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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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2
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Mathieson W, Thomas G. Using FFPE Tissue in Genomic Analyses: Advantages, Disadvantages and the Role of Biospecimen Science. CURRENT PATHOBIOLOGY REPORTS 2019. [DOI: 10.1007/s40139-019-00194-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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3
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Evaluation of a DNA Extraction and Purification Protocol Using Archived Formalin-fixed Paraffin-embedded Tissues for BRAF Mutations Analysis in Papillary Thyroid Microcarcinomas. Appl Immunohistochem Mol Morphol 2019; 27:70-76. [DOI: 10.1097/pai.0000000000000535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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4
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Delgado Ramos GM, Cotter TG, Flor Ramos L, Torres Floril V, Ramos Martinez GA, Ruiz-Cabezas JC. A pilot study on the identification of human papillomavirus genotypes in tongue cancer samples from a single institution in Ecuador. ACTA ACUST UNITED AC 2018; 51:e7810. [PMID: 30304096 PMCID: PMC6180349 DOI: 10.1590/1414-431x20187810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 08/07/2018] [Indexed: 02/06/2023]
Abstract
The relationship between human papillomavirus (HPV) and oropharyngeal squamous cell carcinoma has been established. However, data from Ecuador is limited. The objective of this study was to characterize HPV infection in Ecuadorian patients with tongue cancer. Fifty-three patients with tongue cancer treated at the tertiary referral center Sociedad de Lucha Contra el Cancer (SOLCA), Guayaquil, between 2006 and 2011 were identified. Linear Array® HPV genotyping was used to identify the presence and types of HPV on formalin-fixed paraffin-embedded biopsy samples from these patients with tongue cancer. HPV was identified in 42% (n=22) and high-risk (HR) HPV in 17% (n=9), with 18 different HPV types identified. The most common types were the HR HPV 33 (14%) and low-risk HPV 67 (14%), followed by the HR HPV 58. More than one HPV type was identified in 27.3% of cases. HPV 33 was frequently associated with other HPV types. No statistically significant differences in gender (P=0.58) and age (P=0.12) were observed between HPV-positive and HPV-negative cases. HPV was identified in almost half of the tongue cancer samples, with subtypes 33 and 67 being the most common. This suggested that HPV played an important role in this disease in the population studied. Given these results, current HPV vaccines may not be as effective in reducing tongue cancer rates in this population.
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Affiliation(s)
- G M Delgado Ramos
- School of Medicine, Universidad Católica de Santiago de Guayaquil, Guayaquil, Ecuador
| | - T G Cotter
- Department of Medicine, University of Chicago Medical Center, Chicago, IL, USA
| | - L Flor Ramos
- School of Medicine, Universidad Católica de Santiago de Guayaquil, Guayaquil, Ecuador
| | - V Torres Floril
- Department of Hematology and Oncology, Instituto Oncológico Nacional de la Sociedad de Lucha Contra el Cancer, Guayaquil, Ecuador
| | - G A Ramos Martinez
- Department of Hematology and Oncology, Instituto Oncológico Nacional de la Sociedad de Lucha Contra el Cancer, Guayaquil, Ecuador
| | - J C Ruiz-Cabezas
- Department of Molecular Biology, Instituto Oncológico Nacional de la Sociedad de Lucha Contra el Cancer, Guayaquil, Ecuador
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5
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Kresse SH, Namløs HM, Lorenz S, Berner JM, Myklebost O, Bjerkehagen B, Meza-Zepeda LA. Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples. PLoS One 2018; 13:e0197456. [PMID: 29771965 PMCID: PMC5957415 DOI: 10.1371/journal.pone.0197456] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 05/02/2018] [Indexed: 12/21/2022] Open
Abstract
Nucleic acid material of adequate quality is crucial for successful high-throughput sequencing (HTS) analysis. DNA and RNA isolated from archival FFPE material are frequently degraded and not readily amplifiable due to chemical damage introduced during fixation. To identify optimal nucleic acid extraction kits, DNA and RNA quantity, quality and performance in HTS applications were evaluated. DNA and RNA were isolated from five sarcoma archival FFPE blocks, using eight extraction protocols from seven kits from three different commercial vendors. For DNA extraction, the truXTRAC FFPE DNA kit from Covaris gave higher yields and better amplifiable DNA, but all protocols gave comparable HTS library yields using Agilent SureSelect XT and performed well in downstream variant calling. For RNA extraction, all protocols gave comparable yields and amplifiable RNA. However, for fusion gene detection using the Archer FusionPlex Sarcoma Assay, the truXTRAC FFPE RNA kit from Covaris and Agencourt FormaPure kit from Beckman Coulter showed the highest percentage of unique read-pairs, providing higher complexity of HTS data and more frequent detection of recurrent fusion genes. truXTRAC simultaneous DNA and RNA extraction gave similar outputs as individual protocols. These findings show that although successful HTS libraries could be generated in most cases, the different protocols gave variable quantity and quality for FFPE nucleic acid extraction. Selecting the optimal procedure is highly valuable and may generate results in borderline quality specimens.
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Affiliation(s)
- Stine H. Kresse
- Department of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Heidi M. Namløs
- Department of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Susanne Lorenz
- Department of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- Genomics Core Facility, Department of Core Facilities, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Jeanne-Marie Berner
- Department of Pathology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Ola Myklebost
- Department of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Norwegian Cancer Genomics Consortium (cancergenomics.no), Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Bodil Bjerkehagen
- Department of Pathology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Leonardo A. Meza-Zepeda
- Department of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- Genomics Core Facility, Department of Core Facilities, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- Department of Pathology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- Norwegian Cancer Genomics Consortium (cancergenomics.no), Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- * E-mail:
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6
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Susman S, Berindan-Neagoe I, Petrushev B, Pirlog R, Florian IS, Mihu CM, Berce C, Craciun L, Grewal R, Tomuleasa C. The role of the pathology department in the preanalytical phase of molecular analyses. Cancer Manag Res 2018; 10:745-753. [PMID: 29695931 PMCID: PMC5903845 DOI: 10.2147/cmar.s150851] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
After introducing the new molecules for the treatment of patients with tumoral pathology, the therapeutical decision will be taken depending on the molecular profile performed upon the harvested tissues. This major modification makes the molecular and morphological analysis an essential part in the clinical management of patients and the pathologist plays an important role in this process. The quality and reproducibility of the results are imperative today and they depend on both the reliability of the molecular techniques and the quality of the tissue we use in the process. Also, the genomics and proteomics techniques, used increasingly often, require high-quality tissues, and pathology laboratories play a very significant role in the management of all phases of this process. In this paper the parameters which must be followed in order to obtain optimal results within the techniques which analyze nucleic acids and proteins were reviewed.
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Affiliation(s)
- Sergiu Susman
- Department of Pathology, Imogen Research Center.,Department of Morphological Sciences
| | | | - Bobe Petrushev
- Research Center for Functional Genomics and Translational Medicine
| | | | - Ioan-Stefan Florian
- Department of Neurosurgery, Iuliu Hatieganu University of Medicine and Pharmacy
| | | | - Cristian Berce
- Research Center for Functional Genomics and Translational Medicine
| | | | - Ravnit Grewal
- Department of Hematology, Ion Chiricuta Oncology Institute
| | - Ciprian Tomuleasa
- Research Center for Functional Genomics and Translational Medicine.,Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Department of Haematopathology, Tygerberg Academic Hospital, Tygerberg, South Africa
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7
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Almotwaa S, Elrobh M, AbdulKarim H, Alanazi M, Aldaihan S, Shaik J, Arafa M, Warsy AS. Genetic polymorphism and expression of HSF1 gene is significantly associated with breast cancer in Saudi females. PLoS One 2018; 13:e0193095. [PMID: 29494616 PMCID: PMC5832201 DOI: 10.1371/journal.pone.0193095] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 02/05/2018] [Indexed: 12/20/2022] Open
Abstract
The transcription factor, heat shock factor 1 (HSF1), influences the expression of heat shock proteins as well as other activities like the induction of tumor suppressor genes, signal transduction pathway, and glucose metabolism. We hypothesized that single nucleotide polymorphisms (SNPs) in HSF1 gene might affect its expression or function which might have an influence on the development of breast cancer. The study group included 242 individuals (146 breast cancer patients and 96 healthy controls). From the cancer patients, genomic DNA was extracted from 96 blood samples and 50 Formalin-Fixed Paraffin Embedded (FFPE) tissues, while from the controls DNA were extracted from blood only. Genotype was carried out for four SNPs in the HSF1 gene (rs78202224, rs35253356, rs4977219 and rs34404564) using Taqman genotyping assay method. The HSF1 expression was investigated using immunohistochemistry on FFPE tissues (cancer tissue and adjacent normal tissue). The SNP rs78202224 (G>T) was significantly associated with increased risk of breast cancer. The combined TT + GT genotype (OR: 6.91; p: 0.035) and the T allele showed high risk (OR: 5.81; p:0.0085) for breast cancer development. The SNP rs34404564 (A>G) had a protective effect against the development of breast cancer. The genotype AG (OR: 0.41; p = 0.0059) and GG+AG (OR: 0.52; p: 0.026) occurred at a significantly lower frequency in the breast cancer patients compared to the frequency in healthy controls. No significant relationship was identified between either rs35253356 (A>G) or rs4977219 (A>C) and breast cancer in Saudi. The HSF1 protein expression was higher in all invasive and in situ breast carcinoma compared to the normal tissue. A stronger positive staining for HSF1 was found in the nucleus compared to the cytoplasm. Our results show that HSF1 gene expression is elevated in breast cancer tissue and two of the studied SNPs correlate significantly with cancer development.
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Affiliation(s)
- Sahar Almotwaa
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed Elrobh
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Huda AbdulKarim
- Head of the Hematology/Oncology Unit at King Fahad Medical City Hospital, Comprehensive Cancer Center, Riyadh, Saudi Arabia
| | - Mohamed Alanazi
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Sooad Aldaihan
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Jilani Shaik
- Genome Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Maha Arafa
- Department of Pathology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Arjumand Sultan Warsy
- Senior Scientist, Central Laboratory, Center for Science and Medical Studies for Girls, King Saud University, Riyadh, Saudi Arabia
- * E-mail:
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8
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Testing for NRAS Mutations in Serous Borderline Ovarian Tumors and Low-Grade Serous Ovarian Carcinomas. DISEASE MARKERS 2018; 2018:1497879. [PMID: 29682098 PMCID: PMC5845515 DOI: 10.1155/2018/1497879] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/31/2017] [Accepted: 01/30/2018] [Indexed: 12/24/2022]
Abstract
The Idylla NRAS Mutation Test, performed on the Biocartis Idylla system, is an in vitro diagnostic tool for the qualitative assessment of 18 NRAS mutations in codons 12, 13, 59, 61, 117, and 146. Low-grade serous ovarian cancer (LGSC) represents less than 10% of all serous ovarian carcinomas. LGSCs are believed to arise from preexisting cystadenomas or serous borderline tumors (SBOTs) that eventually progress to an invasive carcinoma. The molecular analysis of cancer-causing mutations and the development of targeted biological therapies constitute a milestone in the diagnosis and therapy of ovarian malignancies. According to some authors, NRAS may be an important oncogene for the progression of SBOT to a frankly invasive disease. The primary aim of this study was to verify if a fully integrated, real-time PCR-based Idylla system can be used for the rapid determination of the NRAS mutation status in patients with serous borderline ovarian tumors and low-grade serous ovarian carcinomas. The study included tissue specimens from 12 patients with histopathologically verified ovarian masses, operated on at the Department of Obstetrics and Gynecology, Nicolaus Copernicus University, Collegium Medicum in Bydgoszcz (Poland), between January 2009 and June 2012. The mean age of the study patients was 52.5 years (range 27-80 years). NRAS mutation in codon 13 (G13D, p.Gly13Asp; nucleotide: c.38G>A) was found in one patient, a woman with low-grade serous ovarian carcinoma. To the best of our knowledge, our experiment was the first published study using the novel Idylla NRAS Mutation Test for the evaluation of ovarian tumors in a clinical setting. The Idylla platform is an interesting ancillary first-line rapid and fully automated instrument to detect NRAS mutations in SBOTs and LGSCs. However, the clinical usefulness of this method still needs to be verified in larger groups of cancer patients.
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9
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Sadlecki P, Antosik P, Grzanka D, Grabiec M, Walentowicz-Sadlecka M. KRAS mutation testing in borderline ovarian tumors and low-grade ovarian carcinomas with a rapid, fully integrated molecular diagnostic system. Tumour Biol 2017; 39:1010428317733984. [DOI: 10.1177/1010428317733984] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Pawel Sadlecki
- Department of Obstetrics and Gynecology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Paulina Antosik
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Dariusz Grzanka
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Marek Grabiec
- Department of Obstetrics and Gynecology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Malgorzata Walentowicz-Sadlecka
- Department of Obstetrics and Gynecology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
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10
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Sadlecki P, Walentowicz P, Bodnar M, Marszalek A, Grabiec M, Walentowicz-Sadlecka M. Determination of BRAF V600E (VE1) protein expression and BRAF gene mutation status in codon 600 in borderline and low-grade ovarian cancers. Tumour Biol 2017; 39:1010428317706230. [PMID: 28488545 DOI: 10.1177/1010428317706230] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Epithelial ovarian tumors are a group of morphologically and genetically heterogeneous neoplasms. Based on differences in clinical phenotype and genetic background, ovarian neoplasms are classified as low-grade and high-grade tumor. Borderline ovarian tumors represent approximately 10%-20% of all epithelial ovarian masses. Various histological subtypes of ovarian malignancies differ in terms of their risk factor profiles, precursor lesions, clinical course, patterns of spread, molecular genetics, response to conventional chemotherapy, and prognosis. The most frequent genetic aberrations found in low-grade serous ovarian carcinomas and serous borderline tumors, as well as in mucinous cancers, are mutations in BRAF and KRAS genes. The most commonly observed BRAF mutation is substitution of glutamic acid for valine in codon 600 (V600E) in exon 15. The primary aim of this study was to determine whether fully integrated, real-time polymerase chain reaction-based Idylla™ system may be useful in determination of BRAF gene mutation status in codon 600 in patients with borderline ovarian tumors and low-grade ovarian carcinomas. The study included tissue specimens from 42 patients with histopathologically verified ovarian masses, who were operated on at the Department of Obstetrics and Gynecology, Nicolaus Copernicus University Collegium Medicum in Bydgoszcz (Poland). Based on histopathological examination of surgical specimens, 35 lesions were classified as low-grade ovarian carcinomas, and 7 as borderline ovarian tumors. Specimens with expression of BRAF V600E (VE1) protein were tested for mutations in codon 600 of the BRAF gene, using an automated molecular diagnostics platform Idylla™. Cytoplasmic immunoexpression of BRAF V600E (VE1) protein was found in three specimens: serous superficial papilloma, serous papillary cystadenoma of borderline malignancy, and partially proliferative serous cystadenoma. All specimens with the expression of BRAF V600E (VE1) protein were tested positively for BRAF V600E/E2/D mutation. No statistically significant relationship (p > 0.05) was found between the presence of BRAF V600E mutation and the probability of 5-year survival. BRAF mutation testing with a rapid, fully integrated molecular diagnostics system Idylla™ may be also a powerful prognostic tool in subjects with newly diagnosed serous borderline tumors, identifying a subset of patients who are unlikely to progress.
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Affiliation(s)
- Pawel Sadlecki
- 1 Department of Obstetrics and Gynecology, L. Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Pawel Walentowicz
- 1 Department of Obstetrics and Gynecology, L. Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Magdalena Bodnar
- 2 Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland.,3 Department of Otolaryngology and Laryngeal Oncology, K. Marcinkowski University of Medical Sciences, Poznan, Poland
| | - Andrzej Marszalek
- 2 Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland.,4 Chair of Oncologic Pathology and Prophylaxis, Poznan University of Medical Sciences and Greater Poland Cancer Center, Poznan, Poland
| | - Marek Grabiec
- 1 Department of Obstetrics and Gynecology, L. Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Malgorzata Walentowicz-Sadlecka
- 1 Department of Obstetrics and Gynecology, L. Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Bydgoszcz, Poland
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11
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Seiler C, Sharpe A, Barrett JC, Harrington EA, Jones EV, Marshall GB. Nucleic acid extraction from formalin-fixed paraffin-embedded cancer cell line samples: a trade off between quantity and quality? BMC Clin Pathol 2016. [PMID: 28649177 PMCID: PMC5477763 DOI: 10.1186/s12907-016-0039-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Advanced genomic techniques such as Next-Generation-Sequencing (NGS) and gene expression profiling, including NanoString, are vital for the development of personalised medicines, as they enable molecular disease classification. This has become increasingly important in the treatment of cancer, aiding patient selection. However, it requires efficient nucleic acid extraction often from formalin-fixed paraffin-embedded tissue (FFPE). METHODS Here we provide a comparison of several commercially available manual and automated methods for DNA and/or RNA extraction from FFPE cancer cell line samples from Qiagen, life Technologies and Promega. Differing extraction geometric mean yields were evaluated across each of the kits tested, assessing dual DNA/RNA extraction vs. specialised single extraction, manual silica column based extraction techniques vs. automated magnetic bead based methods along with a comparison of subsequent nucleic acid purity methods, providing a full evaluation of nucleic acids isolated. RESULTS Out of the four RNA extraction kits evaluated the RNeasy FFPE kit, from Qiagen, gave superior geometric mean yields, whilst the Maxwell 16 automated method, from Promega, yielded the highest quality RNA by quantitative real time RT-PCR. Of the DNA extraction kits evaluated the PicoPure DNA kit, from Life Technologies, isolated 2-14× more DNA. A miniaturised qPCR assay was developed for DNA quantification and quality assessment. CONCLUSIONS Careful consideration of an extraction kit is necessary dependent on quality or quantity of material required. Here we provide a flow diagram on the factors to consider when choosing an extraction kit as well as how to accurately quantify and QC the extracted material.
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Affiliation(s)
- Caroline Seiler
- AstraZeneca Oncology Innovative Medicines, Alderley Park, Macclesfield, UK.,Leeds University-AZ Sandwich Placement, Leeds, UK
| | - Alan Sharpe
- AstraZeneca Oncology Innovative Medicines, Alderley Park, Macclesfield, UK
| | | | | | | | - Gayle B Marshall
- AstraZeneca Oncology Innovative Medicines, Alderley Park, Macclesfield, UK.,AstraZeneca, 8AF6, Mereside, Alderley Park, Alderley Edge, Cheshire SK10 4TG UK
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12
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Janku F, Claes B, Huang HJ, Falchook GS, Devogelaere B, Kockx M, Bempt IV, Reijans M, Naing A, Fu S, Piha-Paul SA, Hong DS, Holley VR, Tsimberidou AM, Stepanek VM, Patel SP, Kopetz ES, Subbiah V, Wheler JJ, Zinner RG, Karp DD, Luthra R, Roy-Chowdhuri S, Sablon E, Meric-Bernstam F, Maertens G, Kurzrock R. BRAF mutation testing with a rapid, fully integrated molecular diagnostics system. Oncotarget 2016; 6:26886-94. [PMID: 26330075 PMCID: PMC4694960 DOI: 10.18632/oncotarget.4723] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 07/17/2015] [Indexed: 01/07/2023] Open
Abstract
Fast and accurate diagnostic systems are needed for further implementation of precision therapy of BRAF-mutant and other cancers. The novel IdyllaTMBRAF Mutation Test has high sensitivity and shorter turnaround times compared to other methods. We used Idylla to detect BRAF V600 mutations in archived formalin-fixed paraffin-embedded (FFPE) tumor samples and compared these results with those obtained using the cobas 4800 BRAF V600 Mutation Test or MiSeq deep sequencing system and with those obtained by a Clinical Laboratory Improvement Amendments (CLIA)-certified laboratory employing polymerase chain reaction–based sequencing, mass spectrometric detection, or next-generation sequencing. In one set of 60 FFPE tumor samples (15 with BRAF mutations per Idylla), the Idylla and cobas results had an agreement of 97%. Idylla detected BRAF V600 mutations in two additional samples. The Idylla and MiSeq results had 100% concordance. In a separate set of 100 FFPE tumor samples (64 with BRAF mutation per Idylla), the Idylla and CLIA-certified laboratory results demonstrated an agreement of 96% even though the tests were not performed simultaneously and different FFPE blocks had to be used for 9 cases. The IdyllaTMBRAF Mutation Test produced results quickly (sample to results time was about 90 minutes with about 2 minutes of hands on time) and the closed nature of the cartridge eliminates the risk of PCR contamination. In conclusion, our observations demonstrate that the Idylla test is rapid and has high concordance with other routinely used but more complex BRAF mutation–detecting tests.
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Affiliation(s)
- Filip Janku
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Helen J Huang
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gerald S Falchook
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Sarah Cannon Research Institute at HealthONE, Denver, CO 80218, USA
| | | | | | | | | | - Aung Naing
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Siqing Fu
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sarina A Piha-Paul
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - David S Hong
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Veronica R Holley
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Apostolia M Tsimberidou
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Vanda M Stepanek
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sapna P Patel
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - E Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Vivek Subbiah
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jennifer J Wheler
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ralph G Zinner
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Daniel D Karp
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rajyalakshmi Luthra
- Molecular Diagnostics Laboratory, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sinchita Roy-Chowdhuri
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Razelle Kurzrock
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Center for Personalized Cancer Therapy, Moores Cancer Center, The University of California San Diego, La Jolla, CA 92093, USA
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13
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Hassani A, Khan G. A simple procedure for the extraction of DNA from long-term formalin-preserved brain tissues for the detection of EBV by PCR. Exp Mol Pathol 2015; 99:558-63. [PMID: 26450268 DOI: 10.1016/j.yexmp.2015.09.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 09/30/2015] [Indexed: 12/28/2022]
Abstract
Long-term formalin fixed brain tissues are potentially an important source of material for molecular studies. Ironically, very few protocols have been published describing DNA extraction from such material for use in PCR analysis. In our attempt to investigate the role of Epstein-Barr virus (EBV) in the pathogenesis of multiple sclerosis (MS), extracting PCR quality DNA from brain samples fixed in formalin for 2-22 years, proved to be very difficult and challenging. As expected, DNA extracted from these samples was not only of poor quality and quantity, but more importantly, it was frequently found to be non-amplifiable due to the presence of PCR inhibitors. Here, we describe a simple and reproducible procedure for extracting DNA using a modified proteinase K and phenol-chloroform methodology. Central to this protocol is the thorough pre-digestion washing of the tissues in PBS, extensive digestion with proteinase K in low SDS containing buffer, and using low NaCl concentration during DNA precipitation. The optimized protocol was used in extracting DNA from meninges of 26 MS and 6 non-MS cases. Although the quality of DNA from these samples was generally poor, small size amplicons (100-200 nucleotides) of the house-keeping gene, β-globin could be reliably amplified from all the cases. PCR for EBV revealed positivity in 35% (9/26) MS cases, but 0/6 non-MS cases. These findings indicate that the method described here is suitable for PCR detection of viral sequences in long-term formalin persevered brain tissues. Our findings also support a possible role for EBV in the pathogenesis of MS.
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Affiliation(s)
- Asma Hassani
- Department of Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Gulfaraz Khan
- Department of Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
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14
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Pelekanos RA, Sardesai VS, Dekker Nitert M, Callaway LK, Fisk NM, Jeffery PL. Rapid method for growth hormone receptor exon 3 delete (GHRd3) SNP genotyping from archival human placental samples. Endocrine 2015; 49:643-52. [PMID: 26067082 DOI: 10.1007/s12020-015-0647-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 06/01/2015] [Indexed: 12/15/2022]
Abstract
Analysis of archival samples from cohorts of pregnant women may be key to discovering prognosticators of stillbirth and pregnancy/perinatal complications. Growth hormone (GH) and its receptor (GHR) are pivotal in feto-placental development and pregnancy maintenance. We report a rapid, optimized method for genotyping the GHR full-length versus exon 3-deleted isoform (GHRd3). TaqMan single nucleotide polymorphism (SNP) genotyping proved superior to standard multiplex polymerase chain reaction (PCR) in allele detection and GHR genotyping from archived samples, including those with poor genomic deoxyribonucleic acid quality/quantity such as formalin fixed, paraffin embedded, blood, and serum. Furthermore, this assay is suitable for high through put 96 or 384-well plate quantitative PCR machines with automated genotype calling software. The TaqMan genotyping assay can increase the data obtained from precious archival human samples.
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Affiliation(s)
- Rebecca A Pelekanos
- Experimental Fetal Medicine Group, UQ Centre for Clinical Research, The University of Queensland, Herston, QLD, 4029, Australia,
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15
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Frickmann H, Hinz R, Hagen RM. Comparison of an automated nucleic acid extraction system with the column-based procedure. Eur J Microbiol Immunol (Bp) 2015; 5:94-102. [PMID: 25883797 DOI: 10.1556/eujmi-d-14-00040] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 12/23/2014] [Indexed: 12/21/2022] Open
Abstract
Here, we assessed the extraction efficiency of a deployable bench-top nucleic acid extractor EZ1 in comparison to the column-based approach with complex sample matrices. A total of 48 EDTA blood samples and 81 stool samples were extracted by EZ1 automated extraction and the column-based QIAamp DNA Mini Kit. Blood sample extractions were assessed by two real-time malaria PCRs, while stool samples were analyzed by six multiplex real-time PCR assays targeting bacterial, viral, and parasitic stool pathogens. Inhibition control PCR testing was performed as well. In total, 147 concordant and 13 discordant pathogen-specific PCR results were obtained. The latter comprised 11 positive results after column-based extraction only and two positive results after EZ1 extraction only. EZ1 extraction showed a higher frequency of inhibition. This phenomenon was, however, inconsistent for the different PCR schemes. In case of concordant PCR results, relevant differences of cycle threshold numbers for the compared extraction schemes were not observed. Switches from well-established column-based extraction to extraction with the automated EZ1 system do not lead to a relevantly reduced yield of target DNA when complex sample matrices are used. If sample inhibition is observed, column-based extraction from another sample aliquot may be considered.
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16
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Hu YC, Zhang Q, Huang YH, Liu YF, Chen HL. Comparison of two methods to extract DNA from formalin-fixed, paraffin-embedded tissues and their impact on EGFR mutation detection in non-small cell lung carcinoma. Asian Pac J Cancer Prev 2015; 15:2733-7. [PMID: 24761893 DOI: 10.7314/apjcp.2014.15.6.2733] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Molecular pathology tests are often carried for clinicopathological diagnosis and pathologists have established large collections of formalin-fixed, paraffin-embedded tissue (FFPE) banks. However, extraction of DNA from FFPE is a laborious and challenging for researchers in clinical laboratories. The aim of this study was to compare two widely used DNA extraction methods: using a QIAamp DNA FFPE kit from Qiagen and a Cobas Sample Preparation Kit from Roche, and evaluated the effect of the DNA quality on molecular diagnostics. METHODS DNA from FFPE non-small cell lung carcinoma tissues including biopsy and surgical specimens was extracted with both QIAamp DNA FFPE and Cobas Sample Preparation Kits and EGFR mutations of non-small cell lung carcinomas were detected by real-time quantitative PCR using the extracted DNA. RESULTS AND CONCLUSION Our results showed that DNA extracted by QIAamp and Cobas methods were both suitable to detect downstream EGFR mutation in surgical specimens. Howover, Cobas method could yield more DNA from biopsy specimens, and gain much better EGFR mutation results.
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Affiliation(s)
- Yu-Chang Hu
- Department of Pathology, The First College of Clinical Medical Sciences, China Three Gorges University, Yichang, China E-mail :
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17
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Chen YL, Lu CC, Yang SC, Su WP, Lin YL, Chen WL, Huang W, Su WC, Chow NH, Ho CL. Verification of wild-type EGFR status in non-small cell lung carcinomas using a mutant-enriched PCR on selected cases. J Mol Diagn 2014; 16:486-494. [PMID: 25051378 DOI: 10.1016/j.jmoldx.2014.05.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 04/10/2014] [Accepted: 05/27/2014] [Indexed: 01/20/2023] Open
Abstract
EGFR genotyping is required for targeted therapy of lung adenocarcinoma. Because a false-negative result might prevent a patient from receiving appropriate targeted therapies, it is desirable to recheck equivocal results of EGFR genotyping. A cohort of 346 lung cancers was tested with a commercial kit for EGFR mutations; nine of the cases had upward real-time amplification curves at late cycles. They were also investigated using mutant-enriched PCR with peptide nucleic acid-locked nucleic acid (PNA-sequencing). Six of the nine equivocal cases harbored EGFR mutations. These cases likely had a small amount of mutant DNA near the detection limit of the commercial kit. Twenty nonequivocal, wild-type cases were reconfirmed using PNA-sequencing. We noticed a College of American Pathologists proficiency test material that showed a suspicious upward curve and eventually proved to have an H773_V774insPH in exon 20, for which a specific primer was not designed in the commercial kit. Further study using cloned DNA fragments showed that the upward curve most likely resulted from cross-reaction between similar, but nonidentical, sequences. It is desirable to keep the number of false-negative results as low as possible, but rechecking all wild-type cases is impractical. The late upward curves we observed helped identify suspicious cases for rechecking. A second method, such as PNA-sequencing, is recommended to verify wild-type cases.
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Affiliation(s)
- Yi-Lin Chen
- Molecular Diagnosis Laboratory, Department of Pathology, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan; Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan; Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan; Associations of Medical Technologists, Tainan, Taiwan
| | - Cheng-Chan Lu
- Molecular Diagnosis Laboratory, Department of Pathology, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan; Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan; The Institute of Molecular Medicine, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Shu-Ching Yang
- Molecular Diagnosis Laboratory, Department of Pathology, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan; Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Wen-Pin Su
- Department of Internal Medicine, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Ya-Lan Lin
- Molecular Diagnosis Laboratory, Department of Pathology, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan; Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Wan-Li Chen
- Molecular Diagnosis Laboratory, Department of Pathology, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan; Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Wenya Huang
- Molecular Diagnosis Laboratory, Department of Pathology, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan; Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan; Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Wu-Chou Su
- Department of Internal Medicine, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Nan-Haw Chow
- Molecular Diagnosis Laboratory, Department of Pathology, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan; Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan; The Institute of Molecular Medicine, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Chung-Liang Ho
- Molecular Diagnosis Laboratory, Department of Pathology, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan; Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan; Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan.
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18
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Wong SSY, Fung KSC, Chau S, Poon RWS, Wong SCY, Yuen KY. Molecular diagnosis in clinical parasitology: When and why? Exp Biol Med (Maywood) 2014; 239:1443-60. [DOI: 10.1177/1535370214523880] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Microscopic detection and morphological identification of parasites from clinical specimens are the gold standards for the laboratory diagnosis of parasitic infections. The limitations of such diagnostic assays include insufficient sensitivity and operator dependence. Immunoassays for parasitic antigens are not available for most parasitic infections and have not significantly improved the sensitivity of laboratory detection. Advances in molecular detection by nucleic acid amplification may improve the detection in asymptomatic infections with low parasitic burden. Rapidly accumulating genomic data on parasites allow the design of polymerase chain reaction (PCR) primers directed towards multi-copy gene targets, such as the ribosomal and mitochondrial genes, which further improve the sensitivity. Parasitic cell or its free circulating parasitic DNA can be shed from parasites into blood and excreta which may allow its detection without the whole parasite being present within the portion of clinical sample used for DNA extraction. Multiplex nucleic acid amplification technology allows the simultaneous detection of many parasitic species within a single clinical specimen. In addition to improved sensitivity, nucleic acid amplification with sequencing can help to differentiate different parasitic species at different stages with similar morphology, detect and speciate parasites from fixed histopathological sections and identify anti-parasitic drug resistance. The use of consensus primer and PCR sequencing may even help to identify novel parasitic species. The key limitation of molecular detection is the technological expertise and expense which are usually lacking in the field setting at highly endemic areas. However, such tests can be useful for screening important parasitic infections in asymptomatic patients, donors or recipients coming from endemic areas in the settings of transfusion service or tertiary institutions with transplantation service. Such tests can also be used for monitoring these recipients or highly immunosuppressed patients, so that early preemptive treatment can be given for reactivated parasitic infections while the parasitic burden is still low.
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Affiliation(s)
- Samson SY Wong
- Department of Microbiology, The University of Hong Kong, Queen Mary Hospital, Pok Fu Lam, Hong Kong
| | - Kitty SC Fung
- Department of Pathology, United Christian Hospital, Kwun Tong of New Kowloon, Hong Kong
| | - Sandy Chau
- Department of Pathology, United Christian Hospital, Kwun Tong of New Kowloon, Hong Kong
| | - Rosana WS Poon
- Department of Microbiology, The University of Hong Kong, Queen Mary Hospital, Pok Fu Lam, Hong Kong
| | - Sally CY Wong
- Department of Microbiology, The University of Hong Kong, Queen Mary Hospital, Pok Fu Lam, Hong Kong
| | - Kwok-Yung Yuen
- Department of Microbiology, The University of Hong Kong, Queen Mary Hospital, Pok Fu Lam, Hong Kong
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Rabelo-Gonçalves E, Roesler B, Guardia AC, Milan A, Hara N, Escanhoela C, Almeida J, Boin I, Zeitune JM. Evaluation of five DNA extraction methods for detection of H. pylori in formalin-fixed paraffin-embedded (FFPE) liver tissue from patients with hepatocellular carcinoma. Pathol Res Pract 2014; 210:142-6. [DOI: 10.1016/j.prp.2013.11.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 10/11/2013] [Accepted: 11/06/2013] [Indexed: 01/06/2023]
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20
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Bonin S, Stanta G. Nucleic acid extraction methods from fixed and paraffin-embedded tissues in cancer diagnostics. Expert Rev Mol Diagn 2014; 13:271-82. [DOI: 10.1586/erm.13.14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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21
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Dietrich D, Uhl B, Sailer V, Holmes EE, Jung M, Meller S, Kristiansen G. Improved PCR performance using template DNA from formalin-fixed and paraffin-embedded tissues by overcoming PCR inhibition. PLoS One 2013; 8:e77771. [PMID: 24155973 PMCID: PMC3796491 DOI: 10.1371/journal.pone.0077771] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 09/05/2013] [Indexed: 02/06/2023] Open
Abstract
Formalin-fixed and paraffin-embedded (FFPE) tissues represent a valuable source for biomarker studies and clinical routine diagnostics. However, they suffer from degradation of nucleic acids due to the fixation process. Since genetic and epigenetic studies usually require PCR amplification, this degradation hampers its use significantly, impairing PCR robustness or necessitating short amplicons. In routine laboratory medicine a highly robust PCR performance is mandatory for the clinical utility of genetic and epigenetic biomarkers. Therefore, methods to improve PCR performance using DNA from FFPE tissue are highly desired and of wider interest. The effect of template DNA derived from FFPE tissues on PCR performance was investigated by means of qPCR and conventional PCR using PCR fragments of different sizes. DNA fragmentation was analyzed via agarose gel electrophoresis. This study showed that poor PCR amplification was partly caused by inhibition of the DNA polymerase by fragmented DNA from FFPE tissue and not only due to the absence of intact template molecules of sufficient integrity. This PCR inhibition was successfully minimized by increasing the polymerase concentration, dNTP concentration and PCR elongation time thereby allowing for the robust amplification of larger amplicons. This was shown for genomic template DNA as well as for bisulfite-converted template DNA required for DNA methylation analyses. In conclusion, PCR using DNA from FFPE tissue suffers from inhibition which can be alleviated by adaptation of the PCR conditions, therefore allowing for a significant improvement of PCR performance with regard to variability and the generation of larger amplicons. The presented solutions to overcome this PCR inhibition are of tremendous value for clinical chemistry and laboratory medicine.
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Affiliation(s)
- Dimo Dietrich
- University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany
- * E-mail:
| | - Barbara Uhl
- University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany
| | - Verena Sailer
- University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany
| | - Emily Eva Holmes
- University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany
| | - Maria Jung
- University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany
| | - Sebastian Meller
- University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany
| | - Glen Kristiansen
- University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany
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