Taqman genotyping assays can be used on decalcified and paraffin-embedded tissue from patients with osteosarcoma

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Publication year
2011Source
Pediatric Blood & Cancer, 56, 1, (2011), pp. 35-8ISSN
Publication type
Article / Letter to editor

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Organization
Paediatrics - OUD tm 2017
Laboratory of Genetic, Endocrine and Metabolic Diseases
Human Genetics
Pathology
Orthopaedics
Journal title
Pediatric Blood & Cancer
Volume
vol. 56
Issue
iss. 1
Page start
p. 35
Page end
p. 8
Subject
IGMD 3: Genomic disorders and inherited multi-system disorders NCEBP 1: Molecular epidemiology; ONCOL 2: Age-related aspects of cancer; ONCOL 2: Age-related aspects of cancer NCMLS 2: Immune Regulation; ONCOL 3: Translational research; ONCOL 4: Quality of CareAbstract
BACKGROUND: In cancers like osteosarcoma with a 5-year overall survival of 50-60%, archived histological specimens can be a useful source of biological material. However, this material generally has been decalcified and formalin-fixed for many years. In our study, we investigated whether DNA obtained from these tissues can be used for reliable single nucleotide polymorphism (SNP) genotyping. PROCEDURE: We studied two SNPs in the drug transporter MDR1 using Taqman(R) SNP genotyping assays. Genotypes of the germ line DNA derived from freshly isolated DNA of 20 surviving patients with osteosarcoma were compared with genotypes obtained from archived material from decalcified formalin-fixed, paraffin-embedded (FFPE) blocks of the same patients. RESULTS: Decalcified FFPE-derived DNA yielded smaller PCR fragments compared to DNA extracted from peripheral blood cells, with a reliable size of approximately 200 bp. However, we were able to evaluate each SNP in 19 of 20 cases included in this study. All successfully genotyped samples showed 100% concordance between genotypes obtained from DNA of FFPE tissue and the genotypes obtained from DNA of blood from the same patients. CONCLUSIONS: In conclusion, we have demonstrated that decalcified FFPE tissue can be used for genetic polymorphism analysis using Taqman(R) allelic discrimination assays. This forms a unique opportunity to combine new insights in genetic research with historical patient cohorts.
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- Academic publications [227727]
- Electronic publications [107311]
- Faculty of Medical Sciences [86204]
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