Single-Tube Protocol for the Extraction of DNA or RNA from Paraffin-Embedded Tissues Using a Starch-Based Adhesive

Turbett, Gavin R.; Barnett, Timothy C.; Dillon, Elizabeth K.; Sellner, Loryn N.

doi:10.2144/96205st04

Cited by 34 publications

(19 citation statements)

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“…Precise dissection of areas containing the highest tumor cell density in the tissue section was possible using the method of Turbett et al (1996), in which the areas of interest are covered with a starch-based glue, peeled off, and submitted for DNA extraction. The yield and specificity of the multiplex PCR reactions were increased by diluting the forward primers relative to the reverse primers (Berg et al, 2000).…”

Section: Discussionmentioning

confidence: 99%

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Molecular Diagnosis of Oligodendroglioma in Paraffin Sections

Hatanpaa

Burger

Eshleman

et al. 2003

Laboratory Investigation

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SUMMARY:Distinction of oligodendrogliomas from other gliomas is clinically important, but the histologic diagnosis of oligodendroglioma has been a difficult and notoriously subjective task. Testing for loss of heterozygosity (LOH) on chromosomal arms 1p and 19q, the genetic signature of oligodendroglioma, has emerged as a useful, objective adjunct to the traditional histologic evaluation. However, LOH testing of glioma specimens has not yet been widely implemented, presumably because of a lack of a practical LOH assay. We describe a 1p and 19q LOH assay suitable for routine diagnostics. In contrast to traditional microsatellite-based LOH analysis, we show that detection of LOH is usually possible even without normal tissue or blood from the same patient. A small area of tumor on a single paraffin section is sufficient for the assay. The assay protocol consists of a one-step DNA extraction, multiplex PCR for microsatellites on 1p and 19q, and capillary electrophoresis of the PCR products. LOH is detected by analysis of the allelic patterns and by integration of data from multiple highly polymorphic microsatellites. In a validation study on 19 gliomas, the results were concordant with results obtained by established methods and correlated well with histologic diagnoses. Because only a paraffin section is required, the pathologist can perform both the traditional histopathologic evaluation and this supporting molecular assay from the material at hand. (Lab Invest 2003, 83:419 -428).

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Section: Discussionmentioning

confidence: 99%

“…The slide was then air dried for 5 to 10 minutes while protected from dust. The dissection and DNA extraction were performed as follows, according to the method of Turbett et al (1996), with small modifications. The HE slide (or its photocopy) served as a guide for dissection.…”

Section: Dissection Of Tissue and Extraction Of Dnamentioning

confidence: 99%

Molecular Diagnosis of Oligodendroglioma in Paraffin Sections

Hatanpaa

Burger

Eshleman

et al. 2003

Laboratory Investigation

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“…19 A 5-m section, cut from paraffin-embedded tissue, was stained with hematoxylin-eosin (HE). The next two 10-m sections were stained with eosin only.…”

Section: Microdissection and Dna Preparationmentioning

confidence: 99%

An early lesion in hepatic carcinogenesis: Loss of heterozygosity in human cirrhotic livers and dysplastic nodules at the 1p36-p34 region

et al. 2001

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Loss of heterozygosity (LOH) of chromosome 1 has been suggested, by karyotyping, to be an initial episode in human hepatocarcinogenesis. However, this alteration has not yet been investigated in cirrhotic nodules (CNs) or dysplastic nodules (DNs). In an initial study from explanted or resected cirrhotic livers, LOH in 1p36-p32 was examined in 31 hepatocellular carcinomas (HCCs), 25 low-grade dysplastic nodules (LGDNs), and 24 high-grade dysplastic nodules (HGDNs). In HCCs, LOH was detected most frequently at loci D1S2843 (1p36.1) (28.6%), D1S513 (1p34.3) (29.2%), and MYCL1 (1p34.1) (28.6%). In HGDN and LGDN, LOH incidences at D1S513 were 11.1% and 13.6%, respectively. To further refine those results and to determine sequential relationships among CN, DN, and HCC, LOH was next studied in an additional 53 HCCs, 56 HGDNs, 30 LGDNs, and 215 CNs from 11 explanted human cirrhotic livers, including 30 "nodule-in-nodule" lesions. Seven markers between D1S2843 (1p36.12) and MYCL1 (1p34.1), and 1 each at D1S484 (1q24.1), IGF2R-3 (6q26), and TP53 (17p13.1) were used. LOH at D1S2843 and D1S513 was detected in HCCs (20.4% and 23.5%, respectively), HGDNs (7.7% and 18.5%), LGDNs (13.6% and 6.9%), and CNs surrounding either HCCs or DNs (7.4% and 8.3%). These results demonstrate that LOH at D1S2843 and D1S513 are early events in human liver carcinogenesis. Because 85% or more of hepatocellular carcinoma (HCC) occur in cirrhotic livers in Western patients, 1 it is possible that certain cirrhotic nodules (CNs) could become preneoplastic. This could be followed, putatively, by the appearance of dysplastic nodules (DNs) and HCCs. A body of evidence resulting from histology 2 and imaging modalities 3 has, over the past decade, documented the relationship between the dysplastic nodular lesions seen mostly in cirrhotic livers and HCC. [2][3][4] DNs have been classified as low-grade (LGDN) and highgrade (HGDN) according to the criteria proposed by the International Working Party. 5 LGDNs have mild atypia, while HGDNs have one or more of the following: high nuclearcytoplasmic ratio, nuclear hyperchromasia, irregular nuclear contour, plates more than 2 cells wide, pseudoglandular formation, cytoplasmic basophilia, and resistance to iron accumulation. 5 However, the molecular mechanisms implicated in this progression remain unknown. Because of the lack of markers for early genetic changes, the only direct evidence at the molecular level for a DN3 HCC sequence has come from the integrated pattern of hepatitis B virus (HBV) DNA of a HCC located within an HGDN (a so-called "nodule-in-nodule" lesion) in a cirrhotic liver. 6 In this study, the HGDN and HCC were from an identical clone. Examination of the mechanisms of transformation of DN would be more feasible if other early molecular markers were to be found.

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“…In total, 164 specimens from 120 patients were analysed. All DNA was extracted from the paraffin-embedded tissues by methods described elsewhere (Turbett et al, 1996). Normal tissue and either two or three lesional types from the same patient were obtained in 26 cases.…”

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confidence: 99%

Microsatellite instability and loss of heterozygosity in mammary carcinoma and its probable precursors

Dillon

Boer²,

Papadimitriou³

et al. 1997

Br J Cancer

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Summary Microsatellite instability is a form of genetic damage that may be due to defective mismatch repair genes and may be a marker of processes leading to malignancy. We have analysed a series of epithelial hyperplasia of usual type, carcinomas in situ and invasive and metastatic carcinomas from the mammary gland on the assumption that they represent stages in the evolution of mammary carcinoma. Eight markers on chromosomes 3p, 4q, 9p, 11p, 14q, 17p, 17q and Xq were examined for microsatellite instability and loss of heterozygosity. High rates of loss on chromosomes 17p, 17q and Xq indicate that these chromosomal arms contain genes important in mammary carcinogenesis. The rate of microsatellite instability observed in this study was uniformly low, irrespective of the lesion. This implies that microsatellite instability is not a marker of malignancy in most instances of mammary neoplasia.

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Single-Tube Protocol for the Extraction of DNA or RNA from Paraffin-Embedded Tissues Using a Starch-Based Adhesive

Cited by 34 publications

References 0 publications

Molecular Diagnosis of Oligodendroglioma in Paraffin Sections

Molecular Diagnosis of Oligodendroglioma in Paraffin Sections

An early lesion in hepatic carcinogenesis: Loss of heterozygosity in human cirrhotic livers and dysplastic nodules at the 1p36-p34 region

Microsatellite instability and loss of heterozygosity in mammary carcinoma and its probable precursors

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