2
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Nasrallah MP, Binder ZA, Oldridge DA, Zhao J, Lieberman DB, Roth JJ, Watt CD, Sukhadia S, Klinman E, Daber RD, Desai A, Brem S, O'Rourke DM, Morrissette JJD. Molecular Neuropathology in Practice: Clinical Profiling and Integrative Analysis of Molecular Alterations in Glioblastoma. Acad Pathol 2019; 6:2374289519848353. [PMID: 31206012 PMCID: PMC6537274 DOI: 10.1177/2374289519848353] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 02/27/2019] [Accepted: 03/25/2019] [Indexed: 12/20/2022] Open
Abstract
Molecular profiling of glioblastoma has revealed complex cytogenetic, epigenetic, and molecular abnormalities that are necessary for diagnosis, prognosis, and treatment. Our neuro-oncology group has developed a data-driven, institutional consensus guideline for efficient and optimal workup of glioblastomas based on our routine performance of molecular testing. We describe our institution’s testing algorithm, assay development, and genetic findings in glioblastoma, to illustrate current practices and challenges in neuropathology related to molecular and genetic testing. We have found that coordination of test requisition, tissue handling, and incorporation of results into the final pathologic diagnosis by the neuropathologist improve patient care. Here, we present analysis of O6-methylguanine-DNA-methyltransferase promoter methylation and next-generation sequencing results of 189 patients, obtained utilizing our internal processes led by the neuropathology team. Our institutional pathway for neuropathologist-driven molecular testing has streamlined the management of glioblastoma samples for efficient return of results for incorporation of genomic data into the pathological diagnosis and optimal patient care.
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Affiliation(s)
- MacLean P Nasrallah
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zev A Binder
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Derek A Oldridge
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jianhua Zhao
- Bioreference Laboratories, West Deptford, NJ, USA
| | - David B Lieberman
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jacquelyn J Roth
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Christopher D Watt
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Shrey Sukhadia
- University of Maryland School of Medicine, Baltimore, MD, USA
| | - Eva Klinman
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Arati Desai
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Steven Brem
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Donald M O'Rourke
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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3
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Hsu HC, Liao MF, Hsu JL, Lee YL, Ro LS. Genetic Analysis of Hereditary Transthyretin Ala97Ser Related Amyloidosis. J Vis Exp 2018. [PMID: 29939164 DOI: 10.3791/57743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Genetic testing is the most reliable test for hereditary transthyretin related amyloidosis and should be performed in most cases of transthyretin amyloidosis (ATTR). ATTR is a rare but fatal disease with heterogeneous phenotypes; therefore, the diagnosis is sometimes delayed. With increasing attention and broader recognition on early manifestations of ATTR as well as emerging treatments, appropriate diagnostic studies, including the transthyretin (TTR) genetic test, to confirm the types and variants of ATTR are therefore fundamental to improve the prognosis. Genetic analyses with polymerase chain reaction (PCR) methods confirm the presence of TTR point mutations much more quickly and safer than conventional methods such as southern blot. Herein, we demonstrate genetic confirmation of the ATTR Ala97Ser mutation, the most common endemic mutation in Taiwan. The protocol comprises four main steps: collecting whole blood specimen, DNA extraction, genetic analysis of all four TTR exons with PCR, and DNA sequencing.
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Affiliation(s)
- Hui-Ching Hsu
- Department of Traditional Chinese Medicine, Division of Chinese Acupuncture and Traumatology, Chang Gung Memorial Hospital Linkou Medical Center and Chang Gung University College of Medicine
| | - Ming-Feng Liao
- Department of Neurology, Chang Gung Memorial Hospital Linkou Medical Center and Chang Gung University College of Medicine
| | - Jung-Lung Hsu
- Department of Neurology, Chang Gung Memorial Hospital Linkou Medical Center and Chang Gung University College of Medicine
| | - Yun-Lin Lee
- Department of Neurology, Chang Gung Memorial Hospital Linkou Medical Center and Chang Gung University College of Medicine
| | - Long-Sun Ro
- Department of Neurology, Chang Gung Memorial Hospital Linkou Medical Center and Chang Gung University College of Medicine;
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4
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Cho M, Ahn S, Hong M, Bang H, Van Vrancken M, Kim S, Lee J, Park SH, Park JO, Park YS, Lim HY, Kang WK, Sun JM, Lee SH, Ahn MJ, Park K, Kim DH, Lee S, Park W, Kim KM. Tissue recommendations for precision cancer therapy using next generation sequencing: a comprehensive single cancer center's experiences. Oncotarget 2018; 8:42478-42486. [PMID: 28477007 PMCID: PMC5522081 DOI: 10.18632/oncotarget.17199] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/05/2017] [Indexed: 02/02/2023] Open
Abstract
To generate accurate next-generation sequencing (NGS) data, the amount and quality of DNA extracted is critical. We analyzed 1564 tissue samples from patients with metastatic or recurrent solid tumor submitted for NGS according to their sample size, acquisition method, organ, and fixation to propose appropriate tissue requirements. Of the 1564 tissue samples, 481 (30.8%) consisted of fresh-frozen (FF) tissue, and 1,083 (69.2%) consisted of formalin-fixed paraffin-embedded (FFPE) tissue. We obtained successful NGS results in 95.9% of cases. Out of 481 FF biopsies, 262 tissue samples were from lung, and the mean fragment size was 2.4 mm. Compared to lung, GI tract tumor fragments showed a significantly lower DNA extraction failure rate (2.1 % versus 6.1%, p = 0.04). For FFPE biopsy samples, the size of biopsy tissue was similar regardless of tumor type with a mean of 0.8 × 0.3 cm, and the mean DNA yield per one unstained slide was 114 ng. We obtained highest amount of DNA from the colorectum (2353 ng) and the lowest amount from the hepatobiliary tract (760.3 ng) likely due to a relatively smaller biopsy size, extensive hemorrhage and necrosis, and lower tumor volume. On one unstained slide from FFPE operation specimens, the mean size of the specimen was 2.0 × 1.0 cm, and the mean DNA yield per one unstained slide was 1800 ng. In conclusions, we present our experiences on tissue requirements for appropriate NGS workflow: > 1 mm2 for FF biopsy, > 5 unstained slides for FFPE biopsy, and > 1 unstained slide for FFPE operation specimens for successful test results in 95.9% of cases.
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Affiliation(s)
- Minho Cho
- Center for Cancer Companion Diagnostics, The Innovative Cancer Medicine Institute, Samsung Medical Center, Seoul, Korea.,Present address: Department of Integrated Health and Environmental Science, College of Health Science, Korea University, Seoul, Korea
| | - Soomin Ahn
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Mineui Hong
- Center for Cancer Companion Diagnostics, The Innovative Cancer Medicine Institute, Samsung Medical Center, Seoul, Korea.,Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Heejin Bang
- Center for Cancer Companion Diagnostics, The Innovative Cancer Medicine Institute, Samsung Medical Center, Seoul, Korea.,Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Michael Van Vrancken
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Seungtae Kim
- Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jeeyun Lee
- Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Se Hoon Park
- Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Joon Oh Park
- Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Young Suk Park
- Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ho Yeong Lim
- Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Won Ki Kang
- Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jong-Mu Sun
- Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Se Hoon Lee
- Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Myung-Ju Ahn
- Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Keunchil Park
- Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Duk Hwan Kim
- Medical Translational Research Center, Samsung Biological Research Institute, Seoul, Korea
| | - Seunggwan Lee
- Department of Integrated Health and Environmental Science, College of Health Science, Korea University, Seoul, Korea
| | | | - Kyoung-Mee Kim
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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5
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Pihlak R, Weaver JMJ, Valle JW, McNamara MG. Advances in Molecular Profiling and Categorisation of Pancreatic Adenocarcinoma and the Implications for Therapy. Cancers (Basel) 2018; 10:cancers10010017. [PMID: 29329208 PMCID: PMC5789367 DOI: 10.3390/cancers10010017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 01/08/2018] [Accepted: 01/10/2018] [Indexed: 12/20/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) continues to be a disease with poor outcomes and short-lived treatment responses. New information is emerging from genome sequencing identifying potential subgroups based on somatic and germline mutations. A variety of different mutations and mutational signatures have been identified; the driver mutation in around 93% of PDAC is KRAS, with other recorded alterations being SMAD4 and CDKN2A. Mutations in the deoxyribonucleic acid (DNA) damage repair pathway have also been investigated in PDAC and multiple clinical trials are ongoing with DNA-damaging agents. Rare mutations in BRAF and microsatellite instability (MSI) have been reported in about 1–3% of patients with PDAC, and agents used in other cancers to target these have also shown some promise. Immunotherapy is a developing field, but has failed to demonstrate benefits in PDAC to date. While many trials have failed to improve outcomes in this deadly disease, there is optimism that by developing a better understanding of the translational aspects of this cancer, future informed therapeutic strategies may prove more successful.
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Affiliation(s)
- Rille Pihlak
- Division of Cancer Sciences, University of Manchester, Manchester M13 9NT, UK.
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX, UK.
| | - Jamie M J Weaver
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX, UK.
| | - Juan W Valle
- Division of Cancer Sciences, University of Manchester, Manchester M13 9NT, UK.
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX, UK.
| | - Mairéad G McNamara
- Division of Cancer Sciences, University of Manchester, Manchester M13 9NT, UK.
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX, UK.
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