Exploring allelic imbalance within paraffin-embedded tumor biopsies using pyrosequencing technology
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Manuel Hidalgo Pascual
Abstract
Background: The comparison of molecular genetic changes in healthy and pathological tissues has historically led to the identification of oncogenes and tumor suppressor genes. It is very common that studies investigating loss of heterozygosity are carried out retrospectively on paraffin-embedded samples.
Methods: In this study, we evaluated the power of pyrosequencing for determining the loss of heterozygotic regions. The present method uses the fact that pyrosequencing is an accurate, sensitive and reproducible technique. The method is also simple to perform, with results available in 96-well format, making the assays amenable to automation. Thus, we analyzed nine single nucleotide polymorphisms along 1Mb between the EMSY and PAK1 genes on 11q13, a region frequently rearranged in different tumors and cell lines. We assessed the study using samples from breast cancer and thyroid cancer biopsies.
Results and conclusions: We conclude that this technique is capable of detecting variations of >10% in allele loss. However, strong allele imbalances were detected, depending on the origin of the sample. Seven out of the nine markers used exhibited differential allele amplification, depending on the DNA quality (p<0.01).
Clin Chem Lab Med 2006;44:1076–81.
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©2006 by Walter de Gruyter Berlin New York
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- Hereditary hyper-ACE-emia due to the Pro1199Leu mutation of somatic ACE as a potential pitfall in diagnosis: a first family outside Europe
- Molecular assay for detection of the common carnitine palmitoyltransferase 1A 1436(C>T) mutation
- Serum cytokine levels and the expression of estrogen and progesterone receptors in breast cancer patients
- Protein Z levels and prognosis in patients with acute coronary syndromes
- Determination of total bilirubin in whole blood from neonates: results from a French multicenter study
- Analysis of protein S-100B in serum: a methodological study
- Lipid peroxidation and homocysteine levels in Behçet's disease
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