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Muzza M. The clonal origin of multifocal papillary thyroid cancer: intrathyroidal spread or independent tumors? Minerva Endocrinol (Torino) 2020; 46:35-44. [PMID: 33045819 DOI: 10.23736/s2724-6507.20.03302-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Multifocality is a common finding in papillary thyroid cancer but the molecular pathogenesis, prognosis and management of multifocal papillary thyroid cancer are debated. The clonal origin of multifocal papillary thyroid cancer represents a controversial aspect, as two opposite viewpoints have been proposed: independent origin or intraglandular spread. Different approaches have been used for inferring the clonality of multifocal papillary thyroid cancer, including X-chromosome inactivation, mutational analysis, determination of loss of heterozygosity and, more recently, next-generation sequencing. Next-generation sequencing, able to provide information on genetic heterogeneity and phylogenetic evolution in multifocal tumors, represents the most reliable approach. While most evidences indicated an independent origin of multifocal papillary thyroid cancer, a minority of studies suggested that multifocal papillary thyroid tumors might be monoclonally derived. This discrepancy may reflect technical limitations; nevertheless, studies based on next-generation sequencing indicated that both independent and clonal origins are possible. The co-existence of multiple tumors implies a high degree of genetic heterogeneity, which may influence the best and targeted therapeutic strategy. On the other hand, intrathyroidal dissemination may indicate metastatic potential of the dominant tumor, thereby prompting more aggressive treatments. In conclusion, data available in the literature indicated that multifocal papillary thyroid cancer may derived from both intraglandular spread and independent tumor foci. The understanding of the clonal origin of multifocal papillary thyroid tumors might represent an important issue in patient treatment.
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Affiliation(s)
- Marina Muzza
- Division of Endocrine and Metabolic Diseases, IRCCS Istituto Auxologico Italiano, Milan, Italy -
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2
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Detection of Loss of Heterozygosity (LOH) Using Circulating Cell-free DNA (cfDNA) by Fluorescence-based Multiplex PCR for Identification of Patients With Prostate Cancer. Appl Immunohistochem Mol Morphol 2019; 26:749-759. [PMID: 28362710 DOI: 10.1097/pai.0000000000000514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Several lines of evidence suggest that loss of heterozygosity (LOH) in specific chromosomal regions is a common mechanism for the inactivation of tumor-suppressor genes that are implicated in the pathogenesis of prostate cancer (PCa). Short tandem repeat (STR) sequences are extremely reliable genetic markers for the detection of LOH associated with cancers. Hence, in the current study, we investigated the detection of LOH at 6 STR markers (D8S360, D9S1748, D9S171, D8S137, D6S1631, and THRB) using blood circulating cell-free DNA (cfDNA), which can be used to distinguish PCa from benign prostatic hyperplasia (BPH). A total of 136 individuals were included in the study, 76 male patients diagnosed with PCa (50 male patients with localized PCa and 26 male patients with metastatic PCa) as experimental subjects and 60 male patients with BPH as controls. Circulating cfDNA was extracted from plasma samples and amplified with fluorescence-labeled primers specific for known STR markers. We also evaluated the serum prostate-specific antigen in both groups. Our findings revealed that the frequency of LOH at D8S360, D9S1748, D9S171, D8S137, and D6S1631 was significantly higher in PCa subjects than in controls (P<0.05). Of the 6 STR markers, LOH at D8S360 could discriminate metastatic PCa from localized PCa. We found that 71.05% of patients with PCa and 1.66% of BPH subjects had LOH at least at 3 of the markers in cfDNA. Our findings provide additional evidence to support the hypothesis that analysis of LOH at D8S360, D9S1748, D9S171, D8S137, and D6S1631 STR markers using cfDNA can be applied as a noninvasive diagnostic approach for the detection of PCa.
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Abstract
CONTEXT Genomic medicine requires the identification of biomarkers and therapeutic targets, which in turn, requires high-quality biospecimens. Achieving high-quality biospecimens requires implementing standard operating procedures to control the variations of preanalytic variables in biobanking. Currently, most biobanks do not control the variations of preanalytic variables when collecting, processing, and storing their biospecimens. However, those variations have been shown to affect the quality of biospecimens and gene expression profiling. OBJECTIVE To identify evidence-based preanalytic parameters that can be applied and those parameters that need further study. DATA SOURCES We searched the Biospecimen Research and PubMed databases using defined key words. We retrieved and reviewed 212 articles obtained through those searches. We included 58 articles (27%) according to our inclusion and exclusion criteria for this review. CONCLUSION -Preanalytic variables in biobanking can degrade the quality of biospecimens and alter gene expression profiling. Variables that require further study include the effect of surgical manipulation; the effect of warm ischemia; the allowable duration of delayed specimen processing; the optimal type, duration, and temperature of preservation and fixation; and the optimal storage duration of formalin-fixed, paraffin embedded specimens in a fit-for-purpose approach.
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Affiliation(s)
- Jane H Zhou
- From the Departments of Pathology (Drs Zhou and Sahin) and Head and Neck Surgery (Dr Myers), University of Texas MD Anderson Cancer Center, Houston. Dr Zhou is now with Human Genome Sequencing Center, Baylor College of Medicine, Houston
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Ellsworth RE, Toro AL, Blackburn HL, Decewicz A, Deyarmin B, Mamula KA, Costantino NS, Hooke JA, Shriver CD, Ellsworth DL. Molecular Heterogeneity in Primary Breast Carcinomas and Axillary Lymph Node Metastases Assessed by Genomic Fingerprinting Analysis. CANCER GROWTH AND METASTASIS 2015; 8:15-24. [PMID: 26279627 PMCID: PMC4511091 DOI: 10.4137/cgm.s29490] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 06/16/2015] [Accepted: 06/17/2015] [Indexed: 01/06/2023]
Abstract
Molecular heterogeneity within primary breast carcinomas and among axillary lymph node (LN) metastases may impact diagnosis and confound treatment. In this study, we used short tandem repeated sequences to assess genomic heterogeneity and to determine hereditary relationships among primary tumor areas and regional metastases from 30 breast cancer patients. We found that primary carcinomas were genetically heterogeneous and sampling multiple areas was necessary to adequately assess genomic variability. LN metastases appeared to originate at different time periods during disease progression from different sites of the primary tumor and the extent of genomic divergence among regional metastases was associated with a less favorable patient outcome (P = 0.009). In conclusion, metastasis is a complex process influenced by primary tumor heterogeneity and variability in the timing of dissemination. Genomic variation in primary breast tumors and regional metastases may negatively impact clinical diagnostics and contribute to therapeutic resistance.
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Affiliation(s)
| | - Allyson L Toro
- Clinical Breast Care Project, Windber Research Institute, Windber, PA, USA
| | | | - Alisha Decewicz
- Clinical Breast Care Project, Windber Research Institute, Windber, PA, USA
| | - Brenda Deyarmin
- Clinical Breast Care Project, Windber Research Institute, Windber, PA, USA
| | - Kimberly A Mamula
- Clinical Breast Care Project, Windber Research Institute, Windber, PA, USA
| | | | - Jeffrey A Hooke
- Clinical Breast Care Project, Murtha Cancer Center, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Craig D Shriver
- Clinical Breast Care Project, Murtha Cancer Center, Walter Reed National Military Medical Center, Bethesda, MD, USA
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Park HR, Jung WW, Kim HS, Park YK. Microarray-based DNA methylation study of Ewing's sarcoma of the bone. Oncol Lett 2014; 8:1613-1617. [PMID: 25202378 PMCID: PMC4156184 DOI: 10.3892/ol.2014.2322] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 05/13/2014] [Indexed: 12/24/2022] Open
Abstract
Alterations in DNA methylation patterns are a hallmark of malignancy. However, the majority of epigenetic studies of Ewing’s sarcoma have focused on the analysis of only a few candidate genes. Comprehensive studies are thus lacking and are required. The aim of the present study was to identify novel methylation markers in Ewing’s sarcoma using microarray analysis. The current study reports the microarray-based DNA methylation study of 1,505 CpG sites of 807 cancer-related genes from 69 Ewing’s sarcoma samples. The Illumina GoldenGate Methylation Cancer Panel I microarray was used, and with the appropriate controls (n=14), a total of 92 hypermethylated genes were identified in the Ewing’s sarcoma samples. The majority of the hypermethylated genes were associated with cell adhesion, cell regulation, development and signal transduction. The overall methylation mean values were compared between patients who survived and those that did not. The overall methylation mean was significantly higher in the patients who did not survive (0.25±0.03) than in those who did (0.22±0.05) (P=0.0322). However, the overall methylation mean was not found to significantly correlate with age, gender or tumor location. GDF10, OSM, APC and HOXA11 were the most significant differentially-methylated genes, however, their methylation levels were not found to significantly correlate with the survival rate. The DNA methylation profile of Ewing’s sarcoma was characterized and 92 genes that were significantly hypermethylated were detected. A trend towards a more aggressive behavior was identified in the methylated group. The results of this study indicated that methylation may be significant in the development of Ewing’s sarcoma.
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Affiliation(s)
- Hye-Rim Park
- Department of Pathology, College of Medicine, Hallym University, Anyang, Gyeonggi 431-070, Republic of Korea
| | - Woon-Won Jung
- Department of Biomedical Laboratory Science, College of Health Science, Cheongju University, Cheongju, Chungbuk 360-764, Republic of Korea
| | - Hyun-Sook Kim
- Department of Biomedical Laboratory Science, College of Health Science, Korea University, Seoul 136-703, Republic of Korea
| | - Yong-Koo Park
- Department of Pathology, College of Medicine, Kyung Hee University, Seoul 130-702, Republic of Korea
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6
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BRAF V600E does not predict aggressive features of pediatric papillary thyroid carcinoma. Laryngoscope 2014; 124:E389-93. [DOI: 10.1002/lary.24668] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 02/24/2014] [Indexed: 11/07/2022]
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Holliday C, Rummel S, Hooke JA, Shriver CD, Ellsworth DL, Ellsworth RE. Genomic instability in the breast microenvironment? A critical evaluation of the evidence. Expert Rev Mol Diagn 2014; 9:667-78. [DOI: 10.1586/erm.09.55] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Rummel S, Valente AL, Kane JL, Shriver CD, Ellsworth RE. Genomic (in)stability of the breast tumor microenvironment. Mol Cancer Res 2012; 10:1526-31. [PMID: 23038813 DOI: 10.1158/1541-7786.mcr-12-0425] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The breast tumor microenvironment plays an active role in tumorigenesis. Molecular alterations have been identified in tumor-associated stroma; however, there is considerable debate as to whether the stroma is characterized by genomic instability or whether detection of chromosomal alterations reflects technological artifact rather than the true genomic content of the tumor microenvironment. Thus, breast stroma specimens from 112 women undergoing reductive mammoplasty (n = 7), prophylactic mastectomy (n = 6), or mastectomy for a breast disease (n = 99) were frozen in optimal cutting temperature medium. Allelic imbalance (AI) analysis was conducted using a panel of 52 microsatellite markers in 484 stromal specimens from 98 women, of which 92% had no detectable AI events. When compared with previously generated AI data from 77 formalin-fixed, paraffin-embedded (FFPE) stroma specimens, 42% of which harbored at least one detectable AI event, the frequency of AI in the FFPE specimens (4.62%) was significantly higher (P < 0.001) than that found in frozen specimens (0.45%). This comparison of AI between FFPE and research-grade specimens suggests that past reports of AI in breast stroma reflect artifact in the archival specimens caused by formalin-fixation, paraffin-embedding and tissue storage. Furthermore, SNP data were generated from a subset of 86 stromal specimens using SNP arrays and copy number alterations were identified using Partek Genomics Suite. For 95% of the specimens, no detectable copy number alterations were found and the 11 changes that were detected were small and not shared between specimens. These data, therefore, support a model in which the tumor microenvironment is genetically stable.
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Affiliation(s)
- Seth Rummel
- Clinical Breast Care Project, Henry M. Jackson Foundation for the Advancement of Military Medicine, Windber, PA 15963, USA
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Matos AJF, Baptista CS, Gärtner MF, Rutteman GR. Prognostic studies of canine and feline mammary tumours: the need for standardized procedures. Vet J 2012; 193:24-31. [PMID: 22296767 DOI: 10.1016/j.tvjl.2011.12.019] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Revised: 12/23/2011] [Accepted: 12/31/2011] [Indexed: 10/14/2022]
Abstract
For several years, veterinary oncologists have been struggling with the prognosis of mammary tumours in dogs and cats. Translation of tumour characteristics into prognostic information is an invaluable tool for the use of the most appropriate therapies, as well as for planning innovative therapeutic trials. Moreover, canine and feline spontaneous mammary gland tumours are good models for the study of human breast cancer. Collecting and interpreting information regarding the prognosis of canine and feline mammary tumours is difficult due to the fact that different methods have been applied to study various components and characteristics. This review identifies some of the challenges of prognostic studies of spontaneous canine and feline mammary tumours and suggests standardized procedures to overcome these challenges and facilitate reproducibility and assessment of results.
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Affiliation(s)
- A J F Matos
- Institute of Biomedical Sciences of Abel Salazar (ICBAS), University of Porto, Portugal.
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Campbell I, Qiu W, Haviv I. Genetic changes in tumour microenvironments. J Pathol 2011; 223:450-8. [PMID: 21294119 DOI: 10.1002/path.2842] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 12/05/2010] [Accepted: 12/08/2010] [Indexed: 12/21/2022]
Abstract
Numerous in vitro and in vivo studies have established that carcinoma-associated fibroblasts differ phenotypically from fibroblasts associated with normal tissue but the mechanisms underlying these differences are unclear. Since carcinoma-associated fibroblasts can be propagated in vitro for extended periods and still maintain their cancer-promoting phenotype, some investigators have proposed that they might have acquired somatic genetic alterations analogous to those observed in malignant epithelium. Early molecular genetic studies appeared to validate this hypothesis by demonstrating remarkably high frequencies of clonal somatic genetic alterations in carcinoma-associated fibroblasts, including loss of heterozygosity, gene amplification, and point mutations in tumour suppressor genes such as TP53 and PTEN. The initial excitement of these paradigm-changing studies overshadowed concerns that there may have been a more mundane explanation for these observations. In addition to the fact that the data would necessarily invoke an unlikely scenario of the simultaneous generation of two symbiotic malignancies, subsequent molecular genetic studies found no evidence of frequent genomic aberrations. One striking common trait of those studies reporting frequent clonal somatic alterations in carcinoma-associated fibroblasts is the use of tissues and techniques which are well known to be highly prone to generating artefacts such as limiting and poor quality DNA followed by highly multiplexed PCR-based analyses. It is now clear that clonal somatic mutations are not the biological basis of the cancer-promoting attributes of carcinoma-associated fibroblasts.
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Affiliation(s)
- Ian Campbell
- VBCRC Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia.
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High-efficiency genotype analysis from formalin-fixed, paraffin-embedded tumor tissues. THE PHARMACOGENOMICS JOURNAL 2010; 11:348-58. [PMID: 20548328 DOI: 10.1038/tpj.2010.50] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) can be assayed using DNA isolated from archival formalin-fixed, paraffin-embedded (FFPE) samples, making retrospective pharmacogenetic studies possible. In this study, we describe methods that significantly increase the number of SNP determinations possible using FFPE samples. Quantifying the amount of DNA amenable to PCR (amplification-quality DNA, AQ-DNA) allows a significant reduction in the amount of sample required for Taqman-based SNP assays. Optimizing AQ-DNA input increases PCR amplification efficiency and SNP determination accuracy. DNA was extracted from 39 FFPE tumor sections and matched tumor and stromal cores, which were of the type used to generate tissue microarrays. Sections and tumor cores yielded sufficient AQ-DNA for more than 1000 SNP determinations. Seven SNPs were assessed following individual assay optimization for minimal AQ-DNA. Genotypes from tumor cores for single SNPs were 92.3-100% concordant with those obtained from sections. Using these methods, the number of SNP genotypes that can be determined from single FFPE samples is greatly increased expanding the genetic association studies possible from limited archival specimens. The use of tumor cores is of particular importance as the harvesting of tumor cores has minimal impact on the utility of the donor blocks for other purposes.
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Lopez-Garcia MA, Geyer FC, Lacroix-Triki M, Marchió C, Reis-Filho JS. Breast cancer precursors revisited: molecular features and progression pathways. Histopathology 2010; 57:171-92. [PMID: 20500230 DOI: 10.1111/j.1365-2559.2010.03568.x] [Citation(s) in RCA: 215] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Increasingly more coherent data on the molecular characteristics of benign breast lesions and breast cancer precursors have led to the delineation of new multistep pathways of breast cancer progression through genotypic-phenotypic correlations. It has become apparent that oestrogen receptor (ER)-positive and -negative breast lesions are fundamentally distinct diseases. Within the ER-positive group, histological grade is strongly associated with the number and complexity of genetic abnormalities in breast cancer cells. Genomic analyses of high-grade ER-positive breast cancers have revealed that a substantial proportion of these tumours harbour the characteristic genetic aberrations found in low-grade ER-positive disease, suggesting that at least a subgroup of high-grade ER-positive breast cancers may originate from low-grade lesions. The ER-negative group is more complex and heterogeneous, comprising distinct molecular entities, including basal-like, HER2 and molecular apocrine lesions. Importantly, the type and pattern of genetic aberrations found in ER-negative cancers differ from those of ER-positive disease. Here, we review the available molecular data on breast cancer risk indicator and precursor lesions, the putative mechanisms of progression from in situ to invasive disease, and propose a revised model of breast cancer evolution based on the molecular characteristics of distinct subtypes of in situ and invasive breast cancers.
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Affiliation(s)
- Maria A Lopez-Garcia
- Molecular Pathology Team, The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, 237 Fulham Road, London, UK
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van Eijk R, van Puijenbroek M, Chhatta AR, Gupta N, Vossen RHAM, Lips EH, Cleton-Jansen AM, Morreau H, van Wezel T. Sensitive and specific KRAS somatic mutation analysis on whole-genome amplified DNA from archival tissues. J Mol Diagn 2009; 12:27-34. [PMID: 19959798 DOI: 10.2353/jmoldx.2010.090028] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Kirsten RAS (KRAS) is a small GTPase that plays a key role in Ras/mitogen-activated protein kinase signaling; somatic mutations in KRAS are frequently found in many cancers. The most common KRAS mutations result in a constitutively active protein. Accurate detection of KRAS mutations is pivotal to the molecular diagnosis of cancer and may guide proper treatment selection. Here, we describe a two-step KRAS mutation screening protocol that combines whole-genome amplification (WGA), high-resolution melting analysis (HRM) as a prescreen method for mutation carrying samples, and direct Sanger sequencing of DNA from formalin-fixed, paraffin-embedded (FFPE) tissue, from which limited amounts of DNA are available. We developed target-specific primers, thereby avoiding amplification of homologous KRAS sequences. The addition of herring sperm DNA facilitated WGA in DNA samples isolated from as few as 100 cells. KRAS mutation screening using high-resolution melting analysis on wgaDNA from formalin-fixed, paraffin-embedded tissue is highly sensitive and specific; additionally, this method is feasible for screening of clinical specimens, as illustrated by our analysis of pancreatic cancers. Furthermore, PCR on wgaDNA does not introduce genotypic changes, as opposed to unamplified genomic DNA. This method can, after validation, be applied to virtually any potentially mutated region in the genome.
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Affiliation(s)
- Ronald van Eijk
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
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Cradic KW, Milosevic D, Rosenberg AM, Erickson LA, McIver B, Grebe SKG. Mutant BRAF(T1799A) can be detected in the blood of papillary thyroid carcinoma patients and correlates with disease status. J Clin Endocrinol Metab 2009; 94:5001-9. [PMID: 19850689 DOI: 10.1210/jc.2009-1349] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
CONTEXT The BRAF(T1799A) transversion is the most frequent morphotype-specific somatic mutation in papillary thyroid carcinoma (PTC). The ability to detect this mutation in the circulation could aid in diagnosis and follow-up of PTC patients. OBJECTIVE Our objective was to develop and clinically validate a sensitive and specific assay for the detection of BRAF(T1799A) in blood samples from PTC patients. DESIGN We developed an allele-specific real-time PCR method for the detection of BRAF(T1799A) in blood samples and studied prospectively blood samples from 193 patients with thyroid cancer (173 PTC, 20 non-PTC) attending for routine follow-up. The results of molecular testing were correlated with disease status and thyroglobulin measurements. BRAF(T1799A) status of the original tumor samples was also confirmed, where available. RESULTS The assay had a detection sensitivity of fewer than one heterozygote BRAF(T1799A)-carrying cell per 100,000 diploid cells, without detectable cross-reactivity between wild-type BRAF and BRAF(T1799A). Circulating BRAF(T1799A) was detected in 20 of 173 PTC patients and in none of the 20 non-PTC patients. BRAF(T1799A)-positive samples contained between one in 326 and fewer than one in 100,000 copies of BRAF(T1799A). Tissue BRAF status correlated with blood BRAF status, whereas BRAF(T1799A) positivity in blood correlated with the presence of active disease at the time of the blood draw, with eight of the 38 PTC patients with persistent/recurrent disease being positive for circulating BRAF(T1799A) (relative risk vs. circulating BRAF(T1799A)-negative, 2.55; P < 0.04). CONCLUSIONS BRAF(T1799A) can be detected in the blood of PTC patients with residual or metastatic disease and may provide diagnostic information.
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Affiliation(s)
- Kendall W Cradic
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st Street SW, Rochester, Minnesota 55905, USA
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Campbell I, Polyak K, Haviv I. Clonal mutations in the cancer-associated fibroblasts: the case against genetic coevolution. Cancer Res 2009; 69:6765-8; discussion 6769. [PMID: 19706773 DOI: 10.1158/0008-5472.can-08-4253] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
It is well established that carcinoma-associated fibroblasts (CAFs) differ phenotypically from fibroblasts associated with normal tissue, but the mechanisms underlying these differences remain controversial. Because CAFs can be propagated in vitro for extended periods and still maintain their cancer promoting phenotype, it has been proposed that they might have acquired somatic genetic alterations analogous to those observed in malignant epithelium. Whereas some investigators have reported frequent and profound genomic alterations in CAFs, other groups have found no such evidence. One striking common trait of those studies reporting frequent clonal somatic alterations in CAFs is the use of tissues and techniques which are well known to be highly prone to generating artefacts, such as limiting and poor quality DNA followed by highly multiplexed PCR-based analysis. We conclude that reported frequent clonal somatic mutations in CAFs are likely to be artefacts and are not the biological basis of the cancer promoting attributes of CAFs. [corrected]
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Affiliation(s)
- Ian Campbell
- VBCRC Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia.
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Cheng L, MacLennan GT, Zhang S, Wang M, Zhou M, Tan PH, Foster S, Lopez-Beltran A, Montironi R. Evidence for Polyclonal Origin of Multifocal Clear Cell Renal Cell Carcinoma. Clin Cancer Res 2008; 14:8087-93. [DOI: 10.1158/1078-0432.ccr-08-1494] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Lee L, Johnston APR, Caruso F. Manipulating the salt and thermal stability of DNA multilayer films via oligonucleotide length. Biomacromolecules 2008; 9:3070-8. [PMID: 18826323 DOI: 10.1021/bm800593t] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA films are promising materials for diverse applications, including sensing, diagnostics, and drug/gene delivery. However, the ability to tune the stability of DNA films remains a crucial aspect for such applications. Herein, we examine the role of oligonucleotide length on the formation, and salt and thermal stability, of DNA multilayer films using oligonucleotides of homopolymeric diblocks (polyAG and polyTC), with each block (A, G, T, or C) ranging from 5 to 30 bases (10-, 20-, 30-, 40-, and 60-mer). Using a combination of quartz crystal microgravimetry, dual polarization interferometry, and flow cytometry, we demonstrate that at least 10 bases per hybridizing block in the DNA diblocks (that is, 20-mer) are required for successful hybridization and, hence, DNA multilayer film formation. Films assembled using longer oligonucleotide blocks were more stable in low salt conditions, with the DNA multilayer films assembled from the 60-mer oligonucleotides remaining intact in solutions of about 25 mM NaCl. A systematic increase in film melting temperature ( T m) was observed for the DNA multilayer films (assembled on colloids) with increasing oligonucleotide length, ranging from 38.5 degrees C for the 20-mer films to 53 degrees C for the 60-mer films. Further, an alternating trend in T m of the DNA multilayer films was observed with layer number (AG or TC); DNA multilayer films terminated with an AG layer exhibited a higher T m (44-49 degrees C) than films with an outermost TC layer (ca. 38 degrees C), suggesting a rearrangement of the film structure upon hybridization of the outermost layer. This work shows that the stability of DNA multilayer films can be tuned by varying the length of the oligonucleotide building blocks, thus providing a versatile means to tailor the salt and thermal stability of DNA films, which is necessary for the application of such films.
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Affiliation(s)
- Lillian Lee
- Centre for Nanoscience and Nanotechnology, Department of Chemical and Biomolecular Engineering, The University of Melbourne, Victoria 3010, Australia
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Jovanovic L, Delahunt B, McIver B, Eberhardt NL, Grebe SKG. Most multifocal papillary thyroid carcinomas acquire genetic and morphotype diversity through subclonal evolution following the intra-glandular spread of the initial neoplastic clone. J Pathol 2008; 215:145-54. [DOI: 10.1002/path.2342] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Müller I, Beeger C, Alix-Panabières C, Rebillard X, Pantel K, Schwarzenbach H. Identification of loss of heterozygosity on circulating free DNA in peripheral blood of prostate cancer patients: potential and technical improvements. Clin Chem 2008; 54:688-96. [PMID: 18281424 DOI: 10.1373/clinchem.2007.099333] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
BACKGROUND Accurate identification of loss of heterozygosity (LOH) on circulating free DNA is often restricted by technical limitations such as poor quality and quantity of tumor-specific DNA and contamination by normal DNA. However, plasma DNA may harbor tumor-specific genetic alterations and could therefore be an interesting target for noninvasive examinations of tumor DNA. METHODS By PCR-based fluorescence microsatellite analysis using 12 polymorphic markers, we investigated LOH on cell-free DNA in blood plasma from 59 patients with localized prostate cancer (PCa) and 12 with metastatic disease (MPCa). In addition, plasma DNA from 21 PCa patients was fractionated into high- and low-molecular-weight DNA by 2 different column systems. To avoid appearance of artificial allelic loss and stabilize the amplification, TMAC (tetramethylammonium chloride) was added to each PCR. RESULTS Overall incidences of LOH at all markers analyzed were 10% in PCa and 12% in MPCa samples. Highest frequencies were found at markers D11S898 (28%) in PCa and D6S1631 (27%) in MPCa. Statistical evaluation showed significant associations between LOH and increasing Gleason scores for the marker combinations D6S1631*D8S286*D9S171 (P = 0.03) and D8S286*D9S171 (P = 0.05). Fractionation of plasma DNA resulted in a higher overall LOH frequency in the low-molecular-weight DNA fraction (23%) compared with the high-molecular-weight DNA (7%). CONCLUSIONS LOH analysis of circulating DNA can provide tumor-specific genetic information on PCa patients. Fractionation of plasma DNA and addition of TMAC improved LOH detection and general assay performance.
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Affiliation(s)
- Imke Müller
- Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, Germany
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Turrina S, Atzei R, Filippini G, De Leo D. STR typing of archival Bouin's fluid-fixed paraffin-embedded tissue using new sensitive redesigned primers for three STR loci (CSF1P0, D8S1179 and D13S317). J Forensic Leg Med 2007; 15:27-31. [PMID: 17239646 DOI: 10.1016/j.jcfm.2006.10.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2005] [Revised: 10/26/2006] [Accepted: 10/30/2006] [Indexed: 11/18/2022]
Abstract
Three new mini-STR primer sets are suggested for three conventional STRs, CSF1P0, D8S1179 and D13S317, included in multiplex PCR kits commercially available and commonly used for DNA typing in forensic applications. The primer pairs for the three loci were redesigned in order to reduce or eliminate the flanking regions of the polymorphism obtaining amplification products, which have dimensions less than 120bp in size. A comparison of results for typing carried out with the newly designed primers on DNA extracted from 100 blood samples provided by healthy donors, previously typed with conventional STRs, showed no genotype difference underlining their precision and reproducibility. The forensic usefulness of the new mini-STR primers was evaluated on highly degraded DNA from casework samples (e.g. archival post-mortem Bouin's fluid-fixed paraffin-embedded tissue specimens) for which commercial STR kit had proven inefficient.
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Affiliation(s)
- Stefania Turrina
- Department of Medicine and Public Health, Institute of Legal Medicine, Forensic Genetic Laboratory, University of Verona, 37134 Verona, Italy
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Rübben A, Bausch B, Nikkels A. Somatic deletion of the NF1 gene in a neurofibromatosis type 1-associated malignant melanoma demonstrated by digital PCR. Mol Cancer 2006; 5:36. [PMID: 16961930 PMCID: PMC1570477 DOI: 10.1186/1476-4598-5-36] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2006] [Accepted: 09/10/2006] [Indexed: 11/16/2022] Open
Abstract
Background Neurofibromatosis type 1 (NF1) is the most common hereditary neurocutaneous disorder and it is associated with an elevated risk for malignant tumors of tissues derived from neural crest cells. The NF1 gene is considered a tumor suppressor gene and inactivation of both copies can be found in NF1-associated benign and malignant tumors. Melanocytes also derive from neural crest cells but melanoma incidence is not markedly elevated in NF1. In this study we could analyze a typical superficial spreading melanoma of a 15-year-old boy with NF1 for loss of heterozygosity (LOH) within the NF1 gene. Neurofibromatosis in this patient was transmitted by the boy's farther who carried the mutation NF1 c. 5546 G/A. Results Melanoma cells were isolated from formalin-fixed tissue by liquid coverslip laser microdissection. In order to obtain statistically significant LOH data, digital PCR was performed at the intragenic microsatellite IVS27AC28 with DNA of approx. 3500 melanoma cells. Digital PCR detected 23 paternal alleles and one maternal allele. Statistical analysis by SPRT confirmed significance of the maternal allele loss. Conclusion To our knowledge, this is the first molecular evidence of inactivation of both copies of the NF1 gene in a typical superficial spreading melanoma of a patient with NF1. The classical double-hit inactivation of the NF1 gene suggests that the NF1 genetic background promoted melanoma genesis in this patient.
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Affiliation(s)
- Albert Rübben
- Department of Dermatology, University Hospital RWTH Aachen, Pauwelsstrasse 30, D-52074 Aachen, Germany
| | - Birke Bausch
- Department of Nephrology, Albert-Ludwigs-University, Hugstetter Str. 55, D-79106 Freiburg, Germany
| | - Arjen Nikkels
- Department of Dermatopathology, University Medical Center, Sart Tilman, B-4000 Liège, Belgium
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Mojica WD, Rapkiewicz AV, Liotta LA, Espina V. Manual exfoliation of fresh tissue obviates the need for frozen sections for molecular profiling. Cancer 2006; 105:483-91. [PMID: 16015639 DOI: 10.1002/cncr.21347] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Simple, rapid tissue processing that preserves macromolecules will enhance translational research capabilities. Traditional fixative-based approaches for specimen preservation are ideal for histologic evaluation but are not conducive to molecular studies of nucleic acids and protein. Tissue cryosections preserve macromolecule integrity, but the process is labor intensive and technically challenging. To the authors' knowledge to date, an alternative method capable of retrieving cells while providing adequate histologic detail yet preserving macromolecule integrity has been lacking. In the current study, the authors evaluated the utility of using manual exfoliation of clinical tissue samples as a means of obtaining cells for molecular analysis. This technique possesses the advantages of fixed and frozen tissue sections without their drawbacks. This simple, rapid, nonfixative based technique is capable of preparing cells from human clinical material for further isolation without compromising the preservation of macromolecules in the tissue. METHODS Cells from a variety of clinical resection specimens from solid tumors were directly scraped from the tissue samples using the edge of a glass microscope slide and smeared onto another slide for cytologic evaluation. The manually exfoliated cells were evaluated microscopically for cytologic quality and cellular quantity. Pure cell populations were procured by laser capture microdissection (LCM) with subsequent extraction of nucleic acids and proteins. The integrity and suitability of the recovered nucleic acids and proteins for molecular analysis were evaluated using the polymerase chain reaction (PCR), reverse transcriptase-PCR, and reverse-phase protein microarray, respectively. RESULTS Manual exfoliation permits the selection of homogeneous cell populations by LCM based on well established cytologic characteristics. DNA and mRNA, of comparable quality to frozen sections, can be amplified from the manual exfoliation cells. Proteins of similar quality can be recovered using this technique and quantitated via reverse-phase protein microarray. CONCLUSIONS Molecular macromolecules of high quality and sufficient quantity can be retrieved from human clinical samples using manual exfoliation and LCM to procure specific cell populations. The manual exfoliation technique does not destroy the original tissue source, thereby allowing subsequent formalin tissue fixation. The technique of manual exfoliation in conjunction with LCM can enable the molecular profiling of a sampled selected cell population. Because it does not destroy the original tissue, histologic correlation can be combined with molecular profiling.
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Affiliation(s)
- Wilfrido D Mojica
- Department of Pathology, University at Buffalo, State University of New York, Buffalo, New York 14203, USA.
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Erill N, Colomer A, Calvo M, Vidal A, Román R, Verdú M, Cordón-Cardó C, Puig X. A novel multiplexing, polymerase chain reaction-based assay for the analysis of chromosome 18q status in colorectal cancer. J Mol Diagn 2005; 7:478-85. [PMID: 16237217 PMCID: PMC1888490 DOI: 10.1016/s1525-1578(10)60578-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Chromosome 18q allelic loss has been reported to have prognostic significance in stage II colorectal carcinoma. We have developed a fluorescent multiplex polymerase chain reaction assay to analyze five microsatellite markers (D18S55, D18S58, D18S61, D18S64, and D18S69) for allelic loss at the long arm of chromosome 18. Amplicon detection and evaluation was accomplished by capillary electrophoresis using an ABI 310 genetic analyzer. Robustness of the assay when performed on DNA extracted from formalin-fixed, paraffin-embedded tissue sections was confirmed by analyzing its repeatability and reproducibility. Allelic loss was assessed in 61 stage II colorectal tumors and was detected in 58% (31 of 53) of tumors not showing instability. As part of the study, results of 207 previous polymerase chain reaction/polyacrylamide-based assays were re-evaluated by two independent observers to determine the degree of concordance of visual evaluation. In the case of stage II colorectal tumors, when electropherogram results were compared with those obtained from visual evaluation of the same markers after polyacrylamide gel electrophoresis, discrepancies between observers were detected in 16.4% of determinations. In conclusion, we have developed a robust and reliable assay for multiplexed loss of heterozygosity determination that improves assessment of chromosome 18q allelic loss in colorectal tumors processed as routine formalin-fixed, paraffin-embedded specimens.
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Akbari M, Hansen MD, Halgunset J, Skorpen F, Krokan HE. Low copy number DNA template can render polymerase chain reaction error prone in a sequence-dependent manner. J Mol Diagn 2005; 7:36-9. [PMID: 15681472 PMCID: PMC1867510 DOI: 10.1016/s1525-1578(10)60006-2] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Paraffin-embedded tissue is an important source of material for molecular pathology and genetic investigations. We used DNA isolated from microdissected formalin-fixed, paraffin-embedded gastric tumors for mutation analysis of a region of the human gene for uracil-DNA glycosylase (UNG), encoding the UNG catalytic domain, and detected apparent base substitutions which, after further investigation, proved to be polymerase chain reaction (PCR) artifacts. We demonstrate that low DNA template input in PCR can generate false mutations, mainly guanine to adenine transitions, in a sequence-dependent manner. One such mutation is identical to a mutation previously reported in the UNG gene in human glioma. This phenomenon was not caused by microheterogeneity in the sample material because the same artifact was seen after amplification of a homogenous, diluted plasmid. We did not observe genuine mutations in the UNG gene in 16 samples. Our results demonstrate that caution should be taken when interpreting data from PCR-based analysis of somatic mutations using low amounts of template DNA, and that methods used to enrich putative subpopulations of mutant molecules in a sample material could, in essence, be a further amplification of sequence-dependent PCR-generated artifacts.
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Affiliation(s)
- Mansour Akbari
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, N-7489 Trondheim, Norway
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Jaremko M, Justenhoven C, Abraham BK, Schroth W, Fritz P, Brod S, Vollmert C, Illig T, Brauch H. MALDI-TOF MS and TaqMan® assisted SNP genotyping of DNA isolated from formalin-fixed and paraffin-embedded tissues (FFPET). Hum Mutat 2005; 25:232-8. [PMID: 15706592 DOI: 10.1002/humu.20141] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Formalin-fixed paraffin-embedded tissues (FFPET) from archived clinical samples provide an invaluable source for large-scale molecular genetic studies. Pharmacogenetic investigations that require long-term clinical follow-up data of patients may particularly benefit from FFPET analysis. Matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and TaqMan-based (Thermus aquaticus polymerase) methodologies have become standard genotyping procedures. However, no data are available on the applicability of MALDI-TOF MS to the genotyping of low quality DNA, as it is usually obtained from FFPET, and data from TaqMan genotyping are limited. We isolated constitutional DNA from 274 FFPET samples (229 patients with breast cancer and 45 patients with benign breast diseases) and genotyped 15 polymorphic loci in 10 genes. Nine SNPs were genotyped by MALDI-TOF MS, and six were genotyped by the TaqMan methodology. We established rates for successful allele assignment for all FFPET, for FFPET prepared prior to 1990, and for FFPET prepared post-1990. Both methodologies showed high success rates ranging between 70.9 and 99.6% (mean: 91.8%) for MALDI-TOF MS and between 82.3 and 97.7% (mean: 91.0%) for TaqMan genotyping. No significant differences in genotyping performances for FFPET prepared prior to 1990 or post-1990 were observed. With the exception of one, all other genotype frequencies were in Hardy-Weinberg equilibrium. Furthermore, genotype frequencies matched those observed in a German breast cancer population and other Caucasian populations. Our study shows for the first time that MALDI-TOF MS and TaqMan genotyping procedures provide reliable data, and are therefore applicable in studies that require large scale FFPET genotyping.
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Affiliation(s)
- Malgorzata Jaremko
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
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Beetz C, Hartmann A, Kiehntopf M, Wölfl S, Kalff R, Deufel T, Patt S. Rapid generation of detailed loss of heterozygosity profiles for routine diagnosis of gliomas. Clin Chem Lab Med 2004; 42:595-601. [PMID: 15259374 DOI: 10.1515/cclm.2004.103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Aberrations in the genomes of gliomas seem to correlate well with clinical parameters. Pertinent studies, however, rely on highly sophisticated methods, they require large amounts of high-quality sample material and/or they demand profound analytical expertise. Consequently, molecular tumour analysis has not yet been widely implemented in routine laboratory applications. We have developed an easy-to-perform approach for the rapid derivation of a detailed loss-of-heterozygosity profile from individual gliomas. DNA of PCR quality is extracted in a one-step procedure from routinely obtained material. A microsatellite-based marker set is used to detect the deletion status of genomic regions (i) with established diagnostic relevance, (ii) recurrently found deleted in gliomas, or (iii) generally associated with tumour suppressor activity. The complete profile comprises 25 regions and is generated from 64 markers multiplexed into 18 reactions. Illustratively, we present findings from an anaplastic oligodendroglioma; the molecular data for this tumour allow refined diagnostic and prognostic statements that could not be derived from histology alone. Our approach should prove useful in the routine diagnosis of gliomas. Simultaneously, research data for many highly relevant regions are generated in a comparatively simple and inexpensive way.
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Affiliation(s)
- Christian Beetz
- Institut für Pathologie, Klinikum der Friedrich-Schiller-Universität Jena, Jena, Germany
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Abstract
OBJECTIVE/HYPOTHESIS This study was designed to investigate the hypothesis that Meniere's disease is associated with herpes simplex virus (HSV) reactivation in the vestibular ganglion. STUDY DESIGN Case control study. METHODS Vestibular ganglia were obtained from archival surgical pathology specimens from patients undergoing vestibular neurectomy for vertigo caused by Meniere's disease. All patients met criteria for classification as definite Meniere's disease according to American Academy of Otolaryngology/Head and Neck Surgery (AAO-HNS) criteria. Control specimens were obtained from willed body donors. Sections from each ganglion were studied for prevalence of viral DNA using a nested polymerase chain reaction designed to amplify the HSV DNA polymerase gene. Quantitative analysis determined the number of viral copies per standard unit of ganglionic DNA. RESULTS HSV DNA was more prevalent in paraffin embedded ganglia from patients with Meniere's disease (100%) than in fresh-frozen control ganglia (81%) (P =.02). Fixation and paraffin embedding substantially reduced recovery of HSV virus in selected control specimens. Quantitative analysis found no correlation between viral copy number in control ganglia processed frozen versus formalin fixed and paraffin embedded. CONCLUSIONS HSV is more commonly isolated from vestibular ganglia of patients with Meniere's disease than the general population. The routine histologic preparation of formalin fixation and paraffin embedding significantly altered the quantity of virus detected though not in a predictable manner. The study provides supportive evidence for a viral etiology in Meniere's disease.
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Affiliation(s)
- Jeffrey T Vrabec
- Bobby R Alford Department of Otorhinolaryngology and Communicative Sciences, Baylor College of Medicine, Houston, Texas, USA.
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