Reliable high-throughput genotyping and loss-of-heterozygosity detection in formalin-fixed,paraffin-embedded (FFPE) tumors using single nucleotide polymorphism arrays.
Author(s): Lips Esther H, Dierrsen Jan WF, van Eijk Ronald, Oosting Jan, Eilers Paul HC, Tollenaar Rob AEM, de Graaf Eelco J, van't Slot Ruben, Wijmenga Cisca, Morreau Hans, van Wenzel Tom
Publication: Cancer Res, 2005, Vol. 22, Page 10188
PubMed ID: 16288005 PubMed Review Paper? No
Purpose of Paper
Conclusion of Paper
Studies
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Study Purpose
To determine if genomic DNA isolated from FFPE tissue is applicable for genotype and LOH analysis via SNP arrays (BeadArray and GeneChip).
Summary of Findings:
The occurrence of SNPs in FFPE and frozen matched controls were nearly identical (99.9%). Of the 8 LOH regions examined only 2 were not identical among FFPE and frozen specimens (located on chromosomes 3 and 8). Genotyping results were identical among the two SNP arrays (BeadArray and GeneChip).
Biospecimens
Preservative Types
- Formalin
- Frozen
Diagnoses:
- Neoplastic - Carcinoma
- Normal
Platform:
Analyte Technology Platform DNA SNP assay Pre-analytical Factors:
Classification Pre-analytical Factor Value(s) Biospecimen Preservation Type of fixation/preservation Formalin (buffered)
Snap frozen
SNP assay Specific Detection method GeneChip
BeadArray
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Study Purpose
To validate results obtained by SNP analyses via DNA sequencing.
Summary of Findings:
DNA sequence analysis confirmed SNP results.
Biospecimens
Preservative Types
- Formalin
- Frozen
Diagnoses:
- Neoplastic - Carcinoma
- Normal
Platform:
Analyte Technology Platform DNA DNA sequencing Pre-analytical Factors:
Classification Pre-analytical Factor Value(s) Biospecimen Preservation Type of fixation/preservation Formalin (buffered)
Snap frozen