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Yeung CC, Jones DC, Woolston DW, Seaton B, Donato EL, Lin M, Backman C, Oehler V, Robinson KL, Shimp K, Kulikauskas R, Long AN, Sowerby D, Elz AE, Smythe KS, Newell EW. Spatial proteomics and transcriptomics characterization of tissue and multiple cancer types including decalcified marrow. Cancer Biomark 2025; 42:18758592241308757. [PMID: 40109220 DOI: 10.1177/18758592241308757] [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: 03/22/2025]
Abstract
BackgroundRecent technologies enabling the study of spatial biology include multiple high-dimensional spatial imaging methods that have rapidly emerged with different capabilities evaluating tissues at different resolutions for different sample formats. Platforms like Xenium (10x Genomics) and PhenoCycler-Fusion (Akoya Biosciences) enable single-cell resolution analysis of gene and protein expression in archival FFPE tissue slides. However, a key limitation is the absence of systematic methods to ensure tissue quality, marker integrity, and data reproducibility.ObjectiveWe seek to optimize the technical methods for spatial work by addressing preanalytical challenges with various tissue and tumor types, including a decalcification protocol for processing FFPE bone marrow core specimens to preserve nucleic acids for effective spatial proteomics and transcriptomics. This study characterizes a multicancer tissue microarray (TMA) and a molecular- and protein-friendly decalcification protocol that supports downstream spatial biology investigations.MethodsWe developed a multi-cancer tissue microarray (TMA) and processed bone marrow core samples using a molecular- and protein-friendly decalcification protocol. PhenoCycler high-plex immunohistochemistry (IHC) generated spatial proteomics data, analyzed with QuPath and single-cell analysis. Xenium provided spatial transcriptomics data, analyzed via Xenium Explorer and custom pipelines.ResultsResults showed that PhenoCycler and Xenium platforms applied to TMA sections of tonsil and various tumor types achieved good marker concordance. Bone marrow decalcification with our optimized protocol preserved mRNA and protein markers, allowing Xenium analysis to resolve all major cell types while maintaining tissue morphology.ConclusionsWe have shared our preanalytical verification of tissues and demonstrate that both the PhenoCycler-Fusion high-plex spatial proteomics and Xenium spatial transcriptomics platforms work well on various tumor types, including marrow core biopsies decalcified using a molecular- and protein-friendly decalcificationprotocol. We also demonstrate our laboratory's methods for systematic quality assessment of the spatial proteomic and transcriptomic data from these platforms, such that either platform can provide orthogonal confirmation for the other.
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Affiliation(s)
- Cecilia Cs Yeung
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Daniel C Jones
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Immunotherapy Integrated Research Center (I-IRC), Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David W Woolston
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Brandon Seaton
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Elizabeth Lawless Donato
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Minggang Lin
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Coral Backman
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Vivian Oehler
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Kristin L Robinson
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Kristen Shimp
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Rima Kulikauskas
- Department of Dermatology, University of Washington, Seattle, WA, USA
| | - Annalyssa N Long
- Immunotherapy Integrated Research Center (I-IRC), Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David Sowerby
- Immunotherapy Integrated Research Center (I-IRC), Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Anna E Elz
- Immunotherapy Integrated Research Center (I-IRC), Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Kimberly S Smythe
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Evan W Newell
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Immunotherapy Integrated Research Center (I-IRC), Fred Hutchinson Cancer Center, Seattle, WA, USA
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The Effectiveness of Mini Primer STR CODIS in DNA Degradation as the Effect of High-Temperature Exposure. ACTA ACUST UNITED AC 2020; 2020:2417693. [PMID: 33425665 PMCID: PMC7775127 DOI: 10.1155/2020/2417693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 12/10/2020] [Indexed: 11/18/2022]
Abstract
Background More and more today, forensic identification through deoxyribonucleic acid (DNA) examination has achieved greater recognition in supporting Indonesia's law enforcement. Such examination is to determine the origin of a child, paternity cases, genealogical relation, or identifying unknown crime victims. However, along with the development of this DNA material examination, problems arise. DNA undergoes a degradation, commonly known as degraded DNA, which is one of the serious issues frequently encountered by forensic and DNA experts. Some forensic DNA experts take one of the alternatives to overcome this issue by implementing a mini primer set that is through a method to reduce the size of STR assays on DNA core locus examination. Methods In this study, the writers conduct research using the mini primers of CSF1PO, FGA, and D21S11 of the molar teeth exposed to 500°C temperature for 20 and 30 minutes and 750°C for the same amount of time. Result The findings show the DNA contents of molar teeth significantly (p < 0.05) decreased as the effect of high-temperature exposure. PCR result visualization shows CSF1PO is the only locus detected with mini primer exposed to 750°C temperature for 30 minutes (the highest exposure during this research). Conclusions This finding suggests that this locus is potential in examining identification through DNA analysis, especially on a degraded condition as the effect of high-temperature exposure. Besides, this could accelerate the identification process especially on mass disaster events or criminal cases.
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Koldej R, Ritchie D. High multiplex analysis of the immune microenvironment in bone marrow trephine samples using GeoMX™ digital spatial profiling. IMMUNO-ONCOLOGY TECHNOLOGY 2020; 5:1-9. [PMID: 35756143 PMCID: PMC9216341 DOI: 10.1016/j.iotech.2020.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Background To date, studies into the bone marrow (BM) immune microenvironment have been limited due to reliance on the analysis of BM aspirates in which the microenvironmental context is lost. GeoMX™ digital spatial profiling (DSP) is a new technique developed for the analysis of formalin-fixed paraffin-embedded tissue samples which allows high multiplex analysis of protein expression in multiple user-defined regions within a tissue section. We examined the applicability of this technique to the analysis of protein expression in diagnostic BM trephine samples. Materials and methods Archival BM trephines were obtained from patient groups (normal, myelodysplasia and aplastic anaemia). Regions of interest in each section were identified by dual CD3+/CD45+ immunohistochemistry staining to identify immune infiltrates, and DSP was applied. Results Due to variability in cell number within regions of interest and differing cellular composition of the BM trephines, raw protein expression counts were normalised by internal controls and nuclei count to determine the expression level of each protein within each region of interest. In heat map analysis using Spearman's rank correlation, aplastic anaemia samples clustered away from both normal and myelodysplasia samples, demonstrating significant differences in their BM immunology. Conclusions GeoMX™ DSP is an innovative new technique that, for the first time, allows the analysis of archival BM trephines at an unprecedented level of detail. It will allow investigations in large cohorts of patients with haematological malignancies to identify new biomarkers, new mechanisms of disease pathogenesis and new drug targets.
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Affiliation(s)
- R.M. Koldej
- ACRF Translational Haematology Research Laboratory, Royal Melbourne Hospital, Melbourne, Australia
- Department of Medicine, University of Melbourne, Melbourne, Australia
| | - D.S. Ritchie
- ACRF Translational Haematology Research Laboratory, Royal Melbourne Hospital, Melbourne, Australia
- Department of Medicine, University of Melbourne, Melbourne, Australia
- Clinical Haematology, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Australia
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Palacios J, de la Hoya M, Bellosillo B, de Juan I, Matías-Guiu X, Lázaro C, Palanca S, Osorio A, Rojo F, Rosa-Rosa JM, Cigudosa JC. Mutational Screening of BRCA1/2 Genes as a Predictive Factor for Therapeutic Response in Epithelial Ovarian Cancer: A Consensus Guide from the Spanish Society of Pathology (SEAP-IAP) and the Spanish Society of Human Genetics (AEGH). Virchows Arch 2020; 476:195-207. [PMID: 31797087 PMCID: PMC7028830 DOI: 10.1007/s00428-019-02709-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/11/2019] [Accepted: 10/25/2019] [Indexed: 12/21/2022]
Abstract
Germline/somatic BRCA-mutated ovarian carcinomas (OC) are associated to have better response with platinum-based chemotherapy and long-term prognosis than non-BRCA-associated OCs. In addition, these mutations are predictive factors to response to Poly(ADP-ribose) polymerase (PARP) inhibitors. Different positioning papers have addressed the clinical recommendations for BRCA testing in OC. This consensus guide represents a collection of technical recommendations to address the detection of BRCA1/2 mutations in the molecular diagnostic testing strategy for OC. Under the coordination of Spanish Society of Pathology (SEAP-IAP) and the Spanish Society of Human Genetics (AEGH), these recommendations have been developed by pathologists and geneticists taking into account previously published recommendations and their experience in the molecular characterization of these genes. Since the implementation of BRCA testing as a predictive factor can initiate the workflow by testing germline mutations in the blood or by testing both germline and somatic mutations in tumor tissue, distinctive features of both strategies are discussed. Additionally, the recommendations included in this paper provide some references, quality parameters, and genomic tools aimed to standardize and facilitate the clinical genomic diagnosis of OC.
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Affiliation(s)
- J Palacios
- Servicio de Anatomía Patológica, Hospital Universitario Ramón y Cajal, 28034, Madrid, Spain.
- Instituto Ramón y Cajal de Investigación Sanitaria, 28034, Madrid, Spain.
- Universidad de Alcalá, 28801, Alcalá de Henares, Spain.
- CIBER-ONC, Instituto de Salud Carlos III, 28029, Madrid, Spain.
| | - M de la Hoya
- CIBER-ONC, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Molecular Oncology Laboratory, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - B Bellosillo
- CIBER-ONC, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Laboratorio de Diagnóstico Molecular, Servicio de Patología, Hospital del Mar, 08003, Barcelona, Spain
| | - I de Juan
- Unidad de Biología Molecular, Servicio de Análisis Clínicos, Hospital Universitario y Politécnico La Fe, 46026, Valencia, Spain
| | - X Matías-Guiu
- CIBER-ONC, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Servicio de Anatomía Patológica, Hospital Universitario de Bellvitge, 08908, L'Hospitalet, Spain
| | - C Lázaro
- CIBER-ONC, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Unidad de Diagnóstico Molecular, Institut Català d'Oncologia, (ICO-IDIBELL-ONCOBELL), 08908, L'Hospitalet, Spain
| | - S Palanca
- Unidad de Biología Molecular, Servicio de Análisis Clínicos, Hospital Universitario y Politécnico La Fe, 46026, Valencia, Spain
| | - A Osorio
- Human Cancer Genetics Programme, Spanish National Cancer Centre (CNIO), 28029, Madrid, Spain
- CIBER-ER, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - F Rojo
- CIBER-ONC, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Departamento de Patología, Fundación Jímenez-Díaz, 28040, Madrid, Spain
| | - J M Rosa-Rosa
- Instituto Ramón y Cajal de Investigación Sanitaria, 28034, Madrid, Spain
- CIBER-ONC, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - J C Cigudosa
- NIMGenetics, Parque Científico de Madrid, Campus Cantoblanco, 28049, Madrid, Spain
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Zheng G, Lin MT, Lokhandwala PM, Beierl K, Netto GJ, Gocke CD, Eshleman JR, McCarthy E, Illei PB. Clinical mutational profiling of bone metastases of lung and colon carcinoma and malignant melanoma using next-generation sequencing. Cancer Cytopathol 2016; 124:744-753. [PMID: 27286239 DOI: 10.1002/cncy.21743] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 04/29/2016] [Accepted: 04/29/2016] [Indexed: 11/07/2022]
Abstract
BACKGROUND Bone is a common metastatic site for solid tumors and is often the only source for molecular testing. Current routine decalcification protocols for the processing of bone specimens damage nucleic acids, leading to a high failure rate. METHODS In this retrospective quality-assessment analysis, preanalytic factors that contributed to the failure of mutational profiling in metastatic bone specimens were evaluated using a next-generation sequencing assay. RESULTS Mutational profiling was conducted in 33 formalin-fixed, paraffin-embedded bone lesions that were submitted to a clinical laboratory. Adequate depth of coverage was obtained in 21 specimens, of which, 16 had mutations detected. "No results" were reported in 12 specimens because the NGS assay failed. There was a significantly higher failure rate in bone specimens compared with nonbone specimens (36% vs 2.3%, respectively). Although nonbone specimens had a higher failure rate in biopsy/fine-needle aspiration (FNA) specimens, in-house bone biopsy/FNA specimens with or without short-duration surface decalcification had a lower failure rate than resected bone specimens (11% vs 60%, respectively). The high failure rate in resected metastatic bone specimens was associated with regular decalcification but not with low DNA input. CONCLUSIONS Next-generation sequencing assays demonstrated clinical utility in metastatic bone specimens. FNA (smear and cell block) and core-biopsy specimens provided adequate resources of nucleic acids for molecular profiling of metastatic bone lesions. The current findings suggest the need for developing specific tissue procurement and processing protocols for bone metastases and greater use of small biopsy and FNA specimens. Cancer Cytopathol 2016;124:744-53. © 2016 American Cancer Society.
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Affiliation(s)
- Gang Zheng
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ming-Tseh Lin
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Parvez M Lokhandwala
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Katie Beierl
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - George J Netto
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Christopher D Gocke
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - James R Eshleman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Edward McCarthy
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Peter B Illei
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland. .,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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Deparaffinization with mineral oil: a simple procedure for extraction of high-quality DNA from archival formalin-fixed paraffin-embedded samples. Appl Immunohistochem Mol Morphol 2015; 22:623-6. [PMID: 24897067 DOI: 10.1097/pai.0b013e3182a77bfe] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Extracting DNA from formalin-fixed paraffin-embedded (FFPE) archival samples remains difficult. Successful polymerase chain reactions (PCR) with DNA extracted from FFPE samples is still very low. We extracted DNA from 12 recent and old archival FFPE bone marrow trephine biopsies by use of a simple protocol on the basis of deparaffinization with molecular biology-grade mineral oil followed by DNA extraction with the Qiagen FFPE kit. Comparison of this deparaffinization method with standard protocols, for example, xylene or Hemo-D with subsequent rehydration using graded ethanols, was investigated. The quality and quantity of extracted DNA were tested by a combination of ultraviolet spectroscopy, analysis on a Caliper LabChip GX, and real-time PCR combined with high-resolution melt analysis. Highest quality PCR-amplifiable DNA was obtained by deparaffinization with mineral oil, whereas more variable results were obtained for the other 2 deparaffinization procedures. This result was confirmed by real-time PCR and high-resolution melt analysis. Besides improvements in the quality of extracted DNA, use of mineral oil for deparaffinization has the added benefit of decreased time (20 vs. 75 min) and a significant reduction of hands-on labor (1 step vs. multiple hands-on centrifugation and decanting steps).
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Torlakovic EE, Brynes RK, Hyjek E, Lee SH, Kreipe H, Kremer M, McKenna R, Sadahira Y, Tzankov A, Reis M, Porwit A. ICSH guidelines for the standardization of bone marrow immunohistochemistry. Int J Lab Hematol 2015; 37:431-49. [DOI: 10.1111/ijlh.12365] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 03/02/2015] [Indexed: 12/25/2022]
Affiliation(s)
- E. E. Torlakovic
- Department of Laboratory Hematology; University Health Network; University of Toronto; Toronto ON Canada
| | - R. K. Brynes
- Department of Pathology; Keck School of Medicine; University of Southern California; Los Angeles CA USA
| | - E. Hyjek
- Department of Pathology; University of Chicago; Chicago IL USA
| | - S.-H. Lee
- Department of Haematology; St George Hospital; SEALS Central; Sydney NSW Australia
| | - H. Kreipe
- Department of Pathology; Hannover Medical School; Hannover Germany
| | - M. Kremer
- Munich Municipal Hospital; Institute of Pathology; Munich Germany
| | - R. McKenna
- Special Hematology; Department of Laboratory Medicine and Pathology; University of Minnesota; Minneapolis MN USA
| | - Y. Sadahira
- Department of Pathology; Kawasaki Medical School; Kurashiki Japan
| | - A. Tzankov
- Institute of Pathology; University Hospital Basel; Basel Switzerland
| | - M. Reis
- Department of Clinical Pathology; Sunnybrook Health Sciences Centre; Toronto ON Canada
| | - A. Porwit
- Department of Laboratory Hematology; University Health Network; University of Toronto; Toronto ON Canada
- Department of Pathology; Karolinska Institute; Stockholm Sweden
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Cree IA, Deans Z, Ligtenberg MJL, Normanno N, Edsjö A, Rouleau E, Solé F, Thunnissen E, Timens W, Schuuring E, Dequeker E, Murray S, Dietel M, Groenen P, Van Krieken JH. Guidance for laboratories performing molecular pathology for cancer patients. J Clin Pathol 2014; 67:923-31. [PMID: 25012948 PMCID: PMC4215286 DOI: 10.1136/jclinpath-2014-202404] [Citation(s) in RCA: 160] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Molecular testing is becoming an important part of the diagnosis of any patient with cancer. The challenge to laboratories is to meet this need, using reliable methods and processes to ensure that patients receive a timely and accurate report on which their treatment will be based. The aim of this paper is to provide minimum requirements for the management of molecular pathology laboratories. This general guidance should be augmented by the specific guidance available for different tumour types and tests. Preanalytical considerations are important, and careful consideration of the way in which specimens are obtained and reach the laboratory is necessary. Sample receipt and handling follow standard operating procedures, but some alterations may be necessary if molecular testing is to be performed, for instance to control tissue fixation. DNA and RNA extraction can be standardised and should be checked for quality and quantity of output on a regular basis. The choice of analytical method(s) depends on clinical requirements, desired turnaround time, and expertise available. Internal quality control, regular internal audit of the whole testing process, laboratory accreditation, and continual participation in external quality assessment schemes are prerequisites for delivery of a reliable service. A molecular pathology report should accurately convey the information the clinician needs to treat the patient with sufficient information to allow for correct interpretation of the result. Molecular pathology is developing rapidly, and further detailed evidence-based recommendations are required for many of the topics covered here.
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Affiliation(s)
- Ian A Cree
- Warwick Medical School, University Hospital Coventry and Warwickshire, Coventry, UK
- Institute of Ophthalmology, University College London, London, UK
| | - Zandra Deans
- UK NEQAS for Molecular Genetics, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Marjolijn J L Ligtenberg
- Department of Pathology 824, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, INT-Fondazione Pascale, Naples, Italy
| | - Anders Edsjö
- Clinical Molecular Pathology Unit, Clinical Pathology and Genetics, Sahlgrenska University Hospital and Sahlgrenska Cancer Center, the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Etienne Rouleau
- Service de Génétique, Unités de Génétique constitutionnelle et somatique, Paris, France
| | - Francesc Solé
- Institut de Recerca contra la Leucèmia Josep Carreras (IJC), Barcelona, Spain
| | - Erik Thunnissen
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Wim Timens
- Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, The Netherlands
| | - Ed Schuuring
- Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, The Netherlands
| | - Elisabeth Dequeker
- Department of Public Health and Primary Care, Biomedical Quality Assurance Research Unit, KU Leuven—University of Leuven, Leuven, Belgium
| | | | - Manfred Dietel
- Institute of Pathology, Charité—Universitätsmedizin Berlin, Berlin, Germany
| | - Patricia Groenen
- Department of Pathology 824, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - J Han Van Krieken
- Department of Pathology 824, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
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Singh VM, Salunga RC, Huang VJ, Tran Y, Erlander M, Plumlee P, Peterson MR. Analysis of the effect of various decalcification agents on the quantity and quality of nucleic acid (DNA and RNA) recovered from bone biopsies. Ann Diagn Pathol 2013; 17:322-6. [PMID: 23660273 DOI: 10.1016/j.anndiagpath.2013.02.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 02/16/2013] [Indexed: 11/19/2022]
Abstract
Molecular studies are part of standard care for cancer patients. Bone, a common and sometimes sole site of metastasis, requires decalcification for morphological examination. Many commonly used decalcification agents contain strong acids that degrade nucleic acids. The paradigm shift in oncology, with biomarker targeted therapy and gene expression profiling analysis, requires sufficient nucleic acid recovery from bone biopsy specimens. We systematically studied the effects of a spectrum of decalcification agents on the quantity and quality of RNA and DNA recovered from bone biopsies. Multiple bone biopsies of similar size and cellularity were fixed in 10% neutral-buffered formalin, randomized to various decalcification agents for 2 hours then processed, and embedded. Tissue lysates were obtained from unstained sections and nucleic acid isolated. DNA and RNA were quantified. Assessment of DNA and RNA integrity was accomplished by comparison of the average cycle threshold by polymerase chain reaction of selected housekeeping genes for each agent. Results were then analyzed by 2-sample t test. There was a significant decrease in both DNA and RNA yield and integrity with strong acids (hydrochloric, nitric) vs 14% EDTA and formic acid. DNA yield was (mean nanograms) 6.15 vs 68.68 (P<.001) and RNA was (mean nanograms) 121.53 vs 288.89 (P=.003), respectively. DNA integrity (mean cycle threshold) was 35.79 vs 30.16 (P<.001), and RNA was 33.03 vs 26.5 (P<.001), respectively. Decalcification of bone biopsies with EDTA or formic acid agents was associated with a significant improvement in recovered nucleic acid quantity and quality.
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Neat MJ, Moonim MT, Dunn RG, Geoghegan H, Foot NJ. Fluorescence in situ hybridisation analysis of bone marrow trephine biopsy specimens; an additional tool in the diagnostic armoury. J Clin Pathol 2012; 66:54-7. [DOI: 10.1136/jclinpath-2012-201131] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Fluorescence in situ hybridisation (FISH) analysis is now widely employed in the diagnosis and risk stratification of a wide range of malignant diseases. While this technique is used successfully with formalin-fixed paraffin-embedded (FFPE) sections from numerous tissue types, FISH analysis of FFPE tissue sections from trephine biopsy specimens has been less widely reported, possibly due to technical limitations relating to the decalcification protocols employed. During the last 4 years FISH analysis has been carried out successfully in 42 out of 55 (76%) consecutive trephine biopsy specimens received as part of the standard diagnostic service at our institution. Samples decalcified using EDTA-based protocols were analysed successfully in 31/31 cases (100%), whereas only 11/24 samples (46%) decalcified using formic acid-based protocols were successful. In our experience, FISH analysis of trephine biopsy specimens is a highly reproducible technique and a very useful adjunctive tool in the diagnostic armoury; however, its use in a standard diagnostic setting relies on the use of EDTA-based decalcification protocols.
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11
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Use of formalin-fixed paraffin-embedded tumor tissue as a DNA source in molecular epidemiological studies of pediatric CNS tumors. ACTA ACUST UNITED AC 2012; 21:105-13. [PMID: 22555093 DOI: 10.1097/pdm.0b013e3182340a78] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Formalin-fixed paraffin-embedded tissue (FFPET) samples are a potential source of DNA for molecular epidemiological studies. However, the use of FFPET samples can be restricted by the yield and quality of DNA isolated. The aim of this study was to examine whether FFPET biopsies from pediatric central nervous system tumors were a feasible alternative to archival frozen tissue when characterizing common gene polymorphisms. DNA was isolated from 50 frozen pediatric central nervous system tumor biopsies and matched FFPET samples. Real-time polymerase chain reaction (PCR) was used to quantify DNA and characterize GSTT1, GSTM1, GSTP1, and MTHFR gene polymorphisms. The use of whole-genome amplification (WGA) to increase DNA yields was also investigated. The results showed that DNA isolated from FFPET samples was more fragmented and provided smaller yields than DNA isolated from frozen samples. Attempts to increase the DNA yield from FFPET using WGA were unsuccessful. DNA from FFPET samples was successfully genotyped for the GSTP1 Ile105Val and MTHFR 677 C>T polymorphisms in 98% of samples and was 100% concordant with the results from frozen tissue. However, DNA from FFPET performed poorly in real-time PCR assays for GSTM1 and GSTT1 deletion polymorphisms. Our investigations show that DNA extracted from FFPET is substantially fragmented and not readily amplified using WGA. In addition, careful validation of PCR assays should be carried out due to the variable amplification of fragmented FFPET DNA.
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Zhang M, Tavora F, Oliveira JB, Li L, Franco M, Fowler D, Zhao Z, Burke A. PKP2 mutations in sudden death from arrhythmogenic right ventricular cardiomyopathy (ARVC) and sudden unexpected death with negative autopsy (SUDNA). Circ J 2011; 76:189-94. [PMID: 22019812 DOI: 10.1253/circj.cj-11-0747] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Plakophilin2 (PKP2) is a desmosome-related protein with numerous armadillo repeats and has been linked to arrhythmogenic right ventricular cardiomyopathy (ARVC). Fatal arrhythmias resulting in sudden death also occur in the absence of morphologic cardiac abnormalities at autopsy, and have been linked to ion channel mutations in a subset of cases, but so far not to PKP2. METHODS AND RESULTS We sequenced all 14 exons of PKP2 in DNA extracted from postmortem heart tissues of 25 patients dying from ARVC and 25 from sudden unexpected death with negative autopsy (SUDNA). The primers were designed using the Primer Express 3.0 software. Direct sequencing for both sense and antisense strands was performed with a BigDye Terminator DNA sequencing kit on a 3130XL Genetic Analyzer. Mutation damage prediction was made using Mutation Taster, Polyphen and SIFT software. In 6 of the 25 ARVC samples, 6 PKP2 mutations were identified, 4 of which were likely significant, and 3 of which were novel (p.N641del, p.L64PfsX22, p.G269R). In 6 of the 25 cases of SUDNA samples, 6 PKP2 mutations were identified, 3 of which were likely significant, and 4 of which were not previously described (p.P665S, p.Y217TfsX45, p.E540, p.S615T). CONCLUSIONS PKP2 mutations are not specific for ARVC and may result in SUDNA. The link between ARVC and desmosomal mutations may not be causal but related to an association between defective desmosomal proteins and arrhythmias.
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Affiliation(s)
- Mingchang Zhang
- Department of Forensic Medicine, Shanghai Medical College, Fudan University, Shanghai, China
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Baak-Pablo R, Dezentje V, Guchelaar HJ, van der Straaten T. Genotyping of DNA samples isolated from formalin-fixed paraffin-embedded tissues using preamplification. J Mol Diagn 2010; 12:746-9. [PMID: 20847277 DOI: 10.2353/jmoldx.2010.100047] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
DNA isolated from formalin-fixed paraffin-embedded (FFPE) tissue is often fragmented and cross-linked and is therefore difficult to genotype. To enable this source of DNA for genotyping analysis using Taqman probes, we tested whether enrichment of the target genes would increase the amount of available DNA. For enrichment of the target genes, we used preamplification by means of diluted Taqman assays. To establish the appropriateness of preamplification, we used DNA extracted from paraffin-embedded tissue and compared the genotyping results of a series of single nucleotide polymorphisms assessed in DNA samples with and without preamplification. In a subset of patients, DNA was isolated from both blood and FFPE tissue to test the reliability of genotyping results derived after preamplification. We found an increase in call rate after preamplification and a convincing concordance in genotype. Based on our findings, we can safely conclude that preamplification of DNA isolated from paraffin-embedded tissue is a valuable and reliable method to optimize genotyping results.
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Affiliation(s)
- Renee Baak-Pablo
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, P.O. Box 9600, 2300 RA Leiden, The Netherlands
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Okello JBA, Zurek J, Devault AM, Kuch M, Okwi AL, Sewankambo NK, Bimenya GS, Poinar D, Poinar HN. Comparison of methods in the recovery of nucleic acids from archival formalin-fixed paraffin-embedded autopsy tissues. Anal Biochem 2010; 400:110-7. [PMID: 20079706 DOI: 10.1016/j.ab.2010.01.014] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 01/11/2010] [Accepted: 01/11/2010] [Indexed: 11/24/2022]
Abstract
Archival formalin-fixed paraffin-embedded (FFPE) human tissue collections are typically in poor states of storage across the developing world. With advances in biomolecular techniques, these extraordinary and virtually untapped resources have become an essential part of retrospective epidemiological studies. To successfully use such tissues in genomic studies, scientists require high nucleic acid yields and purity. In spite of the increasing number of FFPE tissue kits available, few studies have analyzed their applicability in recovering high-quality nucleic acids from archived human autopsy samples. Here we provide a study involving 10 major extraction methods used to isolate total nucleic acid from FFPE tissues ranging in age from 3 to 13years. Although all 10 methods recovered quantifiable amounts of DNA, only 6 recovered quantifiable RNA, varying considerably and generally yielding lower DNA concentrations. Overall, we show quantitatively that TrimGen's WaxFree method and our in-house phenol-chloroform extraction method recovered the highest yields of amplifiable DNA, with considerable polymerase chain reaction (PCR) inhibition, whereas Ambion's RecoverAll method recovered the most amplifiable RNA.
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Affiliation(s)
- John B A Okello
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Ontario L8S4L9, Canada.
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15
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16
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Hanlon K, Harries LW, Ellard S, Rudin CE. Evaluation of 13q14 status in multiple myeloma by digital single nucleotide polymorphism technology. J Mol Diagn 2009; 11:450-7. [PMID: 19644022 DOI: 10.2353/jmoldx.2009.090027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chromosome 13q deletions are common in multiple myeloma and other cancers, demonstrating the importance of this region in tumorigenesis. We used a novel single nucleotide polymorphism (SNP)-based technique, digital SNP (dSNP), to identify loss of heterozygosity (LOH) at chromosome 13q in paraffin-embedded bone marrow biopsies from 22 patients with multiple myeloma. We analyzed heterozygous SNPs at 13q for the presence of allelic imbalances and examined the results by sequential probability ratio analysis. Where possible, dSNP results were confirmed by fluorescence in situ hybridization. Using dSNP, we identified 13q LOH in 16/18 (89%) (95% Confidence Interval; 65%, 99%) patients without the need for neoplastic cell enrichment. In 8/16 (50%) cases, either partial or interstitial patterns of LOH were observed. Both fluorescence in situ hybridization and dSNP data proved concordant in just 3/9 cases. Five of the six discrepancies showed LOH by dSNP occurring beyond the boundaries of the fluorescence in situ hybridization probes. Our findings show that dSNP represents a useful technique for the analysis of LOH in archival tissue with minimal infiltration of neoplastic cells. The high-resolution screening afforded by the dSNP technology allowed for the identification of complex chromosomal rearrangements, resulting in either partial or interstitial LOH. Digital SNP represents an attractive approach for the investigation of tumors not suitable for genomic-array analysis.
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Affiliation(s)
- Katy Hanlon
- Institute of Biomedical and Clinical Sciences, Peninsula Medical School, Barrack Road, Exeter, EX2 5DW
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Talaulikar D, Shadbolt B, McNiven M, Dahlstrom JE. DNA amplification from formalin-fixed decalcified paraffin-embedded bone marrow trephine specimens: does the duration of storage matter? Pathology 2009; 40:702-6. [PMID: 18985524 DOI: 10.1080/00313020802436410] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
INTRODUCTION Examination of bone marrow (BM) trephines has been traditionally limited to histological analysis. With renewed interest in their use in molecular diagnostics, studies assessing the impact of duration of storage on DNA amplification from archived BM trephines are required. METHODS DNA extraction was performed on 169 formalin-fixed decalcified paraffin-embedded (FFDPE) trephine blocks with a mean duration of storage of 59.4 months (range 4-200 months). An amplification control master mix from the In Vivo Scribe Immunoglobulin Heavy Chain Clonality kit was used to determine DNA amplification at different amplicon sizes [96-600 base pairs (bp)]. RESULTS Amplification at 96 bp was noted in 145 of 169 specimens (85.8%). Progressive reduction in amplification was noted at higher base pairs with 99 of 169 (58.6%) amplifying at 200 bp, 56 cases (33.1%) at 300 bp, 35 (20.7%) at 400 bp and 19 (11.2%) at 600 bp. The impact of duration of storage on DNA amplification was not statistically significant. CONCLUSIONS DNA was obtained from archival BM trephine specimens in approximately 86% of cases, indicating good potential for utilisation in polymerase chain reaction (PCR) techniques. The duration of storage of FFDPE tissue had no impact on the ability to amplify specimens.
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Affiliation(s)
- Dipti Talaulikar
- Department of Haematology, The Canberra Hospital, Yamba Drive, Garran, Canberra, ACT 2606, Australia.
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Hunt JL. Molecular pathology in anatomic pathology practice: a review of basic principles. Arch Pathol Lab Med 2008; 132:248-60. [PMID: 18251585 DOI: 10.5858/2008-132-248-mpiapp] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2007] [Indexed: 11/06/2022]
Abstract
Molecular testing in pathology emerged shortly after polymerase chain reaction became a standard molecular biology assay. Testing efforts began in the clinical laboratories primarily with assays for genetically inherited diseases and assays for clonality in hematologic malignancies. Today, the field has evolved into "molecular diagnostics," which encompasses testing in almost every area of anatomic pathology. Molecular testing is now even making its way definitively into both surgical pathology and cytopathology, although molecular anatomic pathology is still young with few standard tissue-based molecular assays. As more clinically valuable information is gained from molecular pathology testing of tissues, unique challenges are also becoming apparent at the intersection between tissue diagnosis and DNA diagnosis. This review focuses on basic molecular pathology concepts, with particular emphasis on the challenge of tissue-based testing in anatomic pathology.
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Affiliation(s)
- Jennifer L Hunt
- Cleveland Clinic, Department of Pathology, 9500 Euclid Ave L25, Cleveland, OH 44195, USA.
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Shimizu Y, Kondo S, Shirai A, Furukawa M, Yoshizaki T. A single nucleotide polymorphism in the matrix metalloproteinase-1 and interleukin-8 gene promoter predicts poor prognosis in tongue cancer. Auris Nasus Larynx 2008; 35:381-9. [PMID: 18276095 DOI: 10.1016/j.anl.2007.12.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2007] [Revised: 12/06/2007] [Accepted: 12/10/2007] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Matrix metalloproteinase-1 (MMP-1) and interleukin-8 (IL-8) play an important role in cancer development and metastasis. There is a single nucleotide polymorphism (SNP) located in the promoter region of MMP-1 and IL-8 that regulates gene expression. MMP-1 -1607 2G/2G and IL-8 -251 A/A genotypes enhance transcriptional activity and may be associated with increased risk in malignant tumors. We therefore evaluated the impact of these SNPs in tongue squamous cell carcinoma (SCC). METHODS In this study, we genotyped 69 tongue SCC patients. The expression of MMP-1 and IL-8 in tongue SCC patients was analyzed by immunohistochemistry. RESULTS We found a significant difference in IL-8 A/A genotypes with nodal recurrence (P=0.0068). An analysis of disease-free survival rates showed that the presence of both MMP-1 2G/2G and IL-8 A/A genotypes was associated with a particularly poor prognosis (P=0.0032) and was an independent prognostic factor (P=0.001). The expression of MMP-1 was significantly correlated with the frequency of MMP-1 2G/2G genotypes (P=0.049). CONCLUSION These results suggest that SNP in the promoter region of MMP-1 and IL-8 plays an important role in tumor progression and recurrence through its expression in tongue SCC.
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Affiliation(s)
- Yoshinori Shimizu
- Department of Otolaryngology, School of Medicine, Kanazawa University, Takaramachi 13-1, Ishikawa, Japan.
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Modern techniques for the diagnostic evaluation of the trephine bone marrow biopsy: Methodological aspects and applications. ACTA ACUST UNITED AC 2008; 42:203-52. [DOI: 10.1016/j.proghi.2007.10.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2007] [Accepted: 10/08/2007] [Indexed: 12/19/2022]
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Gilbert MTP, Haselkorn T, Bunce M, Sanchez JJ, Lucas SB, Jewell LD, Van Marck E, Worobey M. The isolation of nucleic acids from fixed, paraffin-embedded tissues-which methods are useful when? PLoS One 2007; 2:e537. [PMID: 17579711 PMCID: PMC1888728 DOI: 10.1371/journal.pone.0000537] [Citation(s) in RCA: 274] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Accepted: 05/21/2007] [Indexed: 01/19/2023] Open
Abstract
Museums and pathology collections around the world represent an archive of genetic material to study populations and diseases. For preservation purposes, a large portion of these collections has been fixed in formalin-containing solutions, a treatment that results in cross-linking of biomolecules. Cross-linking not only complicates isolation of nucleic acid but also introduces polymerase "blocks" during PCR. A wide variety of methods exists for the recovery of DNA and RNA from archival tissues, and although a number of previous studies have qualitatively compared the relative merits of the different techniques, very few have undertaken wide scale quantitative comparisons. To help address this issue, we have undertaken a study that investigates the quality of nucleic acids recovered from a test panel of fixed specimens that have been manipulated following a number of the published protocols. These include methods of pre-treating the samples prior to extraction, extraction and nucleic acid purification methods themselves, and a post-extraction enzymatic repair technique. We find that although many of the published methods have distinct positive effects on some characteristics of the nucleic acids, the benefits often come at a cost. In addition, a number of the previously published techniques appear to have no effect at all. Our findings recommend that the extraction methodology adopted should be chosen carefully. Here we provide a quick reference table that can be used to determine appropriate protocols for particular aims.
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Affiliation(s)
- M Thomas P Gilbert
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America.
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Witte J, Lehmann S, Wulfert M, Yang Q, Röher HD. Mitochondrial DNA mutations in differentiated thyroid cancer with respect to the age factor. World J Surg 2007; 31:51-9. [PMID: 17171498 DOI: 10.1007/s00268-005-0447-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
INTRODUCTION Increased numbers of mitochondria in differentiated thyroid cancer and, most strikingly, mutations in human mitochondrial DNA (mtDNA) in older people have led to speculation that mtDNA mutations might contribute to aging or accumulate in postmitotic tissues with age. Mutation analyses of mtDNA in papillary (PTCs) and follicular (FTCs) thyroid carcinomas have been limited to date. The significance and frequency of mtDNA mutations in PTC and FTC are therefore controversial, as is age dependence. METHODS We analyzed eight sample pairs of PTC and six of FTC tissue with the corresponding normal thyroid tissue. DNA was extracted from frozen and formaldehyde-fixed tissue using the QIAmp Tissue Kit. Sequence differences in the mtDNA between tumor and normal tissue were detected using appropriate polymerase chain reaction (PCR) products for heteroduplex analysis in a denaturing high performance liquid chromatography (HPLC) Wave System (Transgenomic). Mutations were confirmed and identified by sequencing the PCR products of conspicuous chromatograms. The samples were obtained from 346 patients with PTC and 105 patients with FTC. We analyzed the whole mitochondrial genome from seven PTC and three FTC tumors along with the corresponding normal thyroid tissue. 3/7 PTC samples showed two heteroplasmic mutations and one polymorphism; all 3 FTCs showed homoplasmic and/or heteroplasmic mutations. RESULTS All but one of these tumors are well documented in the mitochondrial database MITOMAP. MtDNA mutations were found in all three patients aged 45 years and older. There was no correlation, however, in this small group to clinical prognostic factors for recurrence and especially for survival in differentiated thyroid carcinomas, such as histology, tumor size, lymph node metastases, distant metastases, and gender, most likely because of the short follow-up. While univariate analysis of the findings in the whole cohort of 346 patients with PTC suggested that age is a significant prognostic factor for survival (P = 0.0237) but not for recurrence (P = 0.65), this was not the case in the 105 patients with FTC. CONCLUSIONS Although we found accumulation of mutations in two older patients with PTC and one patient with FTC (all three patients older than 45 years had mtDNA mutations), the low frequency of these mutations in the small group of 10 analyzed patients did not correlate with statistically validated clinical prognosticators for recurrence or survival, especially not with age. The low power of our data are therefore not able to support or refute the hypothesis that these mtDNA mutations are related to age-dependent tumor progression in the thyroid or that they "may be involved in thyroid tumorigenesis."
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Affiliation(s)
- Jürgen Witte
- Department of General and Trauma surgery, Heinrich Heine University, Moorenstrasse 5, 40225 Düsseldorf, Germany.
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Lau A, Chen S, Sorrell T, Carter D, Malik R, Martin P, Halliday C. Development and clinical application of a panfungal PCR assay to detect and identify fungal DNA in tissue specimens. J Clin Microbiol 2006; 45:380-5. [PMID: 17122000 PMCID: PMC1829013 DOI: 10.1128/jcm.01862-06] [Citation(s) in RCA: 254] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Given the rise in the incidence of invasive fungal infections (IFIs) and the expanding spectrum of fungal pathogens, early and accurate identification of the causative pathogen is essential. We developed a panfungal PCR assay that targets the internal transcribed spacer 1 (ITS1) region of the ribosomal DNA gene cluster to detect fungal DNA in fresh and formalin-fixed, paraffin-embedded (PE) tissue specimens from patients with culture-proven (n=38) or solely histologically proven (n=24) IFIs. PCR products were sequenced and compared with sequences in the GenBank database to identify the causal pathogen. The molecular identification was correlated with results from histological examination and culture. The assay successfully detected and identified the fungal pathogen in 93.6% and 64.3% of culture-proven and solely histologically proven cases of IFI, respectively. A diverse range of fungal genera were identified, including species of Candida, Cryptococcus, Trichosporon, Aspergillus, Fusarium, Scedosporium, Exophiala, Exserohilum, Apophysomyces, Actinomucor, and Rhizopus. For five specimens, molecular analysis identified a pathogen closely related to that identified by culture. All PCR-negative specimens (n=10) were PE tissues in which fungal hyphae were visualized. The results support the use of the panfungal PCR assay in combination with conventional laboratory tests for accurate identification of fungi in tissue specimens.
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Affiliation(s)
- Anna Lau
- Faculty of Medicine, Centre for Infectious Diseases and Microbiology, Westmead Millennium Institute, University of Sidney, Australia
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Shao YY, Wang L, Hicks DG, Ballock RT. Analysis of gene expression in mineralized skeletal tissues by laser capture microdissection and RT-PCR. J Transl Med 2006; 86:1089-95. [PMID: 16940962 DOI: 10.1038/labinvest.3700459] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The analysis of gene expression by growth plate chondrocytes in vivo has been hampered by the inherent difficulty in performing in situ hybridization on mineralized tissues. The combination of laser capture microdissection and reverse transcription-polymerase chain reaction (RT-PCR) allows analysis of gene expression by cells selectively removed from histologic sections by laser ablation. In order to apply this method to mineralized tissues, a decalcification process is required. The object of this study was to determine the optimal method for tissue decalcification prior to laser capture microdissection RT-PCR that will preserve integrity of the mRNA population. Acetone, 10% formalin, and methacarn were evaluated as fixatives, while Surgipath Decalicifier I, 10% ethylenediaminetetraacetic acid (EDTA), and 20% EDTA were evaluated as decalcifying reagents. Our results demonstrate that the optimal RNA quality was preserved by a decalcification protocol consisting of 20% EDTA for decalcification followed by fixation in methacarn, although this method is also associated with a reduction in RNA quantity.
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Affiliation(s)
- Yvonne Y Shao
- Orthopaedic Research Center, Department of Orthopaedic Surgery, The Cleveland Clinic Foundation, Cleveland, OH 44195, USA
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Lassmann S, Gerlach UV, Technau-Ihling K, Werner M, Fisch P. Application of BIOMED-2 primers in fixed and decalcified bone marrow biopsies: analysis of immunoglobulin H receptor rearrangements in B-cell non-Hodgkin's lymphomas. J Mol Diagn 2006; 7:582-91. [PMID: 16258156 PMCID: PMC1867555 DOI: 10.1016/s1525-1578(10)60591-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
The detection of clonality in lymphomas was recently improved by the BIOMED-2 approach, but analysis of fixed tissues is limited. Here, we adapted the BIOMED-2 protocol for examining immunoglobulin H (IgH) receptor rearrangements in fixed, decalcified bone marrow biopsies (BMBs) for clonality analysis in B-cell non-Hodgkin's lymphomas (B-NHL). The study included 111 decalcified BMBs (12 formalin fixed and 99 glutardialdehyde fixed), with B-NHL (n = 85), T-NHL (n = 8), or reactive infiltrates (n = 18). Initially, IgH FRIII polymerase chain reaction (PCR) analysis of crude DNA extracts from 75 glutardialdehyde-fixed BMBs (B-NHLs) using a standard seminested PCR resulted in clonal peaks in 46 of 75 (61.3%) BMBs compared with 19 of 70 (27.1%) for the original BIOMED-2 protocol. Modifications to both DNA extraction and PCR reaction improved the detection rate to 26 of 36 (72.2%) for BIOMED-2 primers, including 10 of 15 (66.7%) cases not detected by our standard IgH analysis. Moreover, introducing the same modifications for analysis of the FRII region by BIOMED-2 primers revealed clonal peaks in 19 of 36 (52.8%) B-NHLs compared with 5 of 70 (7.1%) for the original BIOMED-2 protocol. Together, analysis of FRII and FRIII regions by the modified BIOMED-2 protocol increased the detection rate to 31 of 36 (86.1%), particularly for BMBs with histological evidence of follicular lymphoma (FRIII, 70%; FRII, 90%). In summary, this study provides an improved protocol for detection of clonality by IgH-specific BIOMED-2 primers in fixed, decalcified bone marrow biopsies.
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Affiliation(s)
- Silke Lassmann
- Pathologisches Institut, Universitätsklinikum Freiburg, Albertstrasse 19, 79104 Freiburg.
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Fend F, Bock O, Kremer M, Specht K, Quintanilla-Martinez L. Ancillary techniques in bone marrow pathology: molecular diagnostics on bone marrow trephine biopsies. Virchows Arch 2005; 447:909-19. [PMID: 16231178 DOI: 10.1007/s00428-005-0069-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2005] [Accepted: 07/11/2005] [Indexed: 10/25/2022]
Abstract
Pathologic examination of trephine bone marrow (BM) biopsies plays a central role in the diagnosis and staging of haematological neoplasms and other disorders affecting haematopoiesis. Haematopathology has been profoundly influenced by the advent of molecular genetic techniques suitable for paraffin-embedded tissues, and certain applications, such as the determination of B- and T-cell clonality, belong to its standard diagnostic repertoire. Many of these molecular tests can be performed successfully with nucleic acids extracted from BM trephine biopsies, if some technical aspects specific to this template source such as various fixation and decalcification procedures are taken into consideration. The current indications for molecular BM diagnostics range from the confirmation of lymphoma involvement with gene rearrangement analysis, demonstration of tumor-specific translocations in lymphoid and chronic myeloproliferative disorders along to the detection of microorganisms or marrow involvement by soft tissue sarcomas. The availability of quantitative polymerase chain reaction techniques for the investigation of allelic imbalances and gene expression levels in paraffin-embedded material also open new avenues for research and advanced diagnostics. The molecular detection of minimal residual disease in haematological neoplasms, especially in the context of new treatment strategies, will provide future challenges. This article summarizes the current state of the art in molecular diagnostics applied to paraffin-embedded BM biopsies.
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Affiliation(s)
- Falko Fend
- Institute of Pathology, Technical University Munich, Ismaningerstrasse 22, 81675 Munich, Germany.
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Chakravorty S, Tyagi JS. Novel multipurpose methodology for detection of mycobacteria in pulmonary and extrapulmonary specimens by smear microscopy, culture, and PCR. J Clin Microbiol 2005; 43:2697-702. [PMID: 15956385 PMCID: PMC1151876 DOI: 10.1128/jcm.43.6.2697-2702.2005] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A novel, robust, reproducible, and multipurpose universal sample processing (USP) methodology for highly sensitive smear microscopy, culturing on solid and liquid media, and inhibition-free PCR which is suitable for the laboratory diagnosis of both pulmonary and extrapulmonary tuberculosis (TB) has been developed. This method exploits the chaotropic properties of guanidinium hydrochloride for sample processing and involves incubating the specimen with USP solution, concentrating bacilli by centrifugation, and using the processed specimen for smear microscopy, culture, and PCR. The detection limit for acid-fast bacilli in spiked sputum by smear microscopy is approximately 300 bacilli per ml of specimen. USP solution-treated specimens are fully compatible with culturing on solid and liquid media. High-quality, PCR-amplifiable mycobacterial DNA can be isolated from all types of clinical specimens processed with USP solution. The method has been extensively validated with both pulmonary and extrapulmonary specimens. Furthermore, the USP method is also compatible with smear microscopy, culture, and PCR of mycobacteria other than tubercle bacilli. In summary, the USP method provides smear microscopy, culture, and nucleic acid amplification technologies with a single sample-processing platform and, to the best of our knowledge, is the only method of its kind described to date. It is expected to be useful for the laboratory diagnosis of TB and other mycobacterial diseases by conventional and modern methods.
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Affiliation(s)
- Soumitesh Chakravorty
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
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Kondo S, Wakisaka N, Schell MJ, Horikawa T, Sheen TS, Sato H, Furukawa M, Pagano JS, Yoshizaki T. Epstein-Barr virus latent membrane protein 1 induces the matrix metalloproteinase-1 promoter via an Ets binding site formed by a single nucleotide polymorphism: enhanced susceptibility to nasopharyngeal carcinoma. Int J Cancer 2005; 115:368-76. [PMID: 15688379 DOI: 10.1002/ijc.20849] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The Epstein-Barr Virus (EBV) latent membrane protein 1 (LMP1) has a significant role in several malignancies, including nasopharyngeal carcinoma (NPC). LMP1 is the principal oncoprotein, and we have shown that it also induces a set of factors that mediates invasion, angiogenesis and metastasis. Matrix metalloproteinase-1 (MMP1) is also involved in several malignancies. A single guanine insertion polymorphism (2G) in the MMP1 promoter creates an Ets binding site that causes high levels of transcription and correlates with risk for some malignancies. Here, we evaluate the impact of this 2G insertion type on NPC. We genotyped 44 Japanese and 39 Taiwanese NPC patients, as well as 58 Japanese and 23 Taiwanese healthy controls. The proportion of 2G homozygotes was higher in the NPC groups than in controls (Japanese: p = 0.02, odds ratio (OR) = 2.49; Taiwanese: p = 0.02, OR = 3.66). An analysis of overall survival rates in the patients with NPC, and the 1G/1G genotype disclosed a favorable prognosis (5-year survival rate = 100%, p = 0.04). Multivariate analysis showed that 1G/1G has independent prognostic significance. We also examined whether LMP1 enhances MMP1 expression in epithelial cells in culture. LMP1-transfected cells with 2G/2G genotype expressed MMP1, which was abolished by activator protein-1 (AP1) dominant-negative (DN) and Ets-DN. LMP1 also induced active MMP3, which can cleave latent MMP1, and AP1-DN and Ets-DN suppressed the MMP3 expression. These results suggest that LMP1-induced MMP1 and MMP3 are closely linked and show that LMP1 activates MMP1 via an Ets binding site formed by 2G, which is a candidate marker for both risk and prognosis of NPC.
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Affiliation(s)
- Satoru Kondo
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Ellard S, Hattersley AT, Brewer CM, Vaidya B. Detection of an MEN1 gene mutation depends on clinical features and supports current referral criteria for diagnostic molecular genetic testing. Clin Endocrinol (Oxf) 2005; 62:169-75. [PMID: 15670192 DOI: 10.1111/j.1365-2265.2005.02190.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Diagnostic molecular genetic testing for multiple endocrine neoplasia type 1 (MEN1) has been available since the identification of the MEN1 gene in 1997. Mutation screening of the MEN1 gene has been recommended for patients who meet clinical criteria for MEN1 (at least two of the following: parathyroid hyperplasia, pancreatic endocrine tumour or pituitary adenoma) and those in whom a diagnosis of MEN1 is suspected. We examined the appropriateness of these clinical criteria. PATIENTS AND METHODS A total of 292 patients were referred for diagnostic testing. The coding region of the MEN1 gene was sequenced in 186 index cases and mutation testing was requested for 106 subjects, including 83 asymptomatic relatives. RESULTS MEN1 gene mutations were identified in 68/186 index cases (37%). Twenty-nine of the 60 MEN1 mutations reported are novel. The likelihood of finding a mutation was correlated with the number of MEN1-related tumours (mutation detection rate of 79%, 37% and 15% in patients with three, two and one main MEN1-related tumours; P < or = 0.00001) and increased in the presence of a family history (mutation detection rate of 91%, 69% and 29%vs. 69%, 23% and 0% in sporadic cases with three, two or one main MEN1-related tumours, respectively; P < or = 0.00001). The pick-up rate in the 83% of subjects who met proposed criteria for diagnostic testing was 42%, but in those who did not meet these criteria this fell to 0%. CONCLUSIONS The likelihood of finding an MEN1 mutation depends on the clinical features of the patient and their family. This large series supports present referral criteria for diagnostic mutation screening, but suggests that patients with sporadic isolated tumours rarely have MEN1 mutations.
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Affiliation(s)
- S Ellard
- Department of Molecular Genetics, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK.
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Inadome Y, Noguchi M. Selection of higher molecular weight genomic DNA for molecular diagnosis from formalin-fixed material. ACTA ACUST UNITED AC 2004; 12:231-6. [PMID: 14639109 DOI: 10.1097/00019606-200312000-00007] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The patterns of DNA degradation in frozen, methanol-fixed, and formalin-fixed tissues were investigated by high-performance liquid chromatography (HPLC). The chromatograms all yielded one major peak with or without several extra minor peaks representing molecular weights of preserved genomic DNA. The most characteristic differences were in the retention times of the major peaks, with the earliest major peak occurring in the formalin-fixed tissues, and followed by the methanol-fixed, and frozen tissue samples, in that order. This means that the molecular weight of the DNA from formalin-fixed tissue is much shortened than that recovered from methanol-fixed tissue and frozen tissue. The results also indicated that a small amount of higher molecular weight DNA is still preserved in formalin-fixed tissues. To improve the amplification efficiency of polymerase chain reaction (PCR) analysis of formalin-fixed material, we isolated the higher molecular weight DNA from formalin-fixed, paraffin-embedded tissue from four different organs and compared the amplification efficiencies with those of the crude DNA extract. We used eight sets of oligonucleotide primers producing 262 to 989 base pair (bp) fragments of beta-globin. The results showed that the PCR amplification analyses were more efficient with the isolated higher molecular weight DNA than with the crude DNA extract. Our study demonstrated that not all the DNA in formalin-fixed, paraffin-embedded tissue samples is totally degraded but that a small amount of higher molecular weight DNA persists. The feasibility of molecular diagnosis using formalin-fixed material can be improved by isolating the preserved higher molecular weight DNA by HPLC.
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Affiliation(s)
- Yukinori Inadome
- Department of Pathology, Ibaraki Cancer Center, Tsukuba Medical Center Hospital, Ibaraki, Japan
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31
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van Dongen JJM, Langerak AW, Brüggemann M, Evans PAS, Hummel M, Lavender FL, Delabesse E, Davi F, Schuuring E, García-Sanz R, van Krieken JHJM, Droese J, González D, Bastard C, White HE, Spaargaren M, González M, Parreira A, Smith JL, Morgan GJ, Kneba M, Macintyre EA. Design and standardization of PCR primers and protocols for detection of clonal immunoglobulin and T-cell receptor gene recombinations in suspect lymphoproliferations: report of the BIOMED-2 Concerted Action BMH4-CT98-3936. Leukemia 2004; 17:2257-317. [PMID: 14671650 DOI: 10.1038/sj.leu.2403202] [Citation(s) in RCA: 2368] [Impact Index Per Article: 112.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In a European BIOMED-2 collaborative study, multiplex PCR assays have successfully been developed and standardized for the detection of clonally rearranged immunoglobulin (Ig) and T-cell receptor (TCR) genes and the chromosome aberrations t(11;14) and t(14;18). This has resulted in 107 different primers in only 18 multiplex PCR tubes: three VH-JH, two DH-JH, two Ig kappa (IGK), one Ig lambda (IGL), three TCR beta (TCRB), two TCR gamma (TCRG), one TCR delta (TCRD), three BCL1-Ig heavy chain (IGH), and one BCL2-IGH. The PCR products of Ig/TCR genes can be analyzed for clonality assessment by heteroduplex analysis or GeneScanning. The detection rate of clonal rearrangements using the BIOMED-2 primer sets is unprecedentedly high. This is mainly based on the complementarity of the various BIOMED-2 tubes. In particular, combined application of IGH (VH-JH and DH-JH) and IGK tubes can detect virtually all clonal B-cell proliferations, even in B-cell malignancies with high levels of somatic mutations. The contribution of IGL gene rearrangements seems limited. Combined usage of the TCRB and TCRG tubes detects virtually all clonal T-cell populations, whereas the TCRD tube has added value in case of TCRgammadelta(+) T-cell proliferations. The BIOMED-2 multiplex tubes can now be used for diagnostic clonality studies as well as for the identification of PCR targets suitable for the detection of minimal residual disease.
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Affiliation(s)
- J J M van Dongen
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
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Phulwinder KG. A simple single-step method for the synthesis of recombinant non-homologous competitor cDNA and its implications for quantitative PCR in biological sciences and molecular diagnostics. Biol Chem 2002; 383:1463-9. [PMID: 12437141 DOI: 10.1515/bc.2002.167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In recent years there has been great interest in quantitative polymerase chain reaction. Consequently, a large number of assays have been developed, of which the one using non-homologous competitors is arguably the most precise. Despite widespread applications, currently there is no simple method to synthesize such competitors. Here a facile and cost-effective, single-step method for synthesis of recombinant, non-homologous, competitor complementary DNA is described. The method can be adapted to generate competitors of any size and sequence. The entire procedure is quick, straightforward and does not require any specialized equipment except a standard thermocycler.
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Affiliation(s)
- K Grover Phulwinder
- Department of Surgery, Flinders University School of Medicine, Flinders Medical Centre, South Australia
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Bialek R, Ernst F, Dietz K, Najvar LK, Knobloch J, Graybill JR, Schaumburg-Lever G. Comparison of staining methods and a nested PCR assay to detect Histoplasma capsulatum in tissue sections. Am J Clin Pathol 2002; 117:597-603. [PMID: 11939735 DOI: 10.1309/mh5b-gaq2-ky19-ft7p] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
To optimize diagnosis of histoplasmosis in tissue sections, 30 spleen specimens from mice, experimentally infected with Histoplasma capsulatum, were examined by H&E, Grocott stain, anti-bacille Calmette-Guerin antibody immunostain, Fungiqual A fluorochrome stain (Drs Reinehr and Rembold, Kandern, Germany), and a nested polymerase chain reaction (PCR) assay. Results were compared with the tissue burden determined by quantitative culture. By applying logistic regression, the nested PCR assay was the most sensitive method, but not significantly more sensitive than the Grocott stain. The 50% quantile to achieve a positive result was determined to be 3 colony-forming units per milligram of spleen tissue for the PCR assay, 11 for the Grocott stain, 27 for the fluorochrome stain, 190 for immunostaining, and 533 for the H&E stain. The Grocott and fluorochrome stains did not differ significantly in detecting fungal elements. The PCR assay unambiguously identified H. capsulatum in tissue sections.
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Affiliation(s)
- Ralf Bialek
- Institute for Tropical Medicine, University Hospital Tübingen, Germany
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Iwen PC, Hinrichs SH, Rupp ME. Utilization of the internal transcribed spacer regions as molecular targets to detect and identify human fungal pathogens. Med Mycol 2002; 40:87-109. [PMID: 11860017 DOI: 10.1080/mmy.40.1.87.109] [Citation(s) in RCA: 213] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Advances in molecular technology show great potential for the rapid detection and identification of fungi for medical, scientific and commercial purposes. Numerous targets within the fungal genome have been evaluated, with much of the current work using sequence areas within the ribosomal DNA (rDNA) gene complex. This section of the genome includes the 18S, 5.8S and 28S genes which code for ribosomal RNA (rRNA) and which have a relatively conserved nucleotide sequence among fungi. It also includes the variable DNA sequence areas of the intervening internal transcribed spacer (ITS) regions called ITS1 and ITS2. Although not translated into proteins, the ITS coding regions have a critical role in the development of functional rRNA, with sequence variations among species showing promise as signature regions for molecular assays. This review of the current literature was conducted to evaluate clinical approaches for using the fungal ITS regions as molecular targets. Multiple applications using the fungal ITS sequences are summarized here including those for culture identification, phylogenetic research, direct detection from clinical specimens or the environment, and molecular typing for epidemiological investigations. The breadth of applications shows that ITS regions have great potential as targets in molecular-based assays for the characterization and identification of fungi. Development of rapid and accurate amplification-based ITS assays to diagnose invasive fungal infections could potentially impact care and improve outcome for affected patients.
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Affiliation(s)
- P C Iwen
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha 68198-6495, USA.
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35
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Brown RSD, Edwards J, Bartlett JW, Jones C, Dogan A. Routine acid decalcification of bone marrow samples can preserve DNA for FISH and CGH studies in metastatic prostate cancer. J Histochem Cytochem 2002; 50:113-5. [PMID: 11748301 DOI: 10.1177/002215540205000113] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Production of paraffin-section material from tissue samples that contain bone requires decalcification. Techniques such as acidic decalcification or EDTA chelation are suitable methods. Acid decalcification is generally quicker than EDTA chelation but studies have suggested that it may result in hydrolysis of DNA. Here we show that limited acid decalcification (less than 24 hr) in 5% formic acid can preserve DNA sufficient for fluorescent in situ hybridization (FISH) or comparative genomic hybridization (CGH) and that prolonged 10% formic acid decalcification results in failure of FISH and only limited retrieval of DNA for CGH studies.
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Affiliation(s)
- R S D Brown
- Institute of Urology, London, United Kingdom.
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Wickham CL, Sarsfield P, Joyner MV, Jones DB, Ellard S, Wilkins B. Formic acid decalcification of bone marrow trephines degrades DNA: alternative use of EDTA allows the amplification and sequencing of relatively long PCR products. Mol Pathol 2000; 53:336. [PMID: 11193054 PMCID: PMC1186990 DOI: 10.1136/mp.53.6.336] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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