutations detected in cfDNA with those detected in the corresponding tumor tissue, and to determine the prognostic significance of cfDNA mutations in ATC patients. Methods: The ATC patients who were diagnosed and treated at The University of Texas MD Anderson Cancer Center between January 2015 and February 2018 and who had cfDNA testing were included in this study. cfDNA was collected by blood draw and was analyzed by next-generation sequencing (NGS) using the Guardant360-73 gene platform. Results: A total of 87 patients were included in the study. The most frequently mutated genes detected in cfDNA were TP53, BRAF, and PIK3CA. In 28 treatment naive ATC patients, the concordance rate of detected mutations in TP53, BRAFV600E, and PIK3CA between cfDNA and matched tissue NGS was 82.1%, 92.9%, and 92.9%, respectively. Patients with a PIK3CA mutation detected on cfDNA had worse overall survival (OS) (p = 0.03). This association was observed across various treatment modalities, including surgery, cytotoxic chemotherapy, radiation, and BRAF inhibitor (BRAFi) therapy. With regard to treatment, BRAFi therapy significantly improved ATC OS (p = 0.003). Conclusions: cfDNA is a valuable tool to evaluate a tumor's molecular profile in ATC patients. We identified high concordance rates between the gene mutations identified via cfDNA analysis and those identified from the NGS of the corresponding tumor tissue sequencing. Identified mutations in cfDNA can potentially provide timely information to guide treatment selection and evaluate the prognosis in patients with ATC.
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Affiliation(s)
- Yu Qin
- Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Endocrinology, Diabetes and Metabolism, Baylor College of Medicine, Houston, Texas, USA
| | - Jennifer R. Wang
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ying Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Priyanka Iyer
- Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Endocrinology, Diabetes and Metabolism, Baylor College of Medicine, Houston, Texas, USA
| | - Gilbert J. Cote
- Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Naifa L. Busaidy
- Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ramona Dadu
- Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mark Zafereo
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Michelle D. Williams
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Renata Ferrarotto
- Department of Thoracic Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - G. Brandon Gunn
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Peng Wei
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Keyur Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Marie-Claude Hofmann
- Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Maria E. Cabanillas
- Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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20
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Bensussan AV, Lin J, Guo C, Katz R, Krishnamurthy S, Cressman E, Eberlin LS. Distinguishing Non-Small Cell Lung Cancer Subtypes in Fine Needle Aspiration Biopsies by Desorption Electrospray Ionization Mass Spectrometry Imaging. Clin Chem 2021; 66:1424-1433. [PMID: 33141910 DOI: 10.1093/clinchem/hvaa207] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 08/17/2020] [Indexed: 11/13/2022]
Abstract
BACKGROUND Distinguishing adenocarcinoma and squamous cell carcinoma subtypes of non-small cell lung cancers is critical to patient care. Preoperative minimally-invasive biopsy techniques, such as fine needle aspiration (FNA), are increasingly used for lung cancer diagnosis and subtyping. Yet, histologic distinction of lung cancer subtypes in FNA material can be challenging. Here, we evaluated the usefulness of desorption electrospray ionization mass spectrometry imaging (DESI-MSI) to diagnose and differentiate lung cancer subtypes in tissues and FNA samples. METHODS DESI-MSI was used to analyze 22 normal, 26 adenocarcinoma, and 25 squamous cell carcinoma lung tissues. Mass spectra obtained from the tissue sections were used to generate and validate statistical classifiers for lung cancer diagnosis and subtyping. Classifiers were then tested on DESI-MSI data collected from 16 clinical FNA samples prospectively collected from 8 patients undergoing interventional radiology guided FNA. RESULTS Various metabolites and lipid species were detected in the mass spectra obtained from lung tissues. The classifiers generated from tissue sections yielded 100% accuracy, 100% sensitivity, and 100% specificity for lung cancer diagnosis, and 73.5% accuracy for lung cancer subtyping for the training set of tissues, per-patient. On the validation set of tissues, 100% accuracy for lung cancer diagnosis and 94.1% accuracy for lung cancer subtyping were achieved. When tested on the FNA samples, 100% diagnostic accuracy and 87.5% accuracy on subtyping were achieved per-slide. CONCLUSIONS DESI-MSI can be useful as an ancillary technique to conventional cytopathology for diagnosis and subtyping of non-small cell lung cancers.
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Affiliation(s)
- Alena V Bensussan
- Department of Chemistry, The University of Texas at Austin, Austin, TX
| | - John Lin
- Department of Chemistry, The University of Texas at Austin, Austin, TX
| | - Chunxiao Guo
- Department of Interventional Radiology, Division of Diagnostic Imaging, MD Anderson Cancer Center, Houston, TX
| | - Ruth Katz
- Department of Pathology, Division of Pathology and Laboratory Medicine, MD Anderson Cancer Center, Houston, TX
| | - Savitri Krishnamurthy
- Department of Pathology, Division of Pathology and Laboratory Medicine, MD Anderson Cancer Center, Houston, TX
| | - Erik Cressman
- Department of Interventional Radiology, Division of Diagnostic Imaging, MD Anderson Cancer Center, Houston, TX
| | - Livia S Eberlin
- Department of Chemistry, The University of Texas at Austin, Austin, TX
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21
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Faber E, Grosu H, Sabir S, San Lucas FA, Barkoh BA, Bassett RL, Luthra R, Stewart J, Roy-Chowdhuri S. Adequacy of small biopsy and cytology specimens for comprehensive genomic profiling of patients with non-small-cell lung cancer to determine eligibility for immune checkpoint inhibitor and targeted therapy. J Clin Pathol 2021; 75:612-619. [PMID: 33952592 DOI: 10.1136/jclinpath-2021-207597] [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: 04/01/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 11/03/2022]
Abstract
AIMS In advanced-stage non-small-cell lung cancer (NSCLC), incomplete genotyping for guideline-recommended genomic biomarkers poses a significant challenge to making informed and timely clinical decisions. We report our institution's experience in assessing the adequacy of small specimens for comprehensive genomic profiling for guideline-recommended lung cancer biomarker testing. METHODS We performed a retrospective evaluation of all image-guided procedures for NSCLC performed in our institution between October 2016 and July 2018, including core needle biopsy (CNB) and fine-needle aspiration (FNA) in patients who had undergone genomic profiling for lung cancer. Lung cancer biomarker adequacy, defined as successful testing of guideline-recommended biomarkers including, epidermal growth factor receptor (EGFR); serine/threonine protein kinase B-Raf (BRAF); anaplastic lymphoma kinase (ALK); proto-oncogene tyrosine protein kinase ROS (ROS1); Rearranged during Transfection (RET); Tyrosine protein kinase Met (MET); and programmed cell death ligand 1 (PD-L1), was evaluated. RESULTS A total of 865 cases were evaluated in this study, 785 of which included testing of all lung cancer biomarkers. Lung tissue was adequate for biomarker testing in 84% of cases; this rate increased to 87% when biomarker testing was combined with concurrently acquired FNA or CNB specimens. Biomarker testing success correlated strongly with DNA concentration (p<0.0001) and the use of 22G needles in endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) procedures (p=0.0035). Biomarker testing of CNB specimens showed a significantly higher success rate than did biomarker testing of cytology FNA specimens (p=0.0005). The adequacy of EBUS-TBNA samples was not significantly different from that of the transthoracic needle aspiration samples (p=0.40). Variables such as age, gender, lesion size, site, diagnosis and number of needle passes showed no significant correlation with success rates in lung cancer biomarker testing. CONCLUSION The growing numbers of therapeutic biomarkers in NSCLC requires judicious triage of limited-volume tissue from small specimens. Our study showed that thoracic small tissue specimens can be used successfully to provide prognostic and predictive information for the current guideline-recommended biomarkers for NSCLC in most cases.
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Affiliation(s)
- Erin Faber
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Horiana Grosu
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sharjeel Sabir
- Department of Interventional Radiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Francis Anthony San Lucas
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Bedia A Barkoh
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Roland L Bassett
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Rajyalakshmi Luthra
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - John Stewart
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sinchita Roy-Chowdhuri
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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22
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Emerging Entities and New Diagnostic Markers for Head and Neck Soft Tissue and Bone Tumors. Adv Anat Pathol 2021; 28:139-149. [PMID: 33559990 DOI: 10.1097/pap.0000000000000295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Bone and soft tissue tumors of the head and neck are relatively uncommon tumors that often represent a diagnostic challenge because of the wide range of entities that must be considered in the differential diagnosis. Over the past few years, classification of bone and soft tissue tumors has evolved primarily because of substantial contributions from molecular genetics, with the identification of new markers that are increasingly used to complement histopathologic findings in the routine diagnostic workup. This review focuses on the recently described mesenchymal tumors that preferentially involve the head and neck region, with a focus on the most relevant novel immunohistochemical and molecular findings, including gene fusions and mutations, that can help in the diagnosis and in the assessment of clinical behavior.
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23
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Amemiya K, Hirotsu Y, Nagakubo Y, Mochizuki H, Higuchi R, Tsutsui T, Kakizaki Y, Miyashita Y, Oyama T, Omata M. Actionable driver DNA variants and fusion genes can be detected in archived cytological specimens with the Oncomine Dx Target Test Multi-CDx system in lung cancer. Cancer Cytopathol 2021; 129:729-738. [PMID: 33872472 DOI: 10.1002/cncy.22434] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/11/2021] [Accepted: 03/23/2021] [Indexed: 01/04/2023]
Abstract
BACKGROUND Molecular testing is critical for identifying actionable variants in lung cancer for precision medicine. When tumor tissue samples are unavailable, archived cytological specimens (ACSs) can be used. The authors examined whether oncogenic variants could be accurately detected in ACSs versus paired formalin-fixed, paraffin-embedded (FFPE) tumor tissues with in vitro diagnostic tests. METHODS The authors collected 18 ACSs and 15 FFPE tissues from 15 patients with lung cancer and investigated genomic profiles with the Oncomine Dx Target Test Multi-CDx system, which is an integrated next-generation sequencing platform that comprehensively examines 4 companion diagnostic target genes (epidermal growth factor receptor [EGFR]; B-Raf proto-oncogene, serine/threonine kinase [BRAF]; anaplastic lymphoma kinase [ALK]; and ROS proto-oncogene 1, receptor tyrosine kinase [ROS1]). They compared the quantity and quality of extracted nucleic acids, the sequencing quality control (QC), and the detected variants between ACSs and FFPE tissues. RESULTS The total amount of DNA and RNA obtained from 1 slide was higher in FFPE tissues than ACSs. The RNA integrity number was higher in ACSs. There were no differences in sequencing QC between ACSs and FFPE tissues. A total of 21 variants, including EGFR mutations and ALK and ROS1 fusion genes, were detected in both ACSs and FFPE tissues with 100% concordance. CONCLUSIONS ACSs can be a feasible alternative with which to identify actionable mutations and fusion genes via the Oncomine Dx Target Test Multi-CDx system.
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Affiliation(s)
- Kenji Amemiya
- Genome Analysis Center, Yamanashi Central Hospital, Kofu, Japan.,Division of Genetics and Clinical Laboratory, Yamanashi Central Hospital, Kofu, Japan
| | - Yosuke Hirotsu
- Genome Analysis Center, Yamanashi Central Hospital, Kofu, Japan
| | - Yuki Nagakubo
- Division of Genetics and Clinical Laboratory, Yamanashi Central Hospital, Kofu, Japan
| | | | - Rumi Higuchi
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Kofu, Japan
| | - Toshiharu Tsutsui
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Kofu, Japan
| | - Yumiko Kakizaki
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Kofu, Japan
| | - Yoshihiro Miyashita
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Kofu, Japan
| | - Toshio Oyama
- Pathology Division, Laboratory Department, Yamanashi Prefectural Central Hospital, Kofu, Japan
| | - Masao Omata
- Department of Gastroenterology, Yamanashi Central Hospital, Kofu, Japan.,Department of Gastroenterology, University of Tokyo, Tokyo, Japan
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Nakashima K, Demura Y, Oi M, Tabata M, Tada T, Shiozaki K, Akai M, Ishizuka T. Utility of Endoscopic Ultrasound with Bronchoscope-guided Fine-needle Aspiration for Detecting Driver Oncogenes in Non-small-cell Lung Cancer during Emergency Situations: Case Series. Intern Med 2021; 60:1061-1065. [PMID: 33132332 PMCID: PMC8079917 DOI: 10.2169/internalmedicine.5594-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Since it is difficult to obtain tumor tissue via airway observation for lung cancer patients with a poor respiratory condition, endoscopic ultrasound with bronchoscope-guided fine-needle-aspiration (EUS-B-FNA), a transesophageal procedure, is effective for such patients. We herein report three patients with driver oncogenes taken to the emergency department because of lung cancer-related symptoms. EUS-B-FNA was performed because of the patients' poor respiratory conditions to detect driver oncogenes. The general conditions improved, and the patients achieved a long-term survival with tyrosine kinase inhibitors. Our findings suggest that EUS-B-FNA should be considered to detect driver oncogenes in lung cancer patients despite poor respiratory conditions in emergency departments.
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Affiliation(s)
- Koki Nakashima
- Department of Respiratory Medicine, Japanese Red Cross Fukui Hospital, Japan
- Third Department of Internal Medicine, Faculty of Medical Sciences, University of Fukui, Japan
| | - Yoshiki Demura
- Department of Respiratory Medicine, Japanese Red Cross Fukui Hospital, Japan
| | - Masahiro Oi
- Department of Respiratory Medicine, Japanese Red Cross Fukui Hospital, Japan
| | - Mio Tabata
- Department of Respiratory Medicine, Japanese Red Cross Fukui Hospital, Japan
| | - Toshihiko Tada
- Department of Respiratory Medicine, Japanese Red Cross Fukui Hospital, Japan
| | - Kohei Shiozaki
- Department of Respiratory Medicine, Japanese Red Cross Fukui Hospital, Japan
| | - Masaya Akai
- Department of Respiratory Medicine, Japanese Red Cross Fukui Hospital, Japan
| | - Tamotsu Ishizuka
- Third Department of Internal Medicine, Faculty of Medical Sciences, University of Fukui, Japan
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25
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Sgariglia R, Nacchio M, Migliatico I, Vigliar E, Malapelle U, Pisapia P, De Luca C, Iaccarino A, Salvatore D, Masone S, Troncone G, Bellevicine C. Moving towards a local testing solution for undetermined thyroid fine-needle aspirates: validation of a novel custom DNA-based NGS panel. J Clin Pathol 2021; 75:465-471. [PMID: 33789920 DOI: 10.1136/jclinpath-2021-207429] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/03/2021] [Accepted: 03/06/2021] [Indexed: 01/04/2023]
Abstract
AIMS In thyroid cytopathology, the undetermined diagnostic categories still pose diagnostic challenges. Although next-generation sequencing (NGS) is a promising technique for the molecular testing of thyroid fine-needle aspiration (FNA) specimens, access to such technology can be difficult because of its prohibitive cost and lack of reimbursement in countries with universal health coverage. To overcome these issues, we developed and validated a novel custom NGS panel, Nexthyro, specifically designed to target 264 clinically relevant mutations involved in thyroid tumourigenesis. Moreover, in this study, we compared its analytical performance with that of our previous molecular testing strategy. METHODS The panel, which includes 15 genes (BRAF, EIF1AX, GNAS, HRAS, IDH1, KRAS, NF2, NRAS, PIK3CA, PPM1D, PTEN, RET, DICER1, CHEK2, TERT promoter), was validated with a cell-line derived reference standard and 72 FNA archival samples previously tested with the 7-gene test. RESULTS Nexthyro yielded 100% specificity and detected mutant alleles at levels as low as 2%. Moreover, in 5/72 (7%) FNAs, it detected more clinically relevant mutations in BRAF and RAS genes compared with the 7-gene test. Nexthyro also revealed better postsequencing metrics than the previously adopted commercial 'generic' NGS panel. CONCLUSION Our comparative analysis indicates that Nexthyro is a reliable NGS panel. The study also implies that a custom-based solution for routine thyroid FNA is sustainable at the local level, allowing patients with undetermined thyroid nodules affordable access to NGS.
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Affiliation(s)
| | | | | | - Elena Vigliar
- Public Health, University of Naples Federico II, Naples, Italy
| | | | | | | | | | | | - Stefania Masone
- Clinical Medicine and Surgery, General Surgery Unit, University of Naples Federico II, Naples, Italy
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26
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SoRelle JA, Wachsmann M, Cantarel BL. Assembling and Validating Bioinformatic Pipelines for Next-Generation Sequencing Clinical Assays. Arch Pathol Lab Med 2020; 144:1118-1130. [PMID: 32045276 DOI: 10.5858/arpa.2019-0476-ra] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2019] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Clinical next-generation sequencing (NGS) is being rapidly adopted, but analysis and interpretation of large data sets prompt new challenges for a clinical laboratory setting. Clinical NGS results rely heavily on the bioinformatics pipeline for identifying genetic variation in complex samples. The choice of bioinformatics algorithms, genome assembly, and genetic annotation databases are important for determining genetic alterations associated with disease. The analysis methods are often tuned to the assay to maximize accuracy. Once a pipeline has been developed, it must be validated to determine accuracy and reproducibility for samples similar to real-world cases. In silico proficiency testing or institutional data exchange will ensure consistency among clinical laboratories. OBJECTIVE.— To provide molecular pathologists a step-by-step guide to bioinformatics analysis and validation design in order to navigate the regulatory and validation standards of implementing a bioinformatic pipeline as a part of a new clinical NGS assay. DATA SOURCES.— This guide uses published studies on genomic analysis, bioinformatics methods, and methods comparison studies to inform the reader on what resources, including open source software tools and databases, are available for genetic variant detection and interpretation. CONCLUSIONS.— This review covers 4 key concepts: (1) bioinformatic analysis design for detecting genetic variation, (2) the resources for assessing genetic effects, (3) analysis validation assessment experiments and data sets, including a diverse set of samples to mimic real-world challenges that assess accuracy and reproducibility, and (4) if concordance between clinical laboratories will be improved by proficiency testing designed to test bioinformatic pipelines.
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Affiliation(s)
- Jeffrey A SoRelle
- Department of Pathology (SoRelle, Wachsmann), University of Texas Southwestern Medical Center, Dallas
| | - Megan Wachsmann
- Department of Pathology (SoRelle, Wachsmann), University of Texas Southwestern Medical Center, Dallas
| | - Brandi L Cantarel
- Bioinformatics Core Facility (Cantarel), University of Texas Southwestern Medical Center, Dallas.,Department of Bioinformatics (Cantarel), University of Texas Southwestern Medical Center, Dallas.,University of Texas Southwestern Medical Center, Dallas
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27
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Gentien D, Piqueret-Stephan L, Henry E, Albaud B, Rapinat A, Koscielny S, Scoazec JY, Vielh P. Digital Multiplexed Gene Expression Analysis of mRNA and miRNA from Routinely Processed and Stained Cytological Smears: A Proof-of-Principle Study. Acta Cytol 2020; 65:88-98. [PMID: 33011718 DOI: 10.1159/000510174] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/14/2020] [Indexed: 12/20/2022]
Abstract
OBJECTIVE Although transcriptomic assessments of small samples using high-throughput techniques are usually performed on fresh or frozen tissues, there is a growing demand for those performed on stained cellular specimens already used for diagnostic purposes. STUDY DESIGN The possibility of detecting mRNAs and microRNAs (miRNAs) from routinely processed cytological samples using nCounter® technology was explored. Fresh samples from pleural and peritoneal effusions were analyzed using 2 parallel methods: samples were smeared and routinely stained using the May-Grünwald-Giemsa or Diff-Quik® method and mounted using conventional methods, and they were also studied following a snap freezing method, in which samples were maintained at -80°C until use. mRNAs and miRNAs were assessed and compared after total RNA extraction from both routinely processed samples and their matched frozen controls. RESULTS A good concordance was found between the gene expression measured in routinely processed samples and their matched frozen controls for the majority of mRNAs and miRNAs tested. However, the standard deviation of low-expressed miRNA was high. CONCLUSIONS Although nCounter® technology is a robust method to measure and characterize both mRNAs and miRNAs from routinely processed cytological samples, caution is recommended for the interpretation of low-expressed miRNA.
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Affiliation(s)
- David Gentien
- Translational Research Department, Genomics Platform, Institut Curie, PSL Research University, Paris, France
| | - Laure Piqueret-Stephan
- INSERM UMR 981, Villejuif, France
- Translational Research Laboratory, AMMICa (CNRS UMS3655, INSERM US23, Paris Sud University) Gustave Roussy, Villejuif, France
| | - Emilie Henry
- Translational Research Department, Genomics Platform, Institut Curie, PSL Research University, Paris, France
| | - Benoît Albaud
- Translational Research Department, Genomics Platform, Institut Curie, PSL Research University, Paris, France
| | - Audrey Rapinat
- Translational Research Department, Genomics Platform, Institut Curie, PSL Research University, Paris, France
| | - Serge Koscielny
- Department of Biostatistics, Gustave Roussy, Villejuif, France
| | - Jean-Yves Scoazec
- Translational Research Laboratory, AMMICa (CNRS UMS3655, INSERM US23, Paris Sud University) Gustave Roussy, Villejuif, France
- Department of Medical Biology and Pathology, Gustave Roussy, Villejuif, France
| | - Philippe Vielh
- INSERM UMR 981, Villejuif, France,
- Translational Research Laboratory, AMMICa (CNRS UMS3655, INSERM US23, Paris Sud University) Gustave Roussy, Villejuif, France,
- Department of Medical Biology and Pathology, Gustave Roussy, Villejuif, France,
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28
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Ono Y, Hayashi A, Maeda C, Suzuki M, Wada R, Sato H, Kawabata H, Okada T, Goto T, Karasaki H, Mizukami Y, Okumura T. Time-saving method for directly amplifying and capturing a minimal amount of pancreatic tumor-derived mutations from fine-needle aspirates using digital PCR. Sci Rep 2020; 10:12332. [PMID: 32704002 PMCID: PMC7378187 DOI: 10.1038/s41598-020-69221-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 06/23/2020] [Indexed: 02/08/2023] Open
Abstract
It is challenging to secure a cytopathologic diagnosis using minute amounts of tumor fluids and tissue fragments. Hence, we developed a rapid, accurate, low-cost method for detecting tumor cell-derived DNA from limited amounts of specimens and samples with a low tumor cellularity, to detect KRAS mutations in pancreatic ductal carcinomas (PDA) using digital PCR (dPCR). The core invention is based on the suspension of tumor samples in pure water, which causes an osmotic burst; the crude suspension could be directly subjected to emulsion PCR in the platform. We examined the feasibility of this process using needle aspirates from surgically resected pancreatic tumor specimens (n = 12). We successfully amplified and detected mutant KRAS in 11 of 12 tumor samples harboring the mutation; the positive mutation frequency was as low as 0.8%. We used residual specimens from fine-needle aspiration/biopsy and needle flush processes (n = 10) for method validation. In 9 of 10 oncogenic KRAS pancreatic tumor samples, the "water-burst" method resulted in a positive mutation call. We describe a dPCR-based, super-sensitive screening protocol for determining KRAS mutation availability using tiny needle aspirates from PDAs processed using simple steps. This method might enable pathologists to secure a more accurate, minimally invasive diagnosis using minute tissue fragments.
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Affiliation(s)
- Yusuke Ono
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido, 065-0033, Japan
- Division of Gastroenterology and Hepatology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, 078-8510, Japan
| | - Akihiro Hayashi
- Division of Gastroenterology and Hepatology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, 078-8510, Japan
| | - Chiho Maeda
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido, 065-0033, Japan
| | - Mayumi Suzuki
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido, 065-0033, Japan
| | - Reona Wada
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido, 065-0033, Japan
| | - Hiroki Sato
- Division of Gastroenterology and Hepatology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, 078-8510, Japan
| | - Hidemasa Kawabata
- Division of Gastroenterology and Hepatology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, 078-8510, Japan
| | - Tetsuhiro Okada
- Division of Gastroenterology and Hepatology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, 078-8510, Japan
| | - Takuma Goto
- Division of Gastroenterology and Hepatology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, 078-8510, Japan
| | - Hidenori Karasaki
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido, 065-0033, Japan
| | - Yusuke Mizukami
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido, 065-0033, Japan.
- Division of Gastroenterology and Hepatology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, 078-8510, Japan.
| | - Toshikatsu Okumura
- Division of Gastroenterology and Hepatology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, 078-8510, Japan
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29
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Hoelz L, Mesgary A, Achar E, Gimenez M, Saieg M. Cytopathology smears from autopsies: A viable storage method for molecular analysis. Cytopathology 2020; 32:617-620. [PMID: 32542774 DOI: 10.1111/cyt.12874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 06/01/2020] [Accepted: 06/06/2020] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Cytology appears to be a viable option to histological samples for proper storage and maintenance of autopsy material for DNA extraction and analysis. In the present study, we tested the feasibility of using archived air-dried smears produced at the time of the autopsy for simple molecular analysis, comparing quantity and quality of the DNA extracted from the smears to that of correspondent histological specimens. METHODS Air-dried cytological smears were obtained from scrapings of exactly the same areas collected for histological study. DNA was extracted using a commercially available protocol from all samples, with calculation of purity ratio and overall concentration. The integrity of the extracted DNA was also verified through conventional polymerase chain reaction (PCR). RESULTS Five cases of lung tumours (2 small cell carcinomas and 3 adenocarcinomas) were collected. Percentage of tumour cells and necrosis ranged from 30% to 90% and from 10% to 40%, respectively, in the cytological preparations, and from 50% to 90% and from 10% to 80%, respectively, in the histological preparations. Purity ratio (260/280) had a median of 1.87 in cytology vs 1.94 in histology. Mean DNA concentration among the cytological preparations was 2653 ng/mL (range 1684-3980 ng/mL) vs 757.2 ng/mL among the histological preparations (range 456-1829 ng/mL. DNA from all five cases of cytology was successfully amplified by conventional PCR, in contrast to none from the histology specimens. CONCLUSIONS Archived air-dried smears scraped from tumoural lesions in autopsies have proven to yield a good concentration of quality DNA for conventional PCR, with better results than formalin-fixed paraffin embedded material.
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Affiliation(s)
- Lucas Hoelz
- Santa Casa Medical School, São Paulo, Brazil
| | | | | | | | - Mauro Saieg
- Santa Casa Medical School, São Paulo, Brazil.,AC Camargo Cancer Center, São Paulo, Brazil
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30
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Kunimasa K, Hirotsu Y, Amemiya K, Nagakubo Y, Goto T, Miyashita Y, Kakizaki Y, Tsutsui T, Otake S, Kobayashi H, Higuchi R, Inomata K, Kumagai T, Mochizuki H, Nakamura H, Nakatsuka SI, Nishino K, Imamura F, Kumagai T, Oyama T, Omata M. Genome analysis of peeling archival cytology samples detects driver mutations in lung cancer. Cancer Med 2020; 9:4501-4511. [PMID: 32351019 PMCID: PMC7333826 DOI: 10.1002/cam4.3089] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/09/2020] [Accepted: 04/13/2020] [Indexed: 12/11/2022] Open
Abstract
INTRODUCTIONS When tumor tissue samples are unavailable to search for actionable driver mutations, archival cytology samples can be useful. We investigate whether archival cytology samples can yield reliable genomic information compared to corresponding formalin-fixed paraffin-embedded (FFPE) tumor samples. PATIENTS AND METHODS Pretreatment class V archival cytology samples with adequate tumor cells were selected from 172 lung cancer patients. The genomic profiles of the primary lung tumors have been analyzed through whole-exome regions of 53 genes. We compared the genomic profiles based on the oncogenicity and variant allele frequency (VAF) between the archival cytology and the corresponding primary tumors. We also analyzed the genomic profiles of serial cytological samples during the treatment of EGFR-TKI. RESULTS A total of 43 patients were analyzed with the paired samples for DNA mutations and other three patients were analyzed for their fusion genes. A total of 672 mutations were detected. Of those, 106 mutations (15.8%) were shared with both samples. Sixty of seventy-seven (77.9%) shared mutations were oncogenic or likely oncogenic mutations with VAF ≧10%. As high as 90% (9/10) actionable driver mutations and ALK and ROS1 fusion genes were successfully detected from archival cytology samples. Sequential analysis revealed the dynamic changes in EGFR-TKI-resistant mutation (EGFR p.T790M) during the course of treatment. CONCLUSION Archival cytology sample with adequate tumor cells can yield genetic information compared to the primary tumors. If tumor tissue samples are unavailable, we can use archival cytology samples to search for actionable driver mutations.
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Affiliation(s)
- Kei Kunimasa
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan.,Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Yosuke Hirotsu
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Kenji Amemiya
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Yuki Nagakubo
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Taichiro Goto
- Department of Surgery, School of Medicine, Keio University, Tokyo, Japan.,Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Yoshihiro Miyashita
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Yumiko Kakizaki
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Toshiharu Tsutsui
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Sotaro Otake
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Hiroaki Kobayashi
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Rumi Higuchi
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Kie Inomata
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Takashi Kumagai
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Hitoshi Mochizuki
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Harumi Nakamura
- Department of Diagnostic Pathology and Cytology, Osaka International Cancer Institute, Osaka, Japan
| | - Shin-Ichi Nakatsuka
- Department of Diagnostic Pathology and Cytology, Osaka International Cancer Institute, Osaka, Japan
| | - Kazumi Nishino
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Fumio Imamura
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Toru Kumagai
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Toshio Oyama
- Department of Pathology, Yamanashi Central Hospital, Yamanashi, Japan
| | - Masao Omata
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan.,The University of Tokyo, Tokyo, Japan
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31
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Ruiz-Cordero R, Ma J, Khanna A, Lyons G, Rinsurongkawong W, Bassett R, Guo M, Routbort MJ, Zhang J, Skoulidis F, Heymach J, Roarty EB, Tang Z, Medeiros LJ, Patel KP, Luthra R, Roy-Chowdhuri S. Simplified molecular classification of lung adenocarcinomas based on EGFR, KRAS, and TP53 mutations. BMC Cancer 2020; 20:83. [PMID: 32005111 PMCID: PMC6995064 DOI: 10.1186/s12885-020-6579-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 01/24/2020] [Indexed: 01/25/2023] Open
Abstract
Background Gene expression profiling has consistently identified three molecular subtypes of lung adenocarcinoma that have prognostic implications. To facilitate stratification of patients with this disease into similar molecular subtypes, we developed and validated a simple, mutually exclusive classification. Methods Mutational status of EGFR, KRAS, and TP53 was used to define seven mutually exclusive molecular subtypes. A development cohort of 283 cytology specimens of lung adenocarcinoma was used to evaluate the associations between the proposed classification and clinicopathologic variables including demographic characteristics, smoking history, fluorescence in situ hybridization and molecular results. For validation and prognostic assessment, 63 of the 283 cytology specimens with available survival data were combined with a separate cohort of 428 surgical pathology specimens of lung adenocarcinoma. Results The proposed classification yielded significant associations between these molecular subtypes and clinical and prognostic features. We found better overall survival in patients who underwent surgery and had tumors enriched for EGFR mutations. Worse overall survival was associated with older age, stage IV disease, and tumors with co-mutations in KRAS and TP53. Interestingly, neither chemotherapy nor radiation therapy showed benefit to overall survival. Conclusions The mutational status of EGFR, KRAS, and TP53 can be used to easily classify lung adenocarcinoma patients into seven subtypes that show a relationship with prognosis, especially in patients who underwent surgery, and these subtypes are similar to classifications based on more complex genomic methods reported previously.
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Affiliation(s)
- Roberto Ruiz-Cordero
- Department of Pathology, University of California San Francisco, 1825 4th Street, Room L2181A, San Francisco, CA, 94158, USA.
| | - Junsheng Ma
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Abha Khanna
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Genevieve Lyons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Waree Rinsurongkawong
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Roland Bassett
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ming Guo
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mark J Routbort
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianjun Zhang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ferdinandos Skoulidis
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John Heymach
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Emily B Roarty
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhenya Tang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - L Jeffrey Medeiros
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Keyur P Patel
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rajyalakshmi Luthra
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sinchita Roy-Chowdhuri
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Targeted Gene Next-Generation Sequencing Panel in Patients with Advanced Lung Adenocarcinoma: Paving the Way for Clinical Implementation. Cancers (Basel) 2019; 11:cancers11091229. [PMID: 31443496 PMCID: PMC6770536 DOI: 10.3390/cancers11091229] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/04/2019] [Accepted: 08/15/2019] [Indexed: 12/24/2022] Open
Abstract
Identification of targetable molecular changes is essential for selecting appropriate treatment in patients with advanced lung adenocarcinoma. Methods: In this study, a Sanger sequencing plus Fluorescence In Situ Hybridization (FISH) sequential approach was compared with a Next-Generation Sequencing (NGS)-based approach for the detection of actionable genomic mutations in an experimental cohort (EC) of 117 patients with advanced lung adenocarcinoma. Its applicability was assessed in small biopsies and cytology specimens previously tested for epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase (ALK) mutational status, comparing the molecular changes identified and the impact on clinical outcomes. Subsequently, an NGS-based approach was applied and tested in an implementation cohort (IC) in clinical practice. Using Sanger and FISH, patients were classified as EGFR-mutated (n = 22, 18.8%), ALK-mutated (n = 9, 7.7%), and unclassifiable (UC) (n = 86, 73.5%). Retesting the EC with NGS led to the identification of at least one gene variant in 56 (47.9%) patients, totaling 68 variants among all samples. Still, in the EC, combining NGS plus FISH for ALK, patients were classified as 23 (19.7%) EGFR; 20 (17.1%) KRAS; five (4.3%) B-Raf proto-oncogene (BRAF); one (0.9%) Erb-B2 Receptor Tyrosine Kinase 2 (ERBB2); one (0.9%) STK11; one (0.9%) TP53, and nine (7.7%) ALK mutated. Only 57 (48.7%) remained genomically UC, reducing the UC rate by 24.8%. Fourteen (12.0%) patients presented synchronous alterations. Concordance between NGS and Sanger for EGFR status was very high (κ = 0.972; 99.1%). In the IC, a combined DNA and RNA NGS panel was used in 123 patients. Genomic variants were found in 79 (64.2%). In addition, eight (6.3%) EML4-ALK, four (3.1%), KIF5B-RET, four (3.1%) CD74-ROS1, one (0.8%) TPM3-NTRK translocations and three (2.4%) exon 14 skipping MET Proto-Oncogene (MET) mutations were detected, and 36% were treatable alterations. Conclusions: This study supports the use of NGS as the first-line test for genomic profiling of patients with advanced lung adenocarcinoma.
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McHugh KE, Dermawan JK, Cheng YW, Cruise M, Sohal DPS, Reynolds JP. Molecular testing in metastatic colorectal adenocarcinoma cytology cell pellets. Diagn Cytopathol 2019; 47:1132-1137. [PMID: 31290252 DOI: 10.1002/dc.24275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/05/2019] [Accepted: 06/25/2019] [Indexed: 01/22/2023]
Abstract
BACKGROUND Mutational status for KRAS, NRAS, and BRAF genes should be performed on all colorectal carcinoma (CRC) specimens in order to guide targeted therapy selection for metastatic disease. Mutations are typically assessed via polymerase chain reaction and/or next generation sequencing (NGS) on formalin-fixed paraffin-embedded tissues. With minimally invasive diagnostic methodologies, the cytology cell pellet obtained by fine-needle aspiration (FNA) can serve as an alternative source of tumor deoxyribonucleic acid. METHODS An electronic record review of the cytopathology files (CoPathPlus, Cerner Corp., North Kansas City, Missouri) from September 1, 2015 through December 31, 2018 was conducted. All cytology specimens obtained via FNA and diagnosed as metastatic CRC on which NGS was performed were included. NGS for KRAS, NRAS, and BRAF mutations using the AmpliSeq Cancer Hotspot Panel v2.0 kit (Thermo Fisher Scientific, Waltham, Massachusetts) was performed on cytology cell pellets. RESULTS Forty-eight cases were identified. Forty-six of 48 specimens (96%) were adequate for molecular testing. Of those adequate specimens, proportion of malignant cells in the sample ranged from 5% to 95% (mean 46%). Twenty-seven of 48 cases (56%) were positive for clinically relevant mutations. Twenty-four of 27 cases (89%) were positive for KRAS mutations, with exon 2 most frequently involved (22/24 cases, 92%). Two of 27 cases (7%) were positive for NRAS mutations and one case (1/27, 4%) was positive for a BRAF mutation involving codon 594. CONCLUSION Mutational analysis performed on cytology cell pellets serves as a useful means of gathering clinically actionable information on tumor mutation status in metastatic CRC.
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Affiliation(s)
- Kelsey E McHugh
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Josephine K Dermawan
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Yu-Wei Cheng
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Michael Cruise
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Davendra P S Sohal
- Department of Hematology and Medical Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio
| | - Jordan P Reynolds
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
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Roy-Chowdhuri S, Pisapia P, Salto-Tellez M, Savic S, Nacchio M, de Biase D, Tallini G, Troncone G, Schmitt F. Invited review-next-generation sequencing: a modern tool in cytopathology. Virchows Arch 2019; 475:3-11. [PMID: 30877381 DOI: 10.1007/s00428-019-02559-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 02/26/2019] [Accepted: 03/04/2019] [Indexed: 02/05/2023]
Abstract
In recent years, cytopathology has established itself as an independent diagnostic modality to guide clinical management in many different settings. The application of molecular techniques to cytological samples to identify prognostic and predictive biomarkers has played a crucial role in achieving this goal. While earlier studies have demonstrated that single biomarker testing is feasible on cytological samples, currently, this provides only limited and increasingly insufficient information in an era where an increasing number of biomarkers are required to guide patient care. More recently, multigene mutational assays, such as next-generation sequencing (NGS), have gained popularity because of their ability to provide genomic information on multiple genes. The cytopathologist plays a key role in ensuring success of NGS in cytological samples by influencing the pre-analytical steps, optimizing preparation types and adequacy requirement in terms of cellularity and tumor fraction, and ensuring optimal nucleic acid extraction for DNA input requirements. General principles of the role and potential of NGS in molecular cytopathology in the universal healthcare (UHC) European environment and examples of principal clinical applications were discussed in the workshop that took place at the 30th European Congress of Pathology in Bilbao, European Society of Pathology, whose content is here comprehensively described.
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Affiliation(s)
- Sinchita Roy-Chowdhuri
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Via Sergio Pansini 5, 80131, Naples, Italy
| | - Manuel Salto-Tellez
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Spasenija Savic
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Mariantonia Nacchio
- Department of Public Health, University of Naples Federico II, Via Sergio Pansini 5, 80131, Naples, Italy
| | - Dario de Biase
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giovanni Tallini
- Anatomic Pathology, University of Bologna Medical Center, Bologna, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Via Sergio Pansini 5, 80131, Naples, Italy.
| | - Fernando Schmitt
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Department of Pathology, Medical Faculty of Porto University, Porto, Portugal
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Lin SC, Lin LH, Yu SY, Kao SY, Chang KW, Cheng HW, Liu CJ. FAT1 somatic mutations in head and neck carcinoma are associated with tumor progression and survival. Carcinogenesis 2019; 39:1320-1330. [PMID: 30102337 DOI: 10.1093/carcin/bgy107] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 08/08/2018] [Indexed: 02/06/2023] Open
Abstract
In recent years, the incidence and mortality rates of head and neck squamous cell carcinoma (HNSCC) have increased worldwide. Therefore, understanding genomic alterations in HNSCC carcinogenesis is crucial for appropriate diagnosis and therapy. Protocadherin FAT1, which encodes 4588 amino acid residues, regulates complex mechanisms to promote oncogenesis or suppression of malignancies. Multiplex PCR-based next-generation sequencing (NGS) revealed FAT1 somatic mutations. The clinicopathologic implications of FAT1 in HNSCC were investigated using expression assays, and the functional role of FAT1 in HNSCC pathogenesis was determined using ectopic expression and knockdown experiments. Approximately 29% patients with HNSCC harbored damaging FAT1 mutations. InVEx algorithm identified FAT1 as a significant functional mutation burden. Each type of mutation (missense, nonsense and frameshift) accounted for nearly one-third of deleterious mutations. FAT1 mutations correlated with lower FAT1 expression in tumors. The knockdown of the endogenous expression of FAT1 and exogenous expression of crucial FAT1 domains unequivocally indicated that FAT1 suppressed the migration and invasion capability of HNSCC cells. Functional analysis suggested that nonsense mutations in FAT1 result in the loss of the suppression of tumor progression. FAT1 mutations and downregulation defined nodal involvement, lymphovascular permeation and tumor recurrence. In addition, FAT1 mutations and downregulation are independent predictors of poor disease-free survival in patients with HNSCC. This study is the first to perform multiplex PCR-based NGS to indicate marked non-synonymous FAT1 mutations in HNSCC, which are prognostic indicators. The gene analysis strategy proposed for detecting FAT1 mutations may be a valid method for mutation screening.
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Affiliation(s)
- Shu-Chun Lin
- Institute of Oral Biology, School of Dentistry, National Yang-Ming University, Taipei, Taiwan.,Stomatology Department, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Li-Han Lin
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | - Ssu-Yu Yu
- Institute of Oral Biology, School of Dentistry, National Yang-Ming University, Taipei, Taiwan
| | - Shou-Yen Kao
- Institute of Oral Biology, School of Dentistry, National Yang-Ming University, Taipei, Taiwan.,Stomatology Department, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Kuo-Wei Chang
- Institute of Oral Biology, School of Dentistry, National Yang-Ming University, Taipei, Taiwan.,Stomatology Department, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Hui-Wen Cheng
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | - Chung-Ji Liu
- Institute of Oral Biology, School of Dentistry, National Yang-Ming University, Taipei, Taiwan.,Department of Oral and Maxillofacial Surgery, MacKay Memorial Hospital, Taipei, Taiwan
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Pisapia P, Bellevicine C, Malapelle U, De Luca C, Vigliar E, Troncone G. Bird’s eye view of modern cytopathology: Report from the seventh international Molecular Cytopathology Meeting in Naples, Italy, 2018. Cancer Cytopathol 2019; 127:350-357. [DOI: 10.1002/cncy.22118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Pasquale Pisapia
- Department of Public Health University of Naples Federico II Naples Italy
| | | | - Umberto Malapelle
- Department of Public Health University of Naples Federico II Naples Italy
| | - Caterina De Luca
- Department of Public Health University of Naples Federico II Naples Italy
| | - Elena Vigliar
- Department of Public Health University of Naples Federico II Naples Italy
| | - Giancarlo Troncone
- Department of Public Health University of Naples Federico II Naples Italy
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Dhawan A, Barberis A, Cheng WC, Domingo E, West C, Maughan T, Scott JG, Harris AL, Buffa FM. Guidelines for using sigQC for systematic evaluation of gene signatures. Nat Protoc 2019; 14:1377-1400. [PMID: 30971781 DOI: 10.1038/s41596-019-0136-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 01/11/2019] [Indexed: 11/09/2022]
Abstract
With the increased use of next-generation sequencing generating large amounts of genomic data, gene expression signatures are becoming critically important tools for the interpretation of these data, and are poised to have a substantial effect on diagnosis, management, and prognosis for a number of diseases. It is becoming crucial to establish whether the expression patterns and statistical properties of sets of genes, or gene signatures, are conserved across independent datasets. Conversely, it is necessary to compare established signatures on the same dataset to better understand how they capture different clinical or biological characteristics. Here we describe how to use sigQC, a tool that enables a streamlined, systematic approach for the evaluation of previously obtained gene signatures across multiple gene expression datasets. We implemented sigQC in an R package, making it accessible to users who have knowledge of file input/output and matrix manipulation in R and a moderate grasp of core statistical principles. SigQC has been adopted in basic biology and translational studies, including, but not limited to, the evaluation of multiple gene signatures for potential clinical use as cancer biomarkers. This protocol uses a previously obtained signature for breast cancer metastasis as an example to illustrate the critical quality control steps involved in evaluating its expression, variability, and structure in breast tumor RNA-sequencing data, a different dataset from that in which the signature was originally derived. We demonstrate how the outputs created from sigQC can be used for the evaluation of gene signatures on large-scale gene expression datasets.
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Affiliation(s)
- Andrew Dhawan
- Computational Biology and Integrative Genomics Lab, MRC/CRUK Oxford Institute and Department of Oncology, University of Oxford, Oxford, UK
| | - Alessandro Barberis
- Computational Biology and Integrative Genomics Lab, MRC/CRUK Oxford Institute and Department of Oncology, University of Oxford, Oxford, UK
| | - Wei-Chen Cheng
- Computational Biology and Integrative Genomics Lab, MRC/CRUK Oxford Institute and Department of Oncology, University of Oxford, Oxford, UK
| | - Enric Domingo
- Computational Biology and Integrative Genomics Lab, MRC/CRUK Oxford Institute and Department of Oncology, University of Oxford, Oxford, UK
| | - Catharine West
- Division of Cancer Studies, University of Manchester, Manchester, UK
| | - Tim Maughan
- Computational Biology and Integrative Genomics Lab, MRC/CRUK Oxford Institute and Department of Oncology, University of Oxford, Oxford, UK
| | - Jacob G Scott
- Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - Adrian L Harris
- Computational Biology and Integrative Genomics Lab, MRC/CRUK Oxford Institute and Department of Oncology, University of Oxford, Oxford, UK
| | - Francesca M Buffa
- Computational Biology and Integrative Genomics Lab, MRC/CRUK Oxford Institute and Department of Oncology, University of Oxford, Oxford, UK.
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38
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Sussman R, Rosenbaum JN. Development and Validation of Molecular Assays for Limited Tissue Samples. Acta Cytol 2019; 64:147-154. [PMID: 30995656 DOI: 10.1159/000499109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 02/23/2019] [Indexed: 12/11/2022]
Abstract
As the value of molecular testing of cancer specimens increases, the number of tests imposed on tumor specimens also increases, often in tension with the amount of tumor material available. To develop and validate molecular assays for limited specimens, there are specific concerns that must be addressed, including DNA quality, quantity, and abundance; the number of targets/ability to multiplex; and the analytical sensitivity and specificity of the assay itself. Ultimately, weighing these considerations during assay validation in the overall context of clinical utility and laboratory workflow is critical for delivering the highest level of personalized care to patients.
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Affiliation(s)
- Robyn Sussman
- Center for Personalized Diagnostics, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jason N Rosenbaum
- Center for Personalized Diagnostics, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA,
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Janaki N, Harbhajanka A, Michael CW, Bomeisl P, Wasman J, Atchley M, Miskiewicz K, Alouani D, Sadri N. Comparison of cytocentrifugation supernatant fluid and formalin‐fixed paraffin‐embedded tissue for targeted next‐generation sequencing. Cancer Cytopathol 2019; 127:297-305. [DOI: 10.1002/cncy.22126] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Nafiseh Janaki
- Department of Pathology University Hospitals Cleveland Medical Center Cleveland Ohio
- Department of Pathology Case Western Reserve University School of Medicine Cleveland Ohio
| | - Aparna Harbhajanka
- Department of Pathology University Hospitals Cleveland Medical Center Cleveland Ohio
- Department of Pathology Case Western Reserve University School of Medicine Cleveland Ohio
| | - Claire W. Michael
- Department of Pathology University Hospitals Cleveland Medical Center Cleveland Ohio
- Department of Pathology Case Western Reserve University School of Medicine Cleveland Ohio
| | - Phillip Bomeisl
- Department of Pathology University Hospitals Cleveland Medical Center Cleveland Ohio
- Department of Pathology Case Western Reserve University School of Medicine Cleveland Ohio
| | - Jay Wasman
- Department of Pathology University Hospitals Cleveland Medical Center Cleveland Ohio
- Department of Pathology Case Western Reserve University School of Medicine Cleveland Ohio
| | - Maureen Atchley
- Department of Pathology University Hospitals Cleveland Medical Center Cleveland Ohio
| | - Kristina Miskiewicz
- Department of Pathology University Hospitals Cleveland Medical Center Cleveland Ohio
| | - David Alouani
- Department of Pathology University Hospitals Cleveland Medical Center Cleveland Ohio
- Department of Pathology Case Western Reserve University School of Medicine Cleveland Ohio
| | - Navid Sadri
- Department of Pathology University Hospitals Cleveland Medical Center Cleveland Ohio
- Department of Pathology Case Western Reserve University School of Medicine Cleveland Ohio
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Fielding D, Kurimoto N. Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration for Diagnosis and Staging of Lung Cancer. Clin Chest Med 2019; 39:111-123. [PMID: 29433708 DOI: 10.1016/j.ccm.2017.11.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS TBNA) is fundamental to the diagnosis of lung cancer, as many patients present with more advanced stages of lung cancer, with enlarged hilar and mediastinal lymph nodes. It also represents a way to sample pulmonary masses directly to make the diagnosis, whereby no other accessible tissue is present and the mass sits adjacent to a large central airway. Very importantly also, EBUS TBNA is the widely accepted first procedure in lung cancer staging. A combined procedure of EUS TBNA can be performed to improve diagnostic accuracy.
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Affiliation(s)
- David Fielding
- Department of Thoracic Medicine, Royal Brisbane and Womens Hospital, Third Floor, James Mayne Building, Butterfield Street, Herston 4029, Australia.
| | - Noriaki Kurimoto
- Division of Medical Oncology and Respiratory Medicine, Shimane University Hospital, 89-1, Enyacho, Izumo, Shimane 693-8501, Japan
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Xie F, Zheng X, Mao X, Zhao R, Ye J, Zhang Y, Sun J. Next-Generation Sequencing for Genotyping of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration Samples in Lung Cancer. Ann Thorac Surg 2019; 108:219-226. [PMID: 30885850 DOI: 10.1016/j.athoracsur.2019.02.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 01/18/2019] [Accepted: 02/04/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) can obtain a small amount of specimen. This study aims to evaluate the feasibility and robustness of using EBUS-EBNA samples to perform capture-based targeted next-generation sequencing (NGS). METHODS Tissue samples from patients with advanced non-small cell lung cancer were collected by EBUS-TBNA and were formalin-fixed paraffin-embedded. Three representative genes, EGFR, ALK, and ROS1, were examined by amplification refractory mutation system polymerase chain reaction, immunohistochemistry, and quantitative reverse transcription polymerase chain reaction. The remaining samples were processed with NGS assay with a 56-gene panel. Classic driver mutations detected by NGS were verified by conventional methods. RESULTS Of the 85 samples from patients with advanced non-small cell lung cancer, 77 were performed successfully with all assays. Forty-one mutations in EGFR, ALK, and ROS1 were detected in both conventional methods and NGS, representing a 100% concordance. In contrast, four EGFR mutations detected by NGS were not covered in the targeted regions of amplification refractory mutation system polymerase chain reaction, leading to a negative call in these patients. Altogether, NGS detected 12 additional variants, including six KRAS mutations, one BRAF mutation, one RET fusion, one MET amplification concurrent with EGFR L858R, one KRAS amplification together with EGFR 19del, and one ERBB2 amplification. The mean number of needle passes per lymph node was 5.2 in samples successfully applied in all assays. CONCLUSIONS NGS assay can be successfully conducted with limited tissue samples obtained from EBUS-TBNA. Compared with conventional methods, NGS assay provides more comprehensive information on genetic alterations in tumors, which greatly assists therapeutic decision making for advanced lung cancer.
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Affiliation(s)
- Fangfang Xie
- Department of Endoscopy, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, P.R. China; Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Xiaoxuan Zheng
- Department of Endoscopy, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Xiaowei Mao
- Department of Endoscopy, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, P.R. China; Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Ruiying Zhao
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Junyi Ye
- Burning Rock Biotech, Guangzhou, P.R. China
| | - Yujun Zhang
- Department of Endoscopy, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, P.R. China; Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Jiayuan Sun
- Department of Endoscopy, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, P.R. China; Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, P.R. China.
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42
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Wang H, Sun L, Sang Y, Yang X, Tian G, Wang Z, Fang J, Sun W, Zhou L, Jia L, Tsao MS, Shi H, Lin D. A study of ALK-positive pulmonary squamous-cell carcinoma: From diagnostic methodologies to clinical efficacy. Lung Cancer 2019; 130:135-142. [PMID: 30885334 DOI: 10.1016/j.lungcan.2019.02.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/03/2019] [Accepted: 02/16/2019] [Indexed: 11/16/2022]
Abstract
BACKGROUND High concordance has been observed between Ventana D5F3 ALK immunohistochemistry (IHC) and fluorescence in-situ hybridization (FISH) in lung adenocarcinoma (LADC). However, whether a similar conclusion can be applied to lung squamous-cell carcinoma (LSCC) has remained unclear. We therefore evaluated the ALK (anaplastic lymphoma kinase) status and the therapeutic effect of an ALK tyrosine kinase inhibitor (TKI) in IHC- or FISH-positive LSCC. MATERIALS AND METHODS A total of 2403 LSCC patients from three institutions were screened for ALK aberration by IHC. All IHC-positive cases were subjected to FISH (with an approximately equal number of negative cases as a control group) and next-generation sequencing (NGS). Clinical efficacy was evaluated for the patients who received TKI therapy. RESULTS In 2403 cases of LSCC, 37 cases were identified as ALK-positive by IHC. After quality control, 28 cases were succeeded by FISH (six with insufficient tissue, three with lack of signals) and 13 by NGS (24 failed due to insufficient samples or poor DNA quality); the percentage of non-diagnostic tests was 24.3% (9/37) and 64.9% (24/37), respectively. Four cases (4/2394, 0.17%) analyzed by FISH were determined as ALK-positive. For the control group (40 ALK IHC), FISH demonstrated no samples with ALK gene fusion. The concordance between ALK IHC- and ALK FISH-positive results was 14.3% (4/28). In the 13 cases studied by NGS, two cases showed ALK-EML4 fusion (consistent with two FISH-positive results), and two cases were interpreted as harboring an ALK-association gene mutation. Among four patients (two FISH-positive and two IHC-positive only cases) receiving TKI therapy, two patients had stable disease and the other two had progressive disease. CONCLUSIONS The positive concordance rate of ALK IHC and FISH in LSCC is far less than that reported for LADC. Therefore, ALK IHC detection in LSCC cannot be used as a diagnostic method for ALK rearrangement.
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Affiliation(s)
- Haiyue Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Leina Sun
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People's Republic of China
| | - Yaxiong Sang
- Oncology Business Division, Beijing Novogene Bioinformatics Technology Co., Ltd, Beijing, People's Republic of China
| | - Xin Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Guangming Tian
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic OncologyⅡ, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Ziping Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic OncologyⅠ, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Jian Fang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic OncologyⅡ, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Wei Sun
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Lixin Zhou
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Ling Jia
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Ming-Sound Tsao
- University Health Network/Princess Margaret Cancer Centre and University of Toronto, Toronto, Canada
| | - Huaiyin Shi
- Pathology Department, Chinese PLA General Hospital and Chinese PLA Medical School, Beijing, People's Republic of China.
| | - Dongmei Lin
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China.
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Lozano MD, Echeveste JI, Abengozar M, Mejías LD, Idoate MA, Calvo A, de Andrea CE. Cytology Smears in the Era of Molecular Biomarkers in Non-Small Cell Lung Cancer: Doing More With Less. Arch Pathol Lab Med 2019; 142:291-298. [PMID: 29494220 DOI: 10.5858/arpa.2017-0208-ra] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT - The rapid advances in targeted therapies in non-small cell lung cancer (NSCLC) make the optimization and implementation of cytology specimens for molecular testing a priority. Up to 70% of patients with NSCLC are diagnosed at advanced stages and tissue biopsies often cannot be taken. Although cytology samples provide high-quality material for molecular testing, molecular cytopathology is not yet well known or widely used. OBJECTIVE - To report the many advances in molecular cytopathology and the suitability and utility of cytology samples in molecular and genetic testing of NSCLC. DATA SOURCES - Data sources comprised published peer-reviewed literature and personal experience of the authors. CONCLUSIONS - Molecular testing can be performed on cytologic specimens, especially on direct smears. Rapid on-site evaluation by cytopathologists has improved the adequacy and the management of cytology samples for molecular testing. Mutational profiling of NSCLC using next-generation sequencing can be performed on cytology samples from very small amounts of DNA. Fluorescence in situ hybridization assays on cytology specimens, including stained direct smear, offer some distinct advantages over their histologic counterpart, and are used to detect ALK and ROS1 rearrangements in NSCLC. Cytology specimens allow assessment of the entire tumor cell nucleus, avoiding signal loss from truncation artifacts. The use of cytology samples for assessing programmed death ligand-1 protein expression is currently being developed. Protocols for bisulfite conversion and DNA droplet digital polymerase chain reaction assays have been optimized for cytology smear to investigate aberrant DNA methylation of several NSCLC-related genes.
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Affiliation(s)
| | | | | | | | | | | | - Carlos E de Andrea
- From the Department of Pathology, Clínica Universidad de Navarra, (Drs Lozano, Echeveste, Abengozar, Mejías, Idoate, and de Andrea), IDISNA and Program in Solid Tumors and Biomarkers, Center for Applied Medical Research (CIMA) (Dr Calvo), and the Department of Histology and Pathology (Drs Calvo and de Andrea), University of Navarra, Pamplona, Spain
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44
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Guerini-Rocco E, Passaro A, Casadio C, De Luca VM, Guarize J, de Marinis F, Vacirca D, Barberis M. Acquired Resistance to Tyrosine Kinase Inhibitors in Non-Small Cell Lung Cancers: The Role of Next-Generation Sequencing on Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration Samples. Arch Pathol Lab Med 2019; 142:465-473. [PMID: 29565206 DOI: 10.5858/arpa.2017-0158-ra] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT - Molecular testing is essential for the diagnostic workup of patients with advanced non-small cell lung cancers. Cytology specimens from minimally invasive procedures, such as endobronchial ultrasound-guided transbronchial needle aspiration, are often the only available samples for these patients. The implementation of molecular diagnostic testing, and in particular next-generation sequencing-based testing, on these cytologic specimens is currently an evolving field for lung cytopathology. The application of these molecular analyses on tyrosine kinase inhibitor-resistant non-small cell lung cancers raises unique technical, biologic, and clinical challenges. OBJECTIVE - To provide an overview of the implementation of next-generation sequencing analysis on endobronchial ultrasound-guided transbronchial needle aspiration samples to detect the molecular aberrations underneath the phenomenon of acquired resistance in patients with non-small cell lung cancers progressing while on the EGFR/ALK tyrosine kinase inhibitor treatment. DATA SOURCES - Peer-reviewed original articles, review articles, and published guidelines and expert opinion reports were reviewed, together with our single-center experience. CONCLUSIONS - Next-generation sequencing analyses and the endobronchial ultrasound-guided transbronchial needle aspiration procedure may represent a valuable strategy to address the unique requirements of molecular testing on tyrosine kinase inhibitor-resistant non-small cell lung cancers.
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Affiliation(s)
| | | | | | | | | | | | | | - Massimo Barberis
- From the Divisions of Pathology (Drs Guerini-Rocco, Casadio, Midolo De Luca, and Barberis, and Mr Vacirca), Thoracic Oncology (Drs Passaro and de Marinis), and Thoracic Surgery (Dr Guarize), European Institute of Oncology, Milan, Italy
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45
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Ye W, Hannigan B, Zalles S, Mehrotra M, Barkoh BA, Williams MD, Cabanillas ME, Edeiken-Monroe B, Hu P, Duose D, Wistuba II, Medeiros LJ, Stewart J, Luthra R, Roy-Chowdhuri S. Centrifuged supernatants from FNA provide a liquid biopsy option for clinical next-generation sequencing of thyroid nodules. Cancer Cytopathol 2019; 127:146-160. [PMID: 30620446 DOI: 10.1002/cncy.22098] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/05/2018] [Accepted: 12/05/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND Molecular testing is recommended as an adjunct to improve the preoperative diagnosis of fine-needle aspiration (FNA) of thyroid nodules. Centrifuged supernatants from FNA samples, which are typically discarded, have recently emerged as a novel liquid-based biopsy for molecular testing. This study evaluates the use of thyroid FNA supernatants for detecting clinically relevant mutations. METHODS Supernatants from thyroid FNA samples (n = 156) were evaluated. A 50-gene next-generation sequencing (NGS) assay was used, and mutation analysis results from a subset of samples were further compared with those of paired FNA smears and/or cell blocks. RESULTS All 156 samples yielded adequate DNA (median, 135 ng; range, 11-3180 ng), and 129 of these samples (83%) were successfully sequenced by NGS. The most frequently detected somatic mutations included BRAF and RAS mutations, which were followed by RET, TP53, PTEN, CDKN2A, and PIK3CA mutations. Eleven of 31 cases with an indeterminate cytologic diagnosis and 9 of 12 cases that were suspicious for malignancy had somatic mutations, including the BRAF V600E mutation, which is highly definitive for papillary thyroid carcinoma (PTC). Seven of the 9 indeterminate and suspicious cases with the BRAF V600E mutation had surgical follow-up, and they were all confirmed to be PTC. A comparison of the mutation profiles derived from supernatants with those of paired smears and/or cell blocks in a small subset of cases (n = 8) showed 100% concordance. CONCLUSIONS This study provides evidence that FNA supernatants can be used as a surrogate for thyroid molecular testing to improve diagnostic accuracy in indeterminate nodules, provide prognostic/predictive information, and improve overall patient management.
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Affiliation(s)
- Wenrui Ye
- Diagnostic Genetics, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Brette Hannigan
- Diagnostic Genetics, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stephanie Zalles
- Diagnostic Genetics, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Meenakshi Mehrotra
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Bedia A Barkoh
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michelle D Williams
- Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Maria E Cabanillas
- Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Beth Edeiken-Monroe
- Department of Diagnostic Radiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Peter Hu
- Diagnostic Genetics, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Dzifa Duose
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - L Jeffrey Medeiros
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John Stewart
- Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rajyalakshmi Luthra
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sinchita Roy-Chowdhuri
- Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
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46
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The utilization of cytologic and small biopsy samples for ancillary molecular testing. Mod Pathol 2019; 32:77-85. [PMID: 30600323 DOI: 10.1038/s41379-018-0138-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 07/22/2018] [Indexed: 11/09/2022]
Abstract
There has recently been an increased emphasis on the utilization of cytologic samples and small biopsies for not only diagnostic purposes but also for ancillary testing. In some instances, the ancillary tests contribute to the diagnosis and in other scenarios, they provide prognostic and theranostic information for the management of patients with advanced stage cancer. These ancillary tests include immunohistochemical biomarker analysis, molecular mutation analysis, and cytogenetic tests. Despite the finite nature of the cellular material procured in cytologic and small tissue biopsies, pathologists are tasked with ordering an increasing number of tests using these limited samples. This requires the pathologists to utilize and triage these samples in an optimal fashion so that as much information can be gleaned from a given specimen. This review will focus on the pre-analytic requirements for ancillary molecular and cytogenetic tests in the context of a discussion of the various preparation methods for cytologic and small biopsy specimens. The goal will be to provide the reader with the necessary concepts that can be utilized to develop optimal specimen selection and triage strategies to maximize the chances of effectively utilizing these samples for comprehensive diagnostic and relevant ancillary testing purposes.
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47
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Young K, da Cunha Santos G, Card P, Leighl N. The role of cytology in molecular testing and personalized medicine in lung cancer: A clinical perspective. Cancer Cytopathol 2018; 127:72-78. [DOI: 10.1002/cncy.22085] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 10/21/2018] [Accepted: 11/01/2018] [Indexed: 12/30/2022]
Affiliation(s)
- Kelvin Young
- Department of Hematology/Oncology St. Michael’s Hospital Toronto Ontario Canada
| | - Gilda da Cunha Santos
- Division of Medical Oncology, Princess Margaret Cancer Center University of Toronto Toronto Ontario Canada
| | - Paul Card
- Kaleidoscope Strategic, Inc Toronto Ontario Canada
| | - Natasha Leighl
- Division of Medical Oncology, Princess Margaret Cancer Center University of Toronto Toronto Ontario Canada
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48
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Sussman RT, Shaffer S, Azzato EM, DeSloover D, Farooqi MS, Meyer A, Lieberman DB, Bigdeli A, Paolillo C, Ganapathy K, Sukhadia S, Rosenbaum JN, Daber RD, Morrissette JJ. Validation of a next-generation sequencing oncology panel optimized for low input DNA. Cancer Genet 2018; 228-229:55-63. [DOI: 10.1016/j.cancergen.2018.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 07/24/2018] [Accepted: 08/19/2018] [Indexed: 12/18/2022]
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49
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Snider JS, Hirschhorn JW, Yang J, Chajewski OS, Houston PM, Lindsey KG. Three-year review of gene sequencing analyses of pulmonary non-small cell lung cancers obtained by fine-needle aspiration or surgical biopsy: mutation and failure rates. J Am Soc Cytopathol 2018; 7:300-305. [PMID: 31043299 DOI: 10.1016/j.jasc.2018.04.007] [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: 03/13/2018] [Revised: 04/27/2018] [Accepted: 04/30/2018] [Indexed: 06/09/2023]
Abstract
INTRODUCTION Mutational analysis is becoming the standard of diagnostic workup. Sufficient amounts of and quality tumor tissue can be challenging when faced with a small biopsy or biopsy by fine-needle aspiration (FNA). MATERIALS AND METHODS We reviewed the failures of FNA and surgical biopsy to yield sequencing data and causes thereof over a 3-year period. We executed a search of the laboratory information system for requests to perform our targeted 50-gene assay by massively parallel sequencing on surgical biopsies and FNAs and compared the results. RESULTS Three failure causes were assigned: insufficient tissue as defined by the pathologist, failure to meet quality control indicating library preparation or sequencing failure, and failure of pre-qualifying step for DNA integrity. A total of 327 of 354 cases were successfully sequenced (92%), including 151 FNA cases and 203 biopsies, with 16 (10.6%) and 11 (5.4%) failures, respectively. The Fisher's exact test two-tailed P-value equals 0.050381, making the difference between FNA and biopsy not statistically significant. Insufficient tissue, quality control failure, and DNA integrity were identified as the cause of the failure in 10 (62%), 3 (19%), and 3 (19%) FNA biopsies, and in 5 (45.5%), 1 (9%), and 5 (45.5%) surgical biopsies. The most common cause of failure of FNA was insufficient tissue. For surgical biopsies, DNA integrity and insufficient tissue were equally as likely to be implicated. Both FNA and surgical biopsy have a low failure rate overall without statistical significance between them. CONCLUSIONS Although surgical biopsy is considered the gold standard, these findings support FNA as an equal modality.
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Affiliation(s)
- Jessica S Snider
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Julie W Hirschhorn
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Jack Yang
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Olga S Chajewski
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Peter M Houston
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Kathryn G Lindsey
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina.
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50
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Aung KL, Bedard PL, Yu C, Boerner SL, Zuzarte PC, Ghai S, Berman HK, Serra S, Giesler A, Ahmed L, Joshua AM, Moore MJ, Oza AM, Amir E, McPherson JD, Zhang T, Sukhai MA, Stockley TL, Kamel-Reid S, Siu LL, Hansen AR. Minimally Invasive Real-Time Detection of Actionable Mutations in Patients With Metastatic Solid Tumors Using Fine-Needle and Liquid Biopsies. JCO Precis Oncol 2018; 2:1-20. [DOI: 10.1200/po.17.00248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Purpose Fine-needle biopsy (FNB) and liquid biopsy are minimally invasive methods of tumor sampling that provide feasible means to assess tumor genotypes in real time. However, more data are needed to establish the strength of these methods by benchmarking against the current gold standard methods, core-needle biopsy (CNB) or surgical excision of the tumor. Patients and Methods Eligible patients with advanced solid tumors were prospectively recruited. We performed mutation profiling using matched tumor DNA obtained by CNB, FNB and liquid biopsy, and matrix-assisted laser desorption/ionization time-of-flight custom mass-spectrometry or targeted next-generation DNA sequencing. The actionability of detected mutations was determined using the OncoKB Web tool. Agreement between mutations detected in CNBs, FNBs, and circulating tumor DNA (ctDNA) was examined. Results Forty-one patients underwent tumor biopsy. Thirty CNBs (73%) and 34 FNBs (83%) had sufficient tumor and DNA for mutation profiling. Median DNA yield from CNB and FNB were 775 ng (interquartile range, 240 to 347 4ng) and 649 ng (interquartile range, 180 to1350 ng), respectively. Of 29 CNB/FNB pairs available for comparison, actionable mutation results were concordant in 28 (96%). Six of nine actionable mutations (67%) that were found by CNB, FNB, or both were detectable in ctDNA. Two additional actionable mutations were found exclusively in ctDNA. Conclusion Optimally processed FNB and liquid biopsy can be used routinely for tumor mutation profiling to identify actionable mutations.
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Affiliation(s)
- Kyaw L. Aung
- Kyaw L. Aung, Philippe L. Bedard, Celeste Yu, Scott L. Boerner, Sangeet Ghai, Hal K. Berman, Stefano Serra, Amanda Giesler, Lailah Ahmed, Anthony M. Joshua, Amit M. Oza, Eitan Amir, Tong Zhang, Mahadeo A. Sukhai, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University Health Network; Philippe L. Bedard, Amit M. Oza, Eitan Amir, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University of Toronto; Philip C. Zuzarte, Ontario Institute of Cancer
| | - Philippe L. Bedard
- Kyaw L. Aung, Philippe L. Bedard, Celeste Yu, Scott L. Boerner, Sangeet Ghai, Hal K. Berman, Stefano Serra, Amanda Giesler, Lailah Ahmed, Anthony M. Joshua, Amit M. Oza, Eitan Amir, Tong Zhang, Mahadeo A. Sukhai, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University Health Network; Philippe L. Bedard, Amit M. Oza, Eitan Amir, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University of Toronto; Philip C. Zuzarte, Ontario Institute of Cancer
| | - Celeste Yu
- Kyaw L. Aung, Philippe L. Bedard, Celeste Yu, Scott L. Boerner, Sangeet Ghai, Hal K. Berman, Stefano Serra, Amanda Giesler, Lailah Ahmed, Anthony M. Joshua, Amit M. Oza, Eitan Amir, Tong Zhang, Mahadeo A. Sukhai, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University Health Network; Philippe L. Bedard, Amit M. Oza, Eitan Amir, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University of Toronto; Philip C. Zuzarte, Ontario Institute of Cancer
| | - Scott L. Boerner
- Kyaw L. Aung, Philippe L. Bedard, Celeste Yu, Scott L. Boerner, Sangeet Ghai, Hal K. Berman, Stefano Serra, Amanda Giesler, Lailah Ahmed, Anthony M. Joshua, Amit M. Oza, Eitan Amir, Tong Zhang, Mahadeo A. Sukhai, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University Health Network; Philippe L. Bedard, Amit M. Oza, Eitan Amir, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University of Toronto; Philip C. Zuzarte, Ontario Institute of Cancer
| | - Philip C. Zuzarte
- Kyaw L. Aung, Philippe L. Bedard, Celeste Yu, Scott L. Boerner, Sangeet Ghai, Hal K. Berman, Stefano Serra, Amanda Giesler, Lailah Ahmed, Anthony M. Joshua, Amit M. Oza, Eitan Amir, Tong Zhang, Mahadeo A. Sukhai, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University Health Network; Philippe L. Bedard, Amit M. Oza, Eitan Amir, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University of Toronto; Philip C. Zuzarte, Ontario Institute of Cancer
| | - Sangeet Ghai
- Kyaw L. Aung, Philippe L. Bedard, Celeste Yu, Scott L. Boerner, Sangeet Ghai, Hal K. Berman, Stefano Serra, Amanda Giesler, Lailah Ahmed, Anthony M. Joshua, Amit M. Oza, Eitan Amir, Tong Zhang, Mahadeo A. Sukhai, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University Health Network; Philippe L. Bedard, Amit M. Oza, Eitan Amir, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University of Toronto; Philip C. Zuzarte, Ontario Institute of Cancer
| | - Hal K. Berman
- Kyaw L. Aung, Philippe L. Bedard, Celeste Yu, Scott L. Boerner, Sangeet Ghai, Hal K. Berman, Stefano Serra, Amanda Giesler, Lailah Ahmed, Anthony M. Joshua, Amit M. Oza, Eitan Amir, Tong Zhang, Mahadeo A. Sukhai, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University Health Network; Philippe L. Bedard, Amit M. Oza, Eitan Amir, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University of Toronto; Philip C. Zuzarte, Ontario Institute of Cancer
| | - Stefano Serra
- Kyaw L. Aung, Philippe L. Bedard, Celeste Yu, Scott L. Boerner, Sangeet Ghai, Hal K. Berman, Stefano Serra, Amanda Giesler, Lailah Ahmed, Anthony M. Joshua, Amit M. Oza, Eitan Amir, Tong Zhang, Mahadeo A. Sukhai, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University Health Network; Philippe L. Bedard, Amit M. Oza, Eitan Amir, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University of Toronto; Philip C. Zuzarte, Ontario Institute of Cancer
| | - Amanda Giesler
- Kyaw L. Aung, Philippe L. Bedard, Celeste Yu, Scott L. Boerner, Sangeet Ghai, Hal K. Berman, Stefano Serra, Amanda Giesler, Lailah Ahmed, Anthony M. Joshua, Amit M. Oza, Eitan Amir, Tong Zhang, Mahadeo A. Sukhai, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University Health Network; Philippe L. Bedard, Amit M. Oza, Eitan Amir, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University of Toronto; Philip C. Zuzarte, Ontario Institute of Cancer
| | - Lailah Ahmed
- Kyaw L. Aung, Philippe L. Bedard, Celeste Yu, Scott L. Boerner, Sangeet Ghai, Hal K. Berman, Stefano Serra, Amanda Giesler, Lailah Ahmed, Anthony M. Joshua, Amit M. Oza, Eitan Amir, Tong Zhang, Mahadeo A. Sukhai, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University Health Network; Philippe L. Bedard, Amit M. Oza, Eitan Amir, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University of Toronto; Philip C. Zuzarte, Ontario Institute of Cancer
| | - Anthony M. Joshua
- Kyaw L. Aung, Philippe L. Bedard, Celeste Yu, Scott L. Boerner, Sangeet Ghai, Hal K. Berman, Stefano Serra, Amanda Giesler, Lailah Ahmed, Anthony M. Joshua, Amit M. Oza, Eitan Amir, Tong Zhang, Mahadeo A. Sukhai, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University Health Network; Philippe L. Bedard, Amit M. Oza, Eitan Amir, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University of Toronto; Philip C. Zuzarte, Ontario Institute of Cancer
| | - Malcolm J. Moore
- Kyaw L. Aung, Philippe L. Bedard, Celeste Yu, Scott L. Boerner, Sangeet Ghai, Hal K. Berman, Stefano Serra, Amanda Giesler, Lailah Ahmed, Anthony M. Joshua, Amit M. Oza, Eitan Amir, Tong Zhang, Mahadeo A. Sukhai, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University Health Network; Philippe L. Bedard, Amit M. Oza, Eitan Amir, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University of Toronto; Philip C. Zuzarte, Ontario Institute of Cancer
| | - Amit M. Oza
- Kyaw L. Aung, Philippe L. Bedard, Celeste Yu, Scott L. Boerner, Sangeet Ghai, Hal K. Berman, Stefano Serra, Amanda Giesler, Lailah Ahmed, Anthony M. Joshua, Amit M. Oza, Eitan Amir, Tong Zhang, Mahadeo A. Sukhai, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University Health Network; Philippe L. Bedard, Amit M. Oza, Eitan Amir, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University of Toronto; Philip C. Zuzarte, Ontario Institute of Cancer
| | - Eitan Amir
- Kyaw L. Aung, Philippe L. Bedard, Celeste Yu, Scott L. Boerner, Sangeet Ghai, Hal K. Berman, Stefano Serra, Amanda Giesler, Lailah Ahmed, Anthony M. Joshua, Amit M. Oza, Eitan Amir, Tong Zhang, Mahadeo A. Sukhai, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University Health Network; Philippe L. Bedard, Amit M. Oza, Eitan Amir, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University of Toronto; Philip C. Zuzarte, Ontario Institute of Cancer
| | - John D. McPherson
- Kyaw L. Aung, Philippe L. Bedard, Celeste Yu, Scott L. Boerner, Sangeet Ghai, Hal K. Berman, Stefano Serra, Amanda Giesler, Lailah Ahmed, Anthony M. Joshua, Amit M. Oza, Eitan Amir, Tong Zhang, Mahadeo A. Sukhai, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University Health Network; Philippe L. Bedard, Amit M. Oza, Eitan Amir, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University of Toronto; Philip C. Zuzarte, Ontario Institute of Cancer
| | - Tong Zhang
- Kyaw L. Aung, Philippe L. Bedard, Celeste Yu, Scott L. Boerner, Sangeet Ghai, Hal K. Berman, Stefano Serra, Amanda Giesler, Lailah Ahmed, Anthony M. Joshua, Amit M. Oza, Eitan Amir, Tong Zhang, Mahadeo A. Sukhai, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University Health Network; Philippe L. Bedard, Amit M. Oza, Eitan Amir, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University of Toronto; Philip C. Zuzarte, Ontario Institute of Cancer
| | - Mahadeo A. Sukhai
- Kyaw L. Aung, Philippe L. Bedard, Celeste Yu, Scott L. Boerner, Sangeet Ghai, Hal K. Berman, Stefano Serra, Amanda Giesler, Lailah Ahmed, Anthony M. Joshua, Amit M. Oza, Eitan Amir, Tong Zhang, Mahadeo A. Sukhai, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University Health Network; Philippe L. Bedard, Amit M. Oza, Eitan Amir, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University of Toronto; Philip C. Zuzarte, Ontario Institute of Cancer
| | - Tracy L. Stockley
- Kyaw L. Aung, Philippe L. Bedard, Celeste Yu, Scott L. Boerner, Sangeet Ghai, Hal K. Berman, Stefano Serra, Amanda Giesler, Lailah Ahmed, Anthony M. Joshua, Amit M. Oza, Eitan Amir, Tong Zhang, Mahadeo A. Sukhai, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University Health Network; Philippe L. Bedard, Amit M. Oza, Eitan Amir, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University of Toronto; Philip C. Zuzarte, Ontario Institute of Cancer
| | - Suzanne Kamel-Reid
- Kyaw L. Aung, Philippe L. Bedard, Celeste Yu, Scott L. Boerner, Sangeet Ghai, Hal K. Berman, Stefano Serra, Amanda Giesler, Lailah Ahmed, Anthony M. Joshua, Amit M. Oza, Eitan Amir, Tong Zhang, Mahadeo A. Sukhai, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University Health Network; Philippe L. Bedard, Amit M. Oza, Eitan Amir, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University of Toronto; Philip C. Zuzarte, Ontario Institute of Cancer
| | - Lillian L. Siu
- Kyaw L. Aung, Philippe L. Bedard, Celeste Yu, Scott L. Boerner, Sangeet Ghai, Hal K. Berman, Stefano Serra, Amanda Giesler, Lailah Ahmed, Anthony M. Joshua, Amit M. Oza, Eitan Amir, Tong Zhang, Mahadeo A. Sukhai, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University Health Network; Philippe L. Bedard, Amit M. Oza, Eitan Amir, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University of Toronto; Philip C. Zuzarte, Ontario Institute of Cancer
| | - Aaron R. Hansen
- Kyaw L. Aung, Philippe L. Bedard, Celeste Yu, Scott L. Boerner, Sangeet Ghai, Hal K. Berman, Stefano Serra, Amanda Giesler, Lailah Ahmed, Anthony M. Joshua, Amit M. Oza, Eitan Amir, Tong Zhang, Mahadeo A. Sukhai, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University Health Network; Philippe L. Bedard, Amit M. Oza, Eitan Amir, Tracy L. Stockley, Suzanne Kamel-Reid, Lillian L. Siu, and Aaron R. Hansen, University of Toronto; Philip C. Zuzarte, Ontario Institute of Cancer
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