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


METHODS
We studied two SNPs in the drug transporter MDR1 using Taqman® 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 ∼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® allelic discrimination assays. This forms a unique opportunity to combine new insights in genetic research with historical patient cohorts.
Hagleitner
Melanie M
MM
Department of Pediatric Hematology and Oncology, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands. mm.hagleitner@cukz.umcn.nl
Coenen
Marieke J H
MJ
Jeuken
Judith W M
JW
Flucke
Uta
U
Schreuder
H W Bart
HW
te Loo
D Maroeska W M
DM
Hoogerbrugge
Peter M
PM
D004252:DNA Mutational Analysis / Q000379:methods*; D004273:DNA, Neoplasm / Q000235:genetics; D005838:Genotype; D006801:Humans; D008722:Methods; D012516:Osteosarcoma / Q000235:genetics* / Q000473:pathology; D016612:Paraffin Embedding; D020641:Polymorphism, Single Nucleotide; D016707:Tissue Fixation
D004273:DNA, Neoplasm