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Böckers A, Schurr L, Schön M, Scholl T, Böckers TM, Steinestel K, Arndt A. Predictive molecular pathology after prolonged fixation: A study on tissue from anatomical body donors. Exp Mol Pathol 2024; 137:104899. [PMID: 38761540 DOI: 10.1016/j.yexmp.2024.104899] [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: 10/16/2023] [Revised: 03/19/2024] [Accepted: 05/06/2024] [Indexed: 05/20/2024]
Abstract
Histopathological assessment of tissue samples after prolonged formalin fixation has been described previously, but currently there is only limited knowledge regarding the feasibility of molecular pathology on such tissue. In this pilot study, we tested routine molecular pathology methods (DNA isolation, DNA pyrosequencing/next-generation sequencing, DNA methylation analysis, RT-PCR, clonality analysis and fluorescence in situ hybridization) on tissue samples from 11 tumor entities as well as non-neoplastic brain tissue from 43 body donors during the gross anatomy course at Ulm University (winter semester 2019/20 and 2020/21). The mean post mortem interval until fixation was 2.5 ± 1.6 days (range, 1-6 days). Fixation was performed with aqueous formaldehyde solution (formalin, 1.5-2%). The mean storage time of body donors was 12.8 ± 5.6 months (range, 7-25 months). While most diagnostic methods were successful, samples showed significant variability in DNA quality and evaluability. DNA pyrosequencing as well as next-generation sequencing was successful in all investigated samples. Methylation analyses were partially not successful in some extend due to limited intact DNA yield for these analyses. Taken together, the use of prolonged formalin-fixed tissue samples from body donors offers new avenues in research and education, as these samples could be used for morpho-molecular studies and the establishment of biobanks, especially for tissue types that cannot be preserved and studied in vivo. Pathological ward rounds, sample collection, and histopathological and molecular workup have been integrated in the gross anatomy course in Ulm as an integral part of the curriculum, linking anatomy and pathology and providing medical students early insight into the broad field of (molecular) pathology.
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Affiliation(s)
- Anja Böckers
- Institute for Anatomy and Cell Biology, Medical Faculty, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Leon Schurr
- Institute for Anatomy and Cell Biology, Medical Faculty, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Michael Schön
- Institute for Anatomy and Cell Biology, Medical Faculty, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Tatjana Scholl
- Institute of Pathology and Molecular Pathology, Federal Army Hospital, Oberer Eselsberg 40, 89081 Ulm, Germany
| | - Tobias M Böckers
- Institute for Anatomy and Cell Biology, Medical Faculty, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Konrad Steinestel
- Institute of Pathology and Molecular Pathology, Federal Army Hospital, Oberer Eselsberg 40, 89081 Ulm, Germany
| | - Annette Arndt
- Institute of Pathology and Molecular Pathology, Federal Army Hospital, Oberer Eselsberg 40, 89081 Ulm, Germany.
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Mimura C, Takamiya R, Fujimoto S, Fukui T, Yatani A, Yamada J, Takayasu M, Takata N, Sato H, Fukuda K, Furukawa K, Hazama D, Katsurada N, Yamamoto M, Matsumoto S, Goto K, Tachihara M. Utility of bronchoscopically obtained frozen cytology pellets for next-generation sequencing. BMC Cancer 2024; 24:489. [PMID: 38632507 PMCID: PMC11022476 DOI: 10.1186/s12885-024-12250-5] [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: 01/18/2024] [Accepted: 04/11/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) is essential for lung cancer treatment. It is important to collect sufficient tissue specimens, but sometimes we cannot obtain large enough samples for NGS analysis. We investigated the yield of NGS analysis by frozen cytology pellets using an Oncomine Comprehensive Assay or Oncomine Precision Assay. METHODS We retrospectively enrolled patients with lung cancer who underwent bronchoscopy at Kobe University Hospital and were enrolled in the Lung Cancer Genomic Screening Project for Individualized Medicine. We investigated the amount of extracted DNA and RNA and determined the NGS success rates. We also compared the amount of DNA and RNA by bronchoscopy methods. To create the frozen cytology pellets, we first effectively collected the cells and then quickly centrifuged and cryopreserved them. RESULTS A total of 132 patients were enrolled in this study between May 2016 and December 2022; of them, 75 were subjected to frozen cytology pellet examinations and 57 were subjected to frozen tissue examinations. The amount of DNA and RNA obtained by frozen cytology pellets was nearly equivalent to frozen tissues. Frozen cytology pellets collected by endobronchial ultrasound-guided transbronchial needle aspiration yielded significantly more DNA than those collected by transbronchial biopsy methods. (P < 0.01) In RNA content, cytology pellets were not inferior to frozen tissue. The success rate of NGS analysis with frozen cytology pellet specimens was comparable to the success rate of NGS analysis with frozen tissue specimens. CONCLUSIONS Our study showed that frozen cytology pellets may have equivalent diagnostic value to frozen tissue for NGS analyses. Bronchial cytology specimens are usually used only for cytology, but NGS analysis is possible if enough cells are collected to create pellet specimens. In particular, the frozen cytology pellets obtained by endobronchial ultrasound-guided transbronchial needle aspiration yielded sufficient amounts of DNA. TRIAL REGISTRATION This was registered with the University Medical Hospital Information Network in Japan (UMINCTR registration no. UMIN000052050).
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Affiliation(s)
- Chihiro Mimura
- Division of Respiratory Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-Cho, Chuo-Ku, Kobe-City, Hyogo, 650-0017, Japan
| | - Rei Takamiya
- Division of Respiratory Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-Cho, Chuo-Ku, Kobe-City, Hyogo, 650-0017, Japan
| | - Shodai Fujimoto
- Division of Respiratory Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-Cho, Chuo-Ku, Kobe-City, Hyogo, 650-0017, Japan
| | - Takafumi Fukui
- Division of Respiratory Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-Cho, Chuo-Ku, Kobe-City, Hyogo, 650-0017, Japan
| | - Atsuhiko Yatani
- Division of Respiratory Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-Cho, Chuo-Ku, Kobe-City, Hyogo, 650-0017, Japan
| | - Jun Yamada
- Division of Respiratory Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-Cho, Chuo-Ku, Kobe-City, Hyogo, 650-0017, Japan
| | - Mizuki Takayasu
- Division of Respiratory Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-Cho, Chuo-Ku, Kobe-City, Hyogo, 650-0017, Japan
| | - Naoya Takata
- Division of Respiratory Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-Cho, Chuo-Ku, Kobe-City, Hyogo, 650-0017, Japan
| | - Hiroki Sato
- Division of Respiratory Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-Cho, Chuo-Ku, Kobe-City, Hyogo, 650-0017, Japan
| | - Kiyoko Fukuda
- Division of Respiratory Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-Cho, Chuo-Ku, Kobe-City, Hyogo, 650-0017, Japan
| | - Koichi Furukawa
- Division of Respiratory Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-Cho, Chuo-Ku, Kobe-City, Hyogo, 650-0017, Japan
| | - Daisuke Hazama
- Division of Respiratory Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-Cho, Chuo-Ku, Kobe-City, Hyogo, 650-0017, Japan
| | - Naoko Katsurada
- Division of Respiratory Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-Cho, Chuo-Ku, Kobe-City, Hyogo, 650-0017, Japan
| | - Masatsugu Yamamoto
- Division of Respiratory Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-Cho, Chuo-Ku, Kobe-City, Hyogo, 650-0017, Japan
| | - Shingo Matsumoto
- Department of Thoracic Oncology, National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa-City, Chiba, 277-8577, Japan
| | - Koichi Goto
- Department of Thoracic Oncology, National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa-City, Chiba, 277-8577, Japan
| | - Motoko Tachihara
- Division of Respiratory Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-Cho, Chuo-Ku, Kobe-City, Hyogo, 650-0017, Japan.
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Ivorová S, Kopčaková A, Pristaš P, Kišidayová S. Morphometric and Molecular Analysis of Five-Spine Epidinium Morphotypes Taken from the Rumen of European Bison, Bison bonasus. Life (Basel) 2023; 13:2350. [PMID: 38137951 PMCID: PMC10744686 DOI: 10.3390/life13122350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
An important feature of ruminal ciliates is their phenotypic plasticity, which makes their identification difficult. The common manifestation of the phenotypic plasticity in rumen ciliates is a change in their cell size and caudal spination. We analyzed various morphotypes of Epidinium with five caudal processes (spines) taken from the rumen of European bison (Bison bonasus). In the study, the cluster analysis and K-means analysis of morphometric data could not distinguish very similar morphotypes of Epidinium with five caudal processes. However, the morphotype of E. parvicaudatum prevailed (70%). The DNA of four individual E. parvicaudatum was isolated successfully from formaldehyde-preserved samples. The partial 18S rDNA gene sequences (about 350-400 bp) were identical to Epidinium sequences in GenBank (E. caudatum, a one-spine morphotype, and E. cattanei, a five-spine morphotype). It can be assumed that these short sequences cannot distinguish the differences between the Epidinium morphospecies. Complete gene sequences from various hosts and various molecular markers are necessary to reveal the validity of the Epidinium five-spine species. In conclusion, classical morphology should be supplemented with molecular data when more morphotypes of the rumen ciliate species are present in samples.
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Affiliation(s)
| | | | | | - Svetlana Kišidayová
- Institute of Animal Physiology, Centre of Biosciences, Slovak Academy of Sciences, 04001 Košice, Slovakia; (S.I.); (A.K.); (P.P.)
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Vitošević K, Todorović D, Slović Ž, Varljen T, Radaković I, Radojević D, Čanović V, Todorović M. The quality of DNA isolated from autopsy formalin-fixed and formalin-fixed paraffin-embedded tissues: study of 1662 samples. Mol Biol Rep 2023; 50:6323-6336. [PMID: 37310548 DOI: 10.1007/s11033-023-08491-5] [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: 01/05/2023] [Accepted: 04/26/2023] [Indexed: 06/14/2023]
Abstract
BACKGROUND There are enormous formalin-fixed paraffin-embedded tissue archives and a constantly growing number of methods for molecular analyses but, the isolation of DNA from this tissue is still challenging due to the damaging effect of formalin on DNA. To determine the extent to which DNA purity, yield and integrity depend on the process of fixation in formalin, and to what extent on the process of tissue paraffin embedding, we compared the quality of DNA isolated from fixed tissues and DNA isolated from tissues embedded in paraffin blocks after fixation. METHODS AND RESULTS Heart, liver and brain tissues obtained from healthy people who suddenly died a violent death were fixed in 10% buffered formalin as well as in 4% unbuffered formalin for 6 h, 1-7 days (every 24 h), 10, 14, 28 days and 2 months. Additionally, the same tissues were fixed in 4% unbuffered formalin embedded in a paraffin block and stored from a few months to 30 years. The yield and purity of the DNA samples isolated from these tissues were measured using spectrophotometry. PCR amplification of the hTERT gene was performed to evaluate the degree of DNA fragmentation. Although the purity of the DNA isolated from almost all tissue samples was satisfactory, the DNA yields changed significantly. There was a decrease in successful PCR amplification of the hTERT gene in DNA samples isolated from tissue fixed in buffered and unbuffered formalin for up to 2 months from 100% to 8.3%. Archiving the tissue in paraffin blocks for up to 30 years also impacts the integrity of DNA, so there was a decrease in PCR amplification of the hTERT gene from 91% success to 3%. CONCLUSION The largest decrease in DNA yield was observed after tissue formalin fixation after 14 days of fixation in buffered and unbuffered formalin. DNA integrity depends on the time of tissue formalin fixation, especially after 6 days for tissue fixed in unbuffered formalin, while for tissue fixed in buffered formalin the time is prolonged up to 28 days. The age of paraffin blocks also impacted DNA integrity, after 1 year and 16 years of archiving the paraffin blocks of tissues, there was a decrease in the success of PCR amplification.
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Affiliation(s)
- Katarina Vitošević
- Faculty of Medical Sciences, Department of Forensic Medicine, University of Kragujevac, Serbia, Kragujevac, Serbia.
- Department of Forensic Medicine and Toxicology, University Clinical Center Kragujevac, Kragujevac, Serbia.
| | - Danijela Todorović
- Faculty of Medical Sciences, Department of Genetics, University of Kragujevac, Serbia, Kragujevac, Serbia
| | - Živana Slović
- Faculty of Medical Sciences, Department of Forensic Medicine, University of Kragujevac, Serbia, Kragujevac, Serbia
- Department of Forensic Medicine and Toxicology, University Clinical Center Kragujevac, Kragujevac, Serbia
| | - Tatjana Varljen
- Institute of Legal Medicine, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Ivana Radaković
- Faculty of Medical Sciences, Department of Forensic Medicine, University of Kragujevac, Serbia, Kragujevac, Serbia
| | - Dušan Radojević
- Faculty of Medical Sciences, Department of Genetics, University of Kragujevac, Serbia, Kragujevac, Serbia
| | - Vanja Čanović
- Faculty of Medical Sciences, University of Kragujevac, Serbia, Kragujevac, Serbia
| | - Miloš Todorović
- Faculty of Medical Sciences, Department of Forensic Medicine, University of Kragujevac, Serbia, Kragujevac, Serbia
- Department of Forensic Medicine and Toxicology, University Clinical Center Kragujevac, Kragujevac, Serbia
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5
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Unkovič A, Boštjančič E, Belič A, Perše M. Selection and Evaluation of mRNA and miRNA Reference Genes for Expression Studies (qPCR) in Archived Formalin-Fixed and Paraffin-Embedded (FFPE) Colon Samples of DSS-Induced Colitis Mouse Model. BIOLOGY 2023; 12:biology12020190. [PMID: 36829468 PMCID: PMC9952917 DOI: 10.3390/biology12020190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/21/2023] [Accepted: 01/25/2023] [Indexed: 01/28/2023]
Abstract
The choice of appropriate reference genes is essential for correctly interpreting qPCR data and results. However, the majority of animal studies use a single reference gene without any prior evaluation. Therefore, many qPCR results from rodent studies can be misleading, affecting not only reproducibility but also translatability. In this study, the expression stability of reference genes for mRNA and miRNA in archived FFPE samples of 117 C57BL/6JOlaHsd mice (males and females) from 9 colitis experiments (dextran sulfate sodium; DSS) were evaluated and their expression analysis was performed. In addition, we investigated whether normalization reduced/neutralized the influence of inter/intra-experimental factors which we systematically included in the study. Two statistical algorithms (NormFinder and Bestkeeper) were used to determine the stability of reference genes. Multivariate analysis was made to evaluate the influence of normalization with different reference genes on target gene expression in regard to inter/intra-experimental factors. Results show that archived FFPE samples are a reliable source of RNA and imply that the FFPE procedure does not change the ranking of stability of reference genes obtained in fresh tissues. Multivariate analysis showed that the histological picture is an important factor affecting the expression levels of target genes.
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Affiliation(s)
- Ana Unkovič
- Medical Experimental Centre, Institute of Pathology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Emanuela Boštjančič
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Aleš Belič
- Statistics and Modelling, Technical Development Biologics, Novartis Technical Research & Development, Lek Pharmaceuticals d.d., 1000 Ljubljana, Slovenia
| | - Martina Perše
- Medical Experimental Centre, Institute of Pathology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
- Correspondence:
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Nguyen HT, Tatipamula VB, Do DN, Huynh TC, Dang MK. Retrieving high-quality genomic DNA from formalin-fixed paraffin-embedded tissues for multiple molecular analyses. Prep Biochem Biotechnol 2021; 52:48-55. [PMID: 34047684 DOI: 10.1080/10826068.2021.1923030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues represent the biggest source of archival materials for molecular biology research and pathology investigations. Nevertheless, fixation by formalin may cause denaturation and modification of macromolecules constraining DNA quality and its downstream applications. In this study, we developed a fast, simple, and cost-effective phenol/chloroform-based protocol for the extraction of high-quality DNA from 101 FFPE colorectal cancer tissue blocks that can be used in multiple molecular studies. DNA samples extracted using this phenol/chloroform protocol and the QIAamp DNA FFPE Tissue kit were evaluated for the quantity, quality, and amplificability. Spectrophotometer analyses revealed significantly higher quality and quantity of DNA samples obtained with the phenol/chloroform protocol as compared to those of the QIAamp DNA FFPE Tissue kit. In addition, the amplificability of these samples as assessed by conventional and multiplex polymerase chain reaction (PCR), followed by sequencing and fragment analyses presented an absolute success rate. Additionally, it is able to amplify a DNA fragment of 725 base-pairs at an adequate amount for downstream applications. This fast, simple, and cost-effective method may facilitate the molecular analyses of a large number of FFPE specimens that best suits the needs of the overall study design in terms of the quality and quantity of the extracted DNA.
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Affiliation(s)
- Ha Thi Nguyen
- Institute of Research and Development, Duy Tan University, Danang, Vietnam.,Faculty of Medicine, Duy Tan University, Danang, Vietnam
| | - Vinay Bharadwaj Tatipamula
- Institute of Research and Development, Duy Tan University, Danang, Vietnam.,Faculty of Medicine, Duy Tan University, Danang, Vietnam
| | - Duy Ngoc Do
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, Nova Scotia, Canada
| | - Thien Chi Huynh
- Faculty of Biotechnology, Ho Chi Minh City University of Technology, Ho Chi Minh, Vietnam
| | - Mai Kim Dang
- Institute of Research and Development, Duy Tan University, Danang, Vietnam
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7
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Shukla NI, Siva N, Sivakumar M, Parveen R, Mishra A, Shah A, Medicherla K, Suravajhala P. Extraction of DNA and RNA from Formalin-fixed Paraffin-embedded Tissue Specimens. Bio Protoc 2021. [DOI: 10.21769/bioprotoc.4095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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8
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Božić L, Jovanović T, Šmitran A, Janković M, Knežević A. Comparison of HPV detection rate in formalin-fixed paraffin-embedded tissues of head and neck carcinoma using two DNA extraction kits and three amplification methods. Eur J Oral Sci 2020; 128:501-507. [PMID: 33200860 DOI: 10.1111/eos.12746] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/23/2020] [Accepted: 10/21/2020] [Indexed: 12/27/2022]
Abstract
The potential problems of DNA extraction from formalin-fixed paraffin-embedded (FFPE) tissue samples and amplification efficiency of Human papilloma virus (HPV) may occur in the molecular studies of head and neck squamous carcinoma (HNSCC). The aim of this study was to compare HPV detection rate in FFPE tissues of oral, oropharyngeal, hypopharyngeal, and laryngeal cancers using two silica-based extraction kits and three amplification methods. A total of 50 FFPE specimens from HNSCC tissues were analyzed. The quality and quantity of the extracted DNA were tested by spectrophotometry. HPV DNA was detected using a single polymerase chain reaction (PCR), a nested PCR, and a Real-time PCR kit. Statistically significantly higher DNA quality and quantity was observed using the QIAamp DNA FFPE Tissue Kit than when using the QIAamp DNA Mini Kit. There was not HPV amplification in any of the 50 FFPE samples using the single PCR and Real-time PCR kits, whereas HPV DNA was detected in 22% of samples using nested PCR. Comparing results of the three different methods showed that HPV DNA was detected only with nested PCR. The results presented imply that nested PCR is the most appropriate method for the detection of HPV DNA in FFPE samples, along with adequate DNA extraction methods.
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Affiliation(s)
- Ljiljana Božić
- Faculty of Medicine, University of Banja Luka, Banja Luka, Bosnia and Herzegovina
| | - Tanja Jovanović
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Republic of Serbia
| | - Aleksandra Šmitran
- Faculty of Medicine, University of Banja Luka, Banja Luka, Bosnia and Herzegovina
| | - Marko Janković
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Republic of Serbia
| | - Aleksandra Knežević
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Republic of Serbia
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9
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Sotoudeh Anvari M, Gharib A, Abolhasani M, Azari-Yam A, Hossieni Gharalari F, Safavi M, Zare Mirzaie A, Vasei M. Pre-analytical Practices in the Molecular Diagnostic Tests, A Concise Review. IRANIAN JOURNAL OF PATHOLOGY 2020; 16:1-19. [PMID: 33391375 PMCID: PMC7691716 DOI: 10.30699/ijp.2020.124315.2357] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/05/2020] [Indexed: 12/17/2022]
Abstract
Molecular assays for detection of nucleic acids in biologic specimens are valuable diagnostic tools supporting clinical diagnoses and therapeutic decisions. Pre-analytical errors, which occur before or during processing of nucleic acid extraction, contribute a significant role in common errors that take place in molecular laboratories. Certain practices in specimen collection, transportation, and storage can affect the integrity of nucleic acids before analysis. Applying best practices in these steps, helps to minimize those errors and leads to better decisions in patient diagnosis and treatment. Widely acceptable recommendations, which are for optimal molecular assays associated with pre-analytic variables, are limited. In this article, we have reviewed most of the important issues in sample handling from bed to bench before starting molecular tests, which can be used in diagnostic as well as research laboratories. We have addressed the most important pre-analytical points in performing molecular analysis in fixed and unfixed solid tissues, whole blood, serum, plasma, as well as most of the body fluids including urine, fecal and bronchial samples, as well as prenatal diagnosis samples.
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Affiliation(s)
- Maryam Sotoudeh Anvari
- Molecular Pathology and Cytogenetics Division, Pathology Department, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Atoosa Gharib
- Department of Pathology, Modarres Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Abolhasani
- Oncopathology Research Center, Iran University of Medical Sciences (IUMS), Tehran, Iran; Hasheminejad Kidney Center, Iran University of Medical Sciences, Tehran, Iran
| | - Aileen Azari-Yam
- Molecular Pathology and Cytogenetics Division, Pathology Department, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Moeinadin Safavi
- Molecular Pathology and Cytogenetics Division, Pathology Department, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Zare Mirzaie
- Department of Pathology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Vasei
- Cell-based Therapies Research Center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
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Vitošević K, Todorović M, Slović Ž, Varljen T, Matić S, Todorović D. DNA isolated from formalin-fixed paraffin-embedded healthy tissue after 30 years of storage can be used for forensic studies. Forensic Sci Med Pathol 2020; 17:47-57. [PMID: 33159288 DOI: 10.1007/s12024-020-00327-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2020] [Indexed: 11/30/2022]
Abstract
Tissue formalin fixation and paraffin embedding (FFPE) is a standard method for long-term preservation and morphological and molecular analysis. The aim of this study was to analyze the effect of storage time on the integrity of DNA isolated from three different healthy FFPE tissues. DNA was isolated from FFPE heart, liver and brain tissues obtained from autopsy and archived from 1988 to 2017 using two different methods of DNA isolation: phenol-chloroform-isoamyl alcohol (PCI) and PureLink Genomic DNA Kit. The quantification and purity of DNA was measured spectrophotometrically at 260 nm and 280 nm. The quality of isolated DNA was evaluated by PCR amplification of GPD1 (150 bp), ACTB (262 bp) and RPL4 (407 bp) genes. The histomorphological characteristics of FFPE tissues were not significantly changed during 30 years of storage. Higher yield (272.9 ± 10.3 µg) and purity (A260/280 = 2.05) of DNA was obtained using the PCI method for DNA isolation from FFPE liver tissue. The PCI extraction method showed reproducible and consistent results in PCR amplification of all of three examined genes. The GPD1 gene can be amplified up to 30 years, the ACTB gene in the same samples up to 26 years and the RPL4 gene up to 6 years of storage in FFPE blocks. Although the best yield and purity of isolated DNA (using both isolation methods) was obtained from FFPE liver tissue, the DNA with the most preserved integrity was obtained from brain tissue archived up to 30 years. This is the first report using long-term archived healthy FFPE tissues (up to 30 years) that shows that the DNA isolated from these tissues is of preserved integrity and can be used in molecular autopsy.
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Affiliation(s)
- Katarina Vitošević
- Faculty of Medical Sciences, Department of Forensic Medicine, University of Kragujevac, Kragujevac, Serbia
| | - Miloš Todorović
- Faculty of Medical Sciences, Department of Forensic Medicine, University of Kragujevac, Kragujevac, Serbia
| | - Živana Slović
- Faculty of Medical Sciences, Department of Forensic Medicine, University of Kragujevac, Kragujevac, Serbia
| | - Tatjana Varljen
- Institute of Forensic Medicine, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Stevan Matić
- Institute of Pathology and Forensic Medicine, Military Medical Academy, Belgrade, Serbia
| | - Danijela Todorović
- Faculty of Medical Sciences, Department of Genetics, University of Kragujevac, Kragujevac, Serbia.
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Shetty O, Pai T, Gurav M, Rekhi B. Comparison between Fluorescence in-situ Hybridization (FISH), Reverse Transcriptase PCR (RT-PCR) and fragment analysis, for detection of t (X; 18) (p11; q11) translocation in synovial sarcomas. INDIAN J PATHOL MICR 2020; 63:64-72. [PMID: 32031125 DOI: 10.4103/ijpm.ijpm_851_18] [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] [Indexed: 11/04/2022] Open
Abstract
Background Synovial sarcoma (SS) is an aggressive, but a relatively chemosensitive soft tissue sarcoma, characterized by a specific, t (X;18)(p11;q11) translocation, leading to formation of SS18-SSX chimeric transcript. This translocation can be detected by various techniques, such as fluorescence in-situ hybridization (FISH), reverse transcriptase PCR (RT-PCR) and fragment analysis. Objectives To compare the results of detection of t (X;18)(p11;q11) translocation, across three different platforms, in order to determine the most optimal and sensitive technique. Methods Formalin-fixed paraffin embedded (FFPE) tissue sections of 45 soft tissue sarcomas were analyzed, including 16 cases of SS confirmed by histopathology, immunohistochemistry and molecular technique (s)(Group 1); 13 cases, wherein SS was one of the differential diagnosis, preceding molecular testing (Group 2) and 16 cases of various other sarcomas (Group 3). Various immunohistochemical (IHC) markers studied, including INI1/SMARCB1. All cases were tested for t (X;18) translocation, by fragment Analysis, FISH and RT-PCR. Results There were 23 cases of SS, including 16 of group 1 and 7 of group 2. By fragment analysis, t (X;18)(p11;q11) translocation was detected in 22/23 cases (95.6%). By FISH, SS18 gene rearrangement was detected in 18/22 cases (78.2%), whereas by RT-PCR, SS18-SSX transcripts were detected in 15/23 cases (65.2%). Immunohistochemically, a unique "weak to absent"/reduced INI1 immunostaining pattern was exclusively observed in 12/13 cases of SS (92.3%). Fragment analysis and FISH were relatively more sensitive techniques. Unique "weak to absent"INI1 immunoexpression significantly correlated with positive t (X;18) translocation results (P = 0.0001). Conclusion The present study constitutes first such study from our subcontinent. Fragment analysis is a promising technique for detection of t (X;18)(p11;q11) translocation. FISH and INI1 immunostaining pattern were also relatively more sensitive, over RT-PCR.
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Affiliation(s)
- Omshree Shetty
- Division of Molecular Pathology and Translational Medicine, Tata Memorial Centre, Mumbai, Maharashtra, India
| | - Trupti Pai
- Division of Molecular Pathology and Translational Medicine; Department of Surgical Pathology, Tata Memorial Centre, Mumbai, Maharashtra, India
| | - Mamta Gurav
- Division of Molecular Pathology and Translational Medicine, Tata Memorial Centre, Mumbai, Maharashtra, India
| | - Bharat Rekhi
- Division of Molecular Pathology and Translational Medicine; Department of Surgical Pathology, Tata Memorial Centre, Mumbai, Maharashtra, India
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12
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Salmani T, Ghaderian SMH, Hajiesmaeili M, Mirghaed OR, Rakhshan A, Nasiri MJ, Mohammadi M. Cyclin dependent kinase inhibitor 2A and miR-671-5p expression profile in Iranian glioblastoma multiforme. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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13
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Formalin Fixation of Human Healthy Autopsied Tissues: The Influence of Type of Tissue, Temperature and Incubation Time on the Quality of Isolated DNA. SERBIAN JOURNAL OF EXPERIMENTAL AND CLINICAL RESEARCH 2020. [DOI: 10.2478/sjecr-2019-0020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Formalin fixation is a widely used method in histopathology that has certain limits. Formalin often leads to the degradation of DNA molecules in cancer tissues, which makes tissues unusable for molecular analysis. The other factors may also affect the quality of DNA isolated from fixed tissues. The aim of this study is to determine the impact of the incubation time and temperature on the quality of DNA molecules isolated from various healthy human tissues. The brain, lung and kidney tissues, excluded during the forensic autopsies of people who died of violent death, were fixed in phosphate-buffered formalin from 24h to two months. After the completion of the incubation period, the DNA was isolated using phenol-chloroform-isoamyl alcohol extraction method and the concentration and purity of the samples were determined spectrophotometrically. The degree of degradation of DNA was assessed by PCR reaction, by amplification of gene fragments which lengths were 150bp (GPD1) and 262bp (β-actin). The highest concentration, purity and preserved integrity of DNA were obtained from the brain samples. With prolonged tissue incubation times in formalin, the concentration and integrity of DNA decreased in all tissue samples, especially in the brain tissue, while the purity of DNA remained unchanged. Also, tissue fixation at +4°C contributed to a better quality of isolated DNA compared to DNA isolated from tissue fixed at room temperature. We can conclude that the type of human healthy tissue, temperature and the incubation time of formalin fixation have important influence on the concentration, purity and integrity of DNA during fixation of tissues excluded in the course of forensic autopsy.
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Bertran K, Pantin-Jackwood MJ, Criado MF, Lee DH, Balzli CL, Spackman E, Suarez DL, Swayne DE. Pathobiology and innate immune responses of gallinaceous poultry to clade 2.3.4.4A H5Nx highly pathogenic avian influenza virus infection. Vet Res 2019; 50:89. [PMID: 31675983 PMCID: PMC6824115 DOI: 10.1186/s13567-019-0704-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/27/2019] [Indexed: 11/10/2022] Open
Abstract
In the 2014-2015 Eurasian lineage clade 2.3.4.4A H5 highly pathogenic avian influenza (HPAI) outbreak in the U.S., backyard flocks with minor gallinaceous poultry and large commercial poultry (chickens and turkeys) operations were affected. The pathogenesis of the first H5N8 and reassortant H5N2 clade 2.3.4.4A HPAI U.S. isolates was investigated in six gallinaceous species: chickens, Japanese quail, Bobwhite quail, Pearl guinea fowl, Chukar partridges, and Ring-necked pheasants. Both viruses caused 80-100% mortality in all species, except for H5N2 virus that caused 60% mortality in chickens. The surviving challenged birds remained uninfected based on lack of clinical disease and lack of seroconversion. Among the infected birds, chickens and Japanese quail in early clinical stages (asymptomatic and listless) lacked histopathologic findings. In contrast, birds of all species in later clinical stages (moribund and dead) had histopathologic lesions and systemic virus replication consistent with HPAI virus infection in gallinaceous poultry. These birds had widespread multifocal areas of necrosis, sometimes with heterophilic or lymphoplasmacytic inflammatory infiltrate, and viral antigen in parenchymal cells of most tissues. In general, lesions and antigen distribution were similar regardless of virus and species. However, endotheliotropism was the most striking difference among species, with only Pearl guinea fowl showing widespread replication of both viruses in endothelial cells of most tissues. The expression of IFN-γ and IL-10 in Japanese quail, and IL-6 in chickens, were up-regulated in later clinical stages compared to asymptomatic birds.
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Affiliation(s)
- Kateri Bertran
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, 30605, USA.,IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Mary J Pantin-Jackwood
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, 30605, USA
| | - Miria F Criado
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, 30605, USA
| | - Dong-Hun Lee
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, 30605, USA.,Department of Pathobiology & Veterinary Science, University of Connecticut, Storrs, CT, 06269, USA
| | - Charles L Balzli
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, 30605, USA.,Battelle National Biodefense Institute, National Biodefense Analysis and Countermeasures Center, 8300 Research PI, Fort Detrick, MD, 21702, USA
| | - Erica Spackman
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, 30605, USA
| | - David L Suarez
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, 30605, USA
| | - David E Swayne
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, 30605, USA.
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DNA extraction from FFPE tissue samples - a comparison of three procedures. Contemp Oncol (Pozn) 2019; 23:52-58. [PMID: 31061638 PMCID: PMC6500389 DOI: 10.5114/wo.2019.83875] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 01/26/2019] [Indexed: 12/29/2022] Open
Abstract
Aim of the study One of the critical steps in molecular oncology diagnostics is obtaining high quality genomic DNA. Therefore, it is important to evaluate and compare the techniques used to extract DNA from tissue samples. Since formalin-fixed, paraffin-embedded (FFPE) tissues are routinely used for both retrospective and prospective studies, we compared three commercially available methods of nucleic acid extraction in terms of quantity and quality of isolated DNA. Material and methods Slides prepared from 42 FFPE blocks were macro-dissected. Resulting material was divided and processed simultaneously using three extraction kits: QIAamp DNA FFPE Tissue Kit (QIAGEN), Cobas DNA Sample Preparation Kit (Roche Molecular Systems) and Maxwell 16 FFPE Plus LEV DNA Purification Kit (Promega). Subsequently, quantity and quality of obtained DNA samples were analysed spectrophotometrically (NanoDrop 2000, Thermo Scientific). Results of quantitative analysis were confirmed by a fluorometric procedure (Qubit 3.0 Fluorometer, Life Technologies). Results The results demonstrated that the yields of total DNA extracted using either Maxwell or Cobas methods were significantly higher compared to the QIAamp method (p < 0.001). The Maxwell Extraction Kit delivered DNA samples of the highest quality (p < 0.01). However, the highest total yield of extracted DNA was achieved with the Cobas technique, which may be due to a higher volume of eluate compared to the Maxwell method. Conclusions To our knowledge, this is the first paper which directly compares three extraction methods: Cobas, Maxwell and QIAamp. The data herein provide information required for the selection of a protocol that best suits the needs of the overall study design in terms of the quantity and quality of the extracted DNA.
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Matsushige T, Kuwamoto S, Matsushita M, Oka Wardhani L, Horie Y, Hayashi K, Kitamura Y. Detection of Disease-specific Fusion Genes of Soft Tissue Tumors Using Formalin-fixed Paraffin-embedded Tissues; Its Diagnostic Usefulness and Factors Affecting the Detection Rates. Yonago Acta Med 2019; 62:115-123. [PMID: 30962753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 01/28/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Recent rapid advances in molecular biology have led the discovery of disease-specific novel fusion genes in a variety of soft tissue tumors. In this study, we attempted to detect these fusion genes using formalin-fixed paraffin-embedded (FFPE) tumor tissues and investigated their clinical utility and factors that affect the results of examination. METHODS Reverse transcription polymerase chain reaction for the detection of tumor-specific fusion genes was performed using 41 FFPE tumor samples obtained from 37 patients representing nine histological types of soft tissue tumors that were diagnosed from 2006 to 2017 in our laboratory. RESULTS Fusion genes in 19 (51.3%) out of 37 cases were detected successfully. Relatively high detection rates were observed in synovial sarcomas (100%, 4/4) and alveolar rhabdomyosarcomas (75%, 3/4). The detection rates of fusion genes were inversely correlated with the storage period of FFPE blocks. Decalcification by Plank-Rychlo solution significantly affected detection rates of the internal control gene (P = 0.0038). In contrast, there was no significant difference in detection rates between primary and metastatic lesion, or biopsy and resection material, or presence and absence of treatment history. CONCLUSION In certain histological types, detection of disease-specific fusion genes of soft tissue tumors using FFPE tissues showed high sensitivity and thus had diagnostic utility. However, due to the diversity of fusion patterns and the low-quality of nucleic acid, the detection rate as a whole was sluggish and required further improvement. For factors affecting the detection results, our results suggested that it was impossible to detect fusion genes by decalcified FFPE tissues, but it may be not necessary to consider factors such as the type of specimen (biopsy or resection) and treatment history of the patients when selecting the FFPE tissues.
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Affiliation(s)
- Takahiro Matsushige
- Department of Pathobiological Science and Technology, Major in Clinical Laboratory Science, School of Health Science, Tottori University Faculty of Medicine, Yonago 683-8503, Japan
| | - Satoshi Kuwamoto
- †Department of Pathology, Tottori University Hospital, Yonago 683-8504, Japan
- ‡Division of Molecular Pathology, Department of Pathology, School of Medicine, Tottori University Faculty of Medicine, Yonago 683-8503, Japan
| | - Michiko Matsushita
- Department of Pathobiological Science and Technology, Major in Clinical Laboratory Science, School of Health Science, Tottori University Faculty of Medicine, Yonago 683-8503, Japan
| | - Lusi Oka Wardhani
- ‡Division of Molecular Pathology, Department of Pathology, School of Medicine, Tottori University Faculty of Medicine, Yonago 683-8503, Japan
| | - Yasushi Horie
- †Department of Pathology, Tottori University Hospital, Yonago 683-8504, Japan
| | - Kazuhiko Hayashi
- ‡Division of Molecular Pathology, Department of Pathology, School of Medicine, Tottori University Faculty of Medicine, Yonago 683-8503, Japan
| | - Yukisato Kitamura
- Department of Pathobiological Science and Technology, Major in Clinical Laboratory Science, School of Health Science, Tottori University Faculty of Medicine, Yonago 683-8503, Japan
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Carithers LJ, Agarwal R, Guan P, Odeh H, Sachs MC, Engel KB, Greytak SR, Barcus M, Soria C, Lih CJJ, Williams PM, Branton PA, Sobin L, Fombonne B, Bocklage T, Andry C, Duffy ER, Sica G, Dhir R, Jewell S, Roche N, Moore HM. The Biospecimen Preanalytical Variables Program: A Multiassay Comparison of Effects of Delay to Fixation and Fixation Duration on Nucleic Acid Quality. Arch Pathol Lab Med 2019; 143:1106-1118. [PMID: 30785788 DOI: 10.5858/arpa.2018-0172-oa] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Despite widespread use of formalin-fixed, paraffin-embedded (FFPE) tissue in clinical and research settings, potential effects of variable tissue processing remain largely unknown. OBJECTIVE.— To elucidate molecular effects associated with clinically relevant preanalytical variability, the National Cancer Institute initiated the Biospecimen Preanalytical Variables (BPV) program. DESIGN.— The BPV program, a well-controlled series of systematic, blind and randomized studies, investigated whether a delay to fixation (DTF) or time in fixative (TIF) affects the quantity and quality of DNA and RNA isolated from FFPE colon, kidney, and ovarian tumors in comparison to case-matched snap-frozen controls. RESULTS.— DNA and RNA yields were comparable among FFPE biospecimens subjected to different DTF and TIF time points. DNA and RNA quality metrics revealed assay- and time point-specific effects of DTF and TIF. A quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assay was superior when assessing RNA quality, consistently detecting differences between FFPE and snap-frozen biospecimens and among DTF and TIF time points. RNA Integrity Number and DV200 (representing the percentage of RNA fragments longer than 200 nucleotides) displayed more limited sensitivity. Differences in DNA quality (Q-ratio) between FFPE and snap-frozen biospecimens and among DTF and TIF time points were detected with a qPCR-based assay. CONCLUSIONS.— DNA and RNA quality may be adversely affected in some tumor types by a 12-hour DTF or a TIF of 72 hours. Results presented here as well as those of additional BPV molecular analyses underway will aid in the identification of acceptable delays and optimal fixation times, and quality assays that are suitable predictors of an FFPE biospecimen's fit-for-purpose.
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Affiliation(s)
- Latarsha J Carithers
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Rachana Agarwal
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Ping Guan
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Hana Odeh
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Michael C Sachs
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Kelly B Engel
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Sarah R Greytak
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Mary Barcus
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Conrado Soria
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Chih-Jian Jason Lih
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - P Mickey Williams
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Philip A Branton
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Leslie Sobin
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Benjamin Fombonne
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Therese Bocklage
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Chris Andry
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Elizabeth R Duffy
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Gabriel Sica
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Rajiv Dhir
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Scott Jewell
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Nancy Roche
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Helen M Moore
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
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Matsushige T, Kuwamoto S, Matsushita M, Oka Wardhani L, Horie Y, Hayashi K, Kitamura Y. Detection of Disease-specific Fusion Genes of Soft Tissue Tumors Using Formalin-fixed Paraffin-embedded Tissues; Its Diagnostic Usefulness and Factors Affecting the Detection Rates. Yonago Acta Med 2019. [DOI: 10.33160/yam.2019.03.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Takahiro Matsushige
- *Department of Pathobiological Science and Technology, Major in Clinical Laboratory Science, School of Health Science, Tottori University Faculty of Medicine, Yonago 683-8503, Japan
| | - Satoshi Kuwamoto
- †Department of Pathology, Tottori University Hospital, Yonago 683-8504, Japan
- ‡Division of Molecular Pathology, Department of Pathology, School of Medicine, Tottori University Faculty of Medicine, Yonago 683-8503, Japan
| | - Michiko Matsushita
- *Department of Pathobiological Science and Technology, Major in Clinical Laboratory Science, School of Health Science, Tottori University Faculty of Medicine, Yonago 683-8503, Japan
| | - Lusi Oka Wardhani
- ‡Division of Molecular Pathology, Department of Pathology, School of Medicine, Tottori University Faculty of Medicine, Yonago 683-8503, Japan
| | - Yasushi Horie
- †Department of Pathology, Tottori University Hospital, Yonago 683-8504, Japan
| | - Kazuhiko Hayashi
- ‡Division of Molecular Pathology, Department of Pathology, School of Medicine, Tottori University Faculty of Medicine, Yonago 683-8503, Japan
| | - Yukisato Kitamura
- *Department of Pathobiological Science and Technology, Major in Clinical Laboratory Science, School of Health Science, Tottori University Faculty of Medicine, Yonago 683-8503, Japan
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19
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Effect of formalin fixation on pcr amplification of DNA isolated from healthy autopsy tissues. Acta Histochem 2018; 120:780-788. [PMID: 30224244 DOI: 10.1016/j.acthis.2018.09.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 09/08/2018] [Accepted: 09/10/2018] [Indexed: 12/23/2022]
Abstract
The aim of this study is to investigate the effects of formalin fixation on the degradation of DNA molecules in five different healthy tissues exempted during the autopsy, as well as the selection of the method that is most suitable for the DNA isolation. Heart muscle, liver, brain, lung and kidney tissue obtained from the healthy people who suddenly died from a violent death were used. The parts of tissue were fixed in 10% phosphate-buffered formalin as well as in 4% unbuffered formalin at room temperature. Morphology of tissue was studied using H&E staining. The DNA was isolated 6 h, 1-7 days (every 24 h), 10, 14, 28 days and 2 months after fixation using two different methods: extraction with phenol-chloroform-isoamyl alcohol as well as with PureLink Genomic DNA Kit. Yield and purity of the DNA samples were measured spectrophotometrically at 260 nm and 280 nm. The PCR amplifications of the glycerol-3-phosphate dehydrogenase 1 (GPD1, 150 bp), ß actin (ACTB, 262 bp) and ribosomal protein L4 (RPL4, 407 bp) genes were performed to evaluate the degree of DNA fragmentation. The RPL4 gene was amplified up to 72 h, ACTB gene up to 14 days and GPD1 gene up to 28 days from tissue fixed in phosphate-buffered formalin using phenol-chloroform-isoamylalcohol protocol for DNA isolation. Liver and kidney gave better results of PCR amplification, but statistical significance between tissues was not found. Preserving period, fixative and DNA extracting method are important factors for successful PCR amplification. The healthy tissue, fixed in phosphate-formalin up to 28 days, can be useful source in molecular studies. Tissues fixed in unbuffered formalin are suitable for molecular analysis up to 7 days.
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20
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Chen R, Guan Q, Cheng J, He J, Liu H, Cai H, Hong G, Zhang J, Li N, Ao L, Guo Z. Robust transcriptional tumor signatures applicable to both formalin-fixed paraffin-embedded and fresh-frozen samples. Oncotarget 2018; 8:6652-6662. [PMID: 28036264 PMCID: PMC5351660 DOI: 10.18632/oncotarget.14257] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 12/02/2016] [Indexed: 12/19/2022] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) samples represent a valuable resource for clinical researches. However, FFPE samples are usually considered an unreliable source for gene expression analysis due to the partial RNA degradation. In this study, through comparing gene expression profiles between FFPE samples and paired fresh-frozen (FF) samples for three cancer types, we firstly showed that expression measurements of thousands of genes had at least two-fold change in FFPE samples compared with paired FF samples. Therefore, for a transcriptional signature based on risk scores summarized from the expression levels of the signature genes, the risk score thresholds trained from FFPE (or FF) samples could not be applied to FF (or FFPE) samples. On the other hand, we found that more than 90% of the relative expression orderings (REOs) of gene pairs in the FF samples were maintained in their paired FFPE samples and largely unaffected by the storage time. The result suggested that the REOs of gene pairs were highly robust against partial RNA degradation in FFPE samples. Finally, as a case study, we developed a REOs-based signature to distinguish liver cirrhosis from hepatocellular carcinoma (HCC) using FFPE samples. The signature was validated in four datasets of FFPE samples and eight datasets of FF samples. In conclusion, the valuable FFPE samples can be fully exploited to identify REOs-based diagnostic and prognostic signatures which could be robustly applicable to both FF samples and FFPE samples with degraded RNA.
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Affiliation(s)
- Rou Chen
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou 350001, China
| | - Qingzhou Guan
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou 350001, China
| | - Jun Cheng
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou 350001, China
| | - Jun He
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou 350001, China
| | - Huaping Liu
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou 350001, China
| | - Hao Cai
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou 350001, China
| | - Guini Hong
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou 350001, China
| | - Jiahui Zhang
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou 350001, China
| | - Na Li
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou 350001, China
| | - Lu Ao
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou 350001, China
| | - Zheng Guo
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou 350001, China
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22
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Tamlin VS, Kessell AE, Mccoy RJ, Dobson EC, Smith TS, Hebart M, Brown L, Mitrovic D, Peaston AE. Prevalence of exon 11 internal tandem duplications in the C-KIT
proto-oncogene in Australian canine mast cell tumours. Aust Vet J 2017; 95:386-391. [DOI: 10.1111/avj.12636] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Revised: 12/05/2016] [Accepted: 12/11/2016] [Indexed: 11/28/2022]
Affiliation(s)
- VS Tamlin
- School of Animal and Veterinary Sciences (SAVS); University of Adelaide; Roseworthy 5371 South Australia Australia
| | - AE Kessell
- Gribbles Veterinary Pathology; Glenside SA Australia
| | - RJ Mccoy
- Gribbles Veterinary Pathology; Clayton VIC Australia
| | - EC Dobson
- Gribbles Veterinary Pathology; Clayton VIC Australia
| | - TS Smith
- School of Animal and Veterinary Sciences (SAVS); University of Adelaide; Roseworthy 5371 South Australia Australia
| | - M Hebart
- School of Animal and Veterinary Sciences (SAVS); University of Adelaide; Roseworthy 5371 South Australia Australia
| | - L Brown
- School of Animal and Veterinary Sciences (SAVS); University of Adelaide; Roseworthy 5371 South Australia Australia
| | - D Mitrovic
- School of Animal and Veterinary Sciences (SAVS); University of Adelaide; Roseworthy 5371 South Australia Australia
| | - AE Peaston
- School of Animal and Veterinary Sciences (SAVS); University of Adelaide; Roseworthy 5371 South Australia Australia
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23
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DNA degrades during storage in formalin-fixed and paraffin-embedded tissue blocks. Virchows Arch 2017; 471:491-500. [PMID: 28812131 DOI: 10.1007/s00428-017-2213-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 05/24/2017] [Accepted: 07/25/2017] [Indexed: 02/02/2023]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissue blocks are widely used to identify clinically actionable molecular alterations or perform retrospective molecular studies. Our goal was to quantify degradation of DNA occurring during mid to long-term storage of samples in usual conditions. We selected 46 FFPE samples of surgically resected carcinomas of lung, colon, and urothelial tract, of which DNA had been previously extracted. We performed a second DNA extraction on the same blocks under identical conditions after a median period of storage of 5.5 years. Quantitation of DNA by fluorimetry showed a 53% decrease in DNA quantity after storage. Quantitative PCR (qPCR) targeting KRAS exon 2 showed delayed amplification of DNA extracted after storage in all samples but one. The qPCR/fluorimetry quantification ratio decreased from 56 to 15% after storage (p < 0.001). Overall, remaining proportion of DNA analyzable by qPCR represented only 11% of the amount obtained at first extraction. Maximal length of amplifiable DNA fragments assessed with a multiplex PCR was reduced in DNA extracted from stored tissue, indicating that DNA fragmentation had increased in the paraffin blocks during storage. Next-generation sequencing was performed on 12 samples and showed a mean 3.3-fold decrease in library yield and a mean 4.5-fold increase in the number of single-nucleotide variants detected after storage. In conclusion, we observed significant degradation of DNA extracted from the same FFPE block after 4 to 6 years of storage. Better preservation strategies should be considered for storage of FFPE biopsy specimens.
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Lee HS, Kim WH, Kwak Y, Koh J, Bae JM, Kim KM, Chang MS, Han HS, Kim JM, Kim HW, Chang HK, Choi YH, Park JY, Gu MJ, Lhee MJ, Kim JY, Kim HS, Cho MY. Molecular Testing for Gastrointestinal Cancer. J Pathol Transl Med 2017; 51:103-121. [PMID: 28219002 PMCID: PMC5357760 DOI: 10.4132/jptm.2017.01.24] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/16/2017] [Accepted: 01/24/2017] [Indexed: 12/20/2022] Open
Abstract
With recent advances in molecular diagnostic methods and targeted cancer therapies, several molecular tests have been recommended for gastric cancer (GC) and colorectal cancer (CRC). Microsatellite instability analysis of gastrointestinal cancers is performed to screen for Lynch syndrome, predict favorable prognosis, and screen patients for immunotherapy. The epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor has been approved in metastatic CRCs with wildtype RAS (KRAS and NRAS exon 2-4). A BRAF mutation is required for predicting poor prognosis. Additionally, amplification of human epidermal growth factor receptor 2 (HER2) and MET is also associated with resistance to EGFR inhibitor in metastatic CRC patients. The BRAF V600E mutation is found in sporadic microsatellite unstable CRCs, and thus is helpful for ruling out Lynch syndrome. In addition, the KRAS mutation is a prognostic biomarker and the PIK3CA mutation is a molecular biomarker predicting response to phosphoinositide 3-kinase/AKT/mammalian target of rapamycin inhibitors and response to aspirin therapy in CRC patients. Additionally, HER2 testing should be performed in all recurrent or metastatic GCs. If the results of HER2 immunohistochemistry are equivocal, HER2 silver or fluorescence in situ hybridization testing are essential for confirmative determination of HER2 status. Epstein-Barr virus-positive GCs have distinct characteristics, including heavy lymphoid stroma, hypermethylation phenotype, and high expression of immune modulators. Recent advances in next-generation sequencing technologies enable us to examine various genetic alterations using a single test. Pathologists play a crucial role in ensuring reliable molecular testing and they should also take an integral role between molecular laboratories and clinicians.
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Affiliation(s)
- Hye Seung Lee
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Korea
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Woo Ho Kim
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Yoonjin Kwak
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Korea
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Jiwon Koh
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Jeong Mo Bae
- Department of Pathology, SMG-SNU Boramae Medical Center, Seoul, Korea
| | - Kyoung-Mee Kim
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Mee Soo Chang
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
- Department of Pathology, SMG-SNU Boramae Medical Center, Seoul, Korea
| | - Hye Seung Han
- Department of Pathology, Konkuk University School of Medicine, Seoul, Korea
| | - Joon Mee Kim
- Department of Pathology, Inha University School of Medicine, Incheon, Korea
| | - Hwal Woong Kim
- Department of Pathology, Seegene Medical Foundation, Busan, Korea
| | - Hee Kyung Chang
- Department of Pathology, Kosin University Gospel Hospital, Kosin University College of Medicine, Busan, Korea
| | - Young Hee Choi
- Department of Pathology, Hallym University Dongtan Sacred Heart Hospital, Hwaseong, Korea
| | - Ji Y. Park
- Department of Pathology, Catholic University of Daegu School of Medicine, Daegu, Korea
| | - Mi Jin Gu
- Department of Pathology, Yeungnam University College of Medicine, Daegu, Korea
| | - Min Jin Lhee
- Department of Pathology, Seoul Red Cross Hospital, Seoul, Korea
| | - Jung Yeon Kim
- Department of Pathology, Inje University Sanggye Paik Hospital, Seoul, Korea
| | - Hee Sung Kim
- Department of Pathology, Chung-Ang University College of Medicine, Seoul, Korea
| | - Mee-Yon Cho
- Department of Pathology, Wonju Severance Christian Hospital, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - The Gastrointestinal Pathology Study Group of Korean Society of Pathologists
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Korea
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
- Department of Pathology, SMG-SNU Boramae Medical Center, Seoul, Korea
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
- Department of Pathology, Konkuk University School of Medicine, Seoul, Korea
- Department of Pathology, Inha University School of Medicine, Incheon, Korea
- Department of Pathology, Seegene Medical Foundation, Busan, Korea
- Department of Pathology, Kosin University Gospel Hospital, Kosin University College of Medicine, Busan, Korea
- Department of Pathology, Hallym University Dongtan Sacred Heart Hospital, Hwaseong, Korea
- Department of Pathology, Catholic University of Daegu School of Medicine, Daegu, Korea
- Department of Pathology, Yeungnam University College of Medicine, Daegu, Korea
- Department of Pathology, Seoul Red Cross Hospital, Seoul, Korea
- Department of Pathology, Inje University Sanggye Paik Hospital, Seoul, Korea
- Department of Pathology, Chung-Ang University College of Medicine, Seoul, Korea
- Department of Pathology, Wonju Severance Christian Hospital, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - The Molecular Pathology Study Group of Korean Society of Pathologists
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Korea
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
- Department of Pathology, SMG-SNU Boramae Medical Center, Seoul, Korea
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
- Department of Pathology, Konkuk University School of Medicine, Seoul, Korea
- Department of Pathology, Inha University School of Medicine, Incheon, Korea
- Department of Pathology, Seegene Medical Foundation, Busan, Korea
- Department of Pathology, Kosin University Gospel Hospital, Kosin University College of Medicine, Busan, Korea
- Department of Pathology, Hallym University Dongtan Sacred Heart Hospital, Hwaseong, Korea
- Department of Pathology, Catholic University of Daegu School of Medicine, Daegu, Korea
- Department of Pathology, Yeungnam University College of Medicine, Daegu, Korea
- Department of Pathology, Seoul Red Cross Hospital, Seoul, Korea
- Department of Pathology, Inje University Sanggye Paik Hospital, Seoul, Korea
- Department of Pathology, Chung-Ang University College of Medicine, Seoul, Korea
- Department of Pathology, Wonju Severance Christian Hospital, Yonsei University Wonju College of Medicine, Wonju, Korea
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Meira-Strejevitch CS, Pereira-Chioccola VL, Maia MM, Carnietto de Hipólito DD, Wang HTL, Motoie G, de Souza Gomes AH, Kanamura CT, Martines RB, de Mattos CCB, Frederico FB, de Mattos LC, de Mattos CCB, Frederico FB, Siqueira RC, Previato M, Barbosa AP, Murata FHA. WITHDRAWN: Selection of reference genes in five types of human tissues for normalization of gene expression studies in infectious diseases. Gene 2016:S0378-1119(16)30816-2. [PMID: 27743995 DOI: 10.1016/j.gene.2016.10.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 10/09/2016] [Indexed: 11/23/2022]
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.
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Affiliation(s)
| | | | - Marta Marques Maia
- Centro de Parasitologia e Micologia, Instituto Adolfo Lutz, Sao Paulo Brazil
| | | | - Hui-Tzu Lin Wang
- Laboratório de Investigação Molecular em Cardiologia, Instituto Dante Pazzanese de Cardiologia, Sao Paulo Brazil
| | - Gabriela Motoie
- Centro de Parasitologia e Micologia, Instituto Adolfo Lutz, Sao Paulo Brazil
| | | | | | | | - Cinara Cássia Brandão de Mattos
- Laboratório de Imunogenética, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, Brazil
| | - Fábio Batista Frederico
- Ambulatório de Oftalmologia, Fundação Faculdade Regional de Medicina-Hospital de Base, São José do Rio Preto, Brazil
| | - Luiz Carlos de Mattos
- Laboratório de Imunogenética, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, Brazil
| | - Cinara Cássia Brandão de Mattos
- Laboratório de Imunogenética, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, Brazil
| | - Fábio Batista Frederico
- Ambulatório de Oftalmologia, Fundação Faculdade Regional de Medicina-Hospital de Base, São José do Rio Preto, Brazil
| | - Rubens Camargo Siqueira
- Laboratório de Imunogenética, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, Brazil
| | - Mariana Previato
- Laboratório de Imunogenética, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, Brazil
| | - Amanda Pires Barbosa
- Ambulatório de Oftalmologia, Fundação Faculdade Regional de Medicina-Hospital de Base, São José do Rio Preto, Brazil
| | - Fernando Henrique Antunes Murata
- Laboratório de Imunogenética, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, Brazil
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Clinical impact of targeted amplicon sequencing for meningioma as a practical clinical-sequencing system. Mod Pathol 2016; 29:708-16. [PMID: 27102344 DOI: 10.1038/modpathol.2016.81] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/21/2016] [Accepted: 03/24/2016] [Indexed: 11/08/2022]
Abstract
Recent genetic analyses using next-generation sequencers have revealed numerous genetic alterations in various tumors including meningioma, which is the most common primary brain tumor. However, their use as routine laboratory examinations in clinical applications for tumor genotyping is not cost effective. To establish a clinical sequencing system for meningioma and investigate the clinical significance of genotype, we retrospectively performed targeted amplicon sequencing on 103 meningiomas and evaluated the association with clinicopathological features. We designed amplicon-sequencing panels targeting eight genes including NF2 (neurofibromin 2), TRAF7, KLF4, AKT1, and SMO. Libraries prepared with genomic DNA extracted from PAXgene-fixed paraffin-embedded tissues of 103 meningioma specimens were sequenced using the Illumina MiSeq. NF2 loss in some cases was also confirmed by interphase-fluorescent in situ hybridization. We identified NF2 loss and/or at least one mutation in NF2, TRAF7, KLF4, AKT1, and SMO in 81 out of 103 cases (79%) by targeted amplicon sequencing. On the basis of genetic status, we categorized meningiomas into three genotype groups: NF2 type, TRAKLS type harboring mutation in TRAF7, AKT1, KLF4, and/or SMO, and 'not otherwise classified' type. Genotype significantly correlated with tumor volume, tumor location, and magnetic resonance imaging findings such as adjacent bone change and heterogeneous gadolinium enhancement, as well as histopathological subtypes. In addition, multivariate analysis revealed that genotype was independently associated with risk of recurrence. In conclusion, we established a rapid clinical sequencing system that enables final confirmation of meningioma genotype within 7 days turnaround time. Our method will bring multiple benefits to neuropathologists and neurosurgeons for accurate diagnosis and appropriate postoperative management.
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Thway K, Wren D, Lee J, Thompson L, Fisher C, Gonzalez D. Evaluation of the optimal provision of formalin-fixed, paraffin-embedded material for reverse transcription-PCR in soft-tissue tumour diagnosis. J Clin Pathol 2016; 70:20-24. [DOI: 10.1136/jclinpath-2016-203691] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 04/23/2016] [Accepted: 04/30/2016] [Indexed: 12/19/2022]
Abstract
AimsMolecular genetic analysis is now a routine ancillary diagnostic modality to the histopathological diagnosis of soft-tissue neoplasms, many of which harbour characteristic gene fusions detectable by reverse transcription-PCR (RT-PCR). As the final diagnosis often depends on the molecular result, it is important to obtain the optimal yield of patient RNA.MethodsWe assessed the most reliable method of providing formalin-fixed, paraffin-embedded material for optimal RNA yield by comparing three consecutive periods in which different preparations (5×10 μm scrolls, 5×5 μm sections and 1×10 μm sections) were used for RNA extraction for RT-PCR, with its technical success rate.ResultsFor ‘2011’, ‘2012’ and ‘2013’, RT-PCR technical failure rates were 13.4%, 4.4% and 7.9%, respectively. The percentage of failed referral cases was 71.4%, 85.7% and 31.3%, and the proportion of core biopsy to excision specimens was 3:15, 2:5 and 13:3.ConclusionsThis study shows that the effectiveness of RNA extraction and purification is dependent on both specimen type and the tissue sectioning strategy. The failure rate has improved over recent years, particularly for large specimens as large numbers of thick 10 μm scrolls can saturate RNA extraction columns. In contrast, recent technical fails are more frequent in core biopsies, where 1×10 μm sections are insufficient for adequate RNA extraction. While previous technical fails occurred mostly in referred cases, this appears no longer the case due to the better fixation and processing of specimens in external surgical pathology departments because of the widespread recognition of the importance of molecular diagnostics as an important part of the patient pathway.
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A Comparison of Fresh Frozen vs. Formalin-Fixed, Paraffin-Embedded Specimens of Canine Mammary Tumors via Branched-DNA Assay. Int J Mol Sci 2016; 17:ijms17050724. [PMID: 27187374 PMCID: PMC4881546 DOI: 10.3390/ijms17050724] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 05/02/2016] [Accepted: 05/04/2016] [Indexed: 12/24/2022] Open
Abstract
Mammary neoplasms are the tumors most affecting female dogs and women. Formalin-fixed, paraffin-embedded (FFPE) tissues are an invaluable source of archived biological material. Fresh frozen (FF) tissue is considered ideal for gene expression analysis. However, strategies based on FFPE material offer several advantages. Branched-DNA assays permit a reliable and fast workflow when analyzing gene expression. The aim of this study was to assess the comparability of the branched-DNA assay when analyzing certain gene expression patterns between FF and FFPE samples in canine mammary tumors. RNA was isolated from 109 FFPE samples and from 93 FF samples of different canine mammary tissues. Sixteen (16) target genes (Tp53; Myc; HMGA1; Pik3ca; Mcl1; MAPK3; FOXO3; PTEN; GATA4; PFDN5; HMGB1; MAPK1; BRCA2; BRCA1; HMGA2; and Her2) were analyzed via branched-DNA assay (b-DNA). ACTB, GAPDH, and HPRT1 were used as data normalizers. Overall, the relative gene expression of the two different origins of samples showed an agreement of 63%. Still, care should be taken, as FFPE specimens showed lower expression of the analyzed targets when compared to FF samples. The fact that the gene expression in FFPE proved to be lower than in FF specimens is likely to have been caused by the effect of storage time. ACTB had the best performance as a data normalizer.
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Kwak Y, Nam SK, Shin E, Ahn SH, Lee HE, Park DJ, Kim WH, Kim HH, Lee HS. Comparison of the Diagnostic Value Between Real-Time Reverse Transcription-Polymerase Chain Reaction Assay and Histopathologic Examination in Sentinel Lymph Nodes for Patients With Gastric Carcinoma. Am J Clin Pathol 2016; 145:651-9. [PMID: 27247370 DOI: 10.1093/ajcp/aqw055] [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] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES Sentinel lymph node (SLN)-based diagnosis in gastric cancers has shown varied sensitivities and false-negative rates in several studies. Application of the reverse transcription-polymerase chain reaction (RT-PCR) in SLN diagnosis has recently been proposed. METHODS A total of 155 SLNs from 65 patients with cT1-2, N0 gastric cancer were examined. The histopathologic results were compared with results obtained by real-time RT-PCR for detecting molecular RNA (mRNA) of cytokeratin (CK)19, carcinoembryonic antigen (CEA), and CK20. RESULTS The sensitivity and specificity of the multiple marker RT-PCR assay standardized against the results of the postoperative histological examination were 0.778 (95% confidence interval [CI], 0.577-0.914) and 0.781 (95% CI, 0.700-0.850), respectively. In comparison, the sensitivity and specificity of intraoperative diagnosis were 0.819 (95% CI, 0.619-0.937) and 1.000 (95% CI, 0.972-1.000), respectively. The positive predictive value of the multiple-marker RT-PCR assay was 0.355 (95% CI, 0.192-0.546) for predicting non-SLN metastasis, which was lower than that of intraoperative diagnosis (0.813, 95% CI, 0.544-0.960). CONCLUSIONS The real-time RT-PCR assay could detect SLN metastasis in gastric cancer. However, the predictive value of the real-time RT-PCR assay was lower than that of precise histopathologic examination and did not outweigh that of our intraoperative SLN diagnosis.
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Affiliation(s)
- Yoonjin Kwak
- From the Departments of Pathology and Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea; Department of Pathology, Seoul National University College of Medicine, Seoul, South Korea; and Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN. From the Departments of Pathology and Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea; Department of Pathology, Seoul National University College of Medicine, Seoul, South Korea; and Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Soo Kyung Nam
- From the Departments of Pathology and Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea; Department of Pathology, Seoul National University College of Medicine, Seoul, South Korea; and Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Eun Shin
- From the Departments of Pathology and Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea; Department of Pathology, Seoul National University College of Medicine, Seoul, South Korea; and Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Sang-Hoon Ahn
- From the Departments of Pathology and Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea; Department of Pathology, Seoul National University College of Medicine, Seoul, South Korea; and Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Hee Eun Lee
- From the Departments of Pathology and Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea; Department of Pathology, Seoul National University College of Medicine, Seoul, South Korea; and Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Do Joong Park
- From the Departments of Pathology and Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea; Department of Pathology, Seoul National University College of Medicine, Seoul, South Korea; and Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Woo Ho Kim
- From the Departments of Pathology and Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea; Department of Pathology, Seoul National University College of Medicine, Seoul, South Korea; and Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Hyung-Ho Kim
- From the Departments of Pathology and Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea; Department of Pathology, Seoul National University College of Medicine, Seoul, South Korea; and Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN.
| | - Hye Seung Lee
- From the Departments of Pathology and Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea; Department of Pathology, Seoul National University College of Medicine, Seoul, South Korea; and Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN.
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Aggerholm-Pedersen N, Safwat A, Bærentzen S, Nordsmark M, Nielsen OS, Alsner J, Sørensen BS. The importance of reference gene analysis of formalin-fixed, paraffin-embedded samples from sarcoma patients - an often underestimated problem. Transl Oncol 2014; 7:687-93. [PMID: 25500077 PMCID: PMC4311021 DOI: 10.1016/j.tranon.2014.09.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 09/24/2014] [Accepted: 09/26/2014] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE Reverse transcription quantitative real-time polymerase chain reaction is efficient for quantification of gene expression, but the choice of reference genes is of paramount importance as it is essential for correct interpretation of data. This is complicated by the fact that the materials often available are routinely collected formalin-fixed, paraffin-embedded (FFPE) samples in which the mRNA is known to be highly degraded. The purpose of this study was to investigate 22 potential reference genes in sarcoma FFPE samples and to study the variation in expression level within different samples taken from the same tumor and between different histologic types. METHODS Twenty-nine patients treated for sarcoma were enrolled. The samples encompassed 82 (FFPE) specimens. Extraction of total RNA from 7-μm FFPE sections was performed using a fully automated, bead-base RNA isolation procedure, and 22 potential reference genes were analyzed by reverse transcription quantitative real-time polymerase chain reaction. The stability of the genes was analyzed by RealTime Statminer. The intrasamples variation and the interclass correlation coefficients were calculated. The linear regression model was used to calculate the degradation of the mRNA over time. RESULTS The quality of RNA was sufficient for analysis in 84% of the samples. Recommended reference genes differed with histologic types. However, PPIA, SF3A1, and MRPL19 were stably expressed regardless of the histologic type included. The variation in ∆Cq value for samples from the same patients was similar to the variation between patients. It was possible to compensate for the time-dependent degradation of the mRNA when normalization was made using the selected reference genes. CONCLUSION PPIA, SF3A1, and MRPL19 are suitable reference genes for normalization in gene expression studies of FFPE samples from sarcoma regardless of the histology.
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Affiliation(s)
| | - Akmal Safwat
- Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Steen Bærentzen
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | | | | | - Jan Alsner
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Brita S Sørensen
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark
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Amptoulach S, Lazaris AC, Giannopoulou I, Kavantzas N, Patsouris E, Tsavaris N. Expression of caspase-3 predicts prognosis in advanced noncardia gastric cancer. Med Oncol 2014; 32:416. [PMID: 25476481 DOI: 10.1007/s12032-014-0416-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 11/27/2014] [Indexed: 12/19/2022]
Abstract
There is strong evidence that tumor growth is not only a result of uncontrolled cell proliferation but also of decreased apoptosis. Caspase-3 is a member of interleukin-1 beta-converting enzyme which is involved in the induction of apoptosis. Data on the expression of caspase-3 in patients with gastric cancer and its association with patient outcome are somewhat contradictory. We aimed to investigate the potential relation of the expression of caspase-3 protein with response to therapy and overall survival in patients with advanced noncardia gastric cancer. Tumor tissue samples collected from 359 consecutive patients with gastric cancer stage IV were retrospectively analyzed for the expression of caspase-3 in the primary tumor. The DNA apoptotic index assessed by the terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate-biotin nick end labeling method. All patients were followed up until death. Caspase-3 was expressed in 43.5 % of tumors. Caspase-3 expression compared to no expression was related with a higher DNA apoptotic index (p < 0.05). In multivariate analysis, tumor expression of caspase-3 was found to be an independent predictor of poor treatment response and survival (p < 0.05). Expression of caspase-3 in advanced gastric cancer is a predictor of poor response to treatment and survival. Further studies are needed to fully elucidate the prognostic value of caspase-3 expression in these patients.
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Affiliation(s)
- Sousana Amptoulach
- Oncology Unit, Department of Pathophysiology, Laikon General Hospital, Athens University School of Medicine, 11527, Athens, Greece,
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Craft WF, Conway JA, Dark MJ. Comparison of histomorphology and DNA preservation produced by fixatives in the veterinary diagnostic laboratory setting. PeerJ 2014; 2:e377. [PMID: 24860702 PMCID: PMC4017885 DOI: 10.7717/peerj.377] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 04/22/2014] [Indexed: 11/20/2022] Open
Abstract
Histopathology is the most useful tool for diagnosis of a number of diseases, especially cancer. To be effective, histopathology requires that tissues be fixed prior to processing. Formalin is currently the most common histologic fixative, offering many advantages: it is cheap, readily available, and pathologists are routinely trained to examine tissues fixed in formalin. However, formalin fixation substantially degrades tissue DNA, hindering subsequent use in diagnostics and research. We therefore evaluated three alternative fixatives, TissueTek® Xpress® Molecular Fixative, modified methacarn, and PAXgene®, all of which have been proposed as formalin alternatives, to determine their suitability for routine use in a veterinary diagnostic laboratory. This was accomplished by examining the histomorphology of sections produced from fixed tissues as well as the ability to amplify fragments from extracted DNA. Tissues were sampled from two dogs and four cats, fixed for 24–48 h, and processed routinely. While all fixatives produced acceptable histomorphology, formalin had significantly better morphologic characteristics than the other three fixatives. Alternative fixatives generally had better DNA amplification than formalin, although results varied somewhat depending on the tissue examined. While no fixative is yet ready to replace formalin, the alternative fixatives examined may be useful as adjuncts to formalin in diagnostic practices.
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Affiliation(s)
- William F Craft
- Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida , Gainesville, FL , USA
| | - Julia A Conway
- Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida , Gainesville, FL , USA
| | - Michael J Dark
- Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida , Gainesville, FL , USA ; Emerging Pathogens Institute, University of Florida , Gainesville, FL , USA
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