TY - JOUR
T1 - Taqman genotyping assays can be used on decalcified and paraffin-embedded tissue from patients with osteosarcoma
AU - Hagleitner, Melanie M.
AU - Coenen, Marieke J.H.
AU - Jeuken, Judith W.M.
AU - Flucke, Uta
AU - Schreuder, H. W.Bart
AU - te Loo, D. Maroeska W.M.
AU - Hoogerbrugge, Peter M.
PY - 2011/1
Y1 - 2011/1
N2 - 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® 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.
AB - 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® 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.
KW - Decalcified formalin-fixed tissue
KW - Osteosarcoma
KW - Single nucleotide polymorphisms
UR - http://www.scopus.com/inward/record.url?scp=78649684167&partnerID=8YFLogxK
U2 - 10.1002/pbc.22654
DO - 10.1002/pbc.22654
M3 - Article
C2 - 20848662
AN - SCOPUS:78649684167
SN - 1545-5009
VL - 56
SP - 35
EP - 38
JO - Pediatric Blood and Cancer
JF - Pediatric Blood and Cancer
IS - 1
ER -