High-resolution copy number analysis of paraffin-embedded archival tissue using SNP BeadArrays.
Author(s): Oosting J, Lips EH, van Eijk R, Eilers PH, Szuhai K, Wijmenga C, Morreau H, van Wezel T
Publication: Genome Res, 2007, Vol. 17, Page 368-76
PubMed ID: 17267813 PubMed Review Paper? No
Purpose of Paper
Conclusion of Paper
Studies
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Study Purpose
The purpose of this study was to determine the effects of using FFPE instead of frozen colorectal tumors and normal adjacent specimens on copy number determination by aCGH and to compare the results obtained between three array types. DNA was extracted from sections of frozen specimens using the genomic Wizard kit and from 0.6 mm punches of FFPE tissue using Chelex-100 and cleaned up with the Wizard kit.
Summary of Findings:
All three platforms slightly overestimated the copy number for normal specimens, and copy numbers for regions with a gain were slightly higher while those with a loss were slightly lower when determined by GeneChip rather than with BAC arrays or BeadArrays. The CNV was comparable between frozen and FFPE specimens using BAC and BeadArrays, but the correlation between frozen and FFPE specimens was 0.85 which was lower than the correlations between arrays (r=0.93-0.95) or between replicates with different intensity (r=0.92). However, exclusion of one specimen increased the correlation between FFPE and frozen specimens using BeadArrays to 0.96. The authors report the BeadArrays allowed for detection of LOH by physical loss as well as copy neutral LOH.
Biospecimens
Preservative Types
- Formalin
- Frozen
Diagnoses:
- Neoplastic - Carcinoma
- Neoplastic - Normal Adjacent
- Neoplastic - Benign
Platform:
Analyte Technology Platform DNA Array CGH DNA DNA microarray Pre-analytical Factors:
Classification Pre-analytical Factor Value(s) Biospecimen Preservation Type of fixation/preservation Formalin (buffered)
Frozen
Array CGH Specific Type of array Illumina Sentrix Beadarray
Affymetrix 10 K Xba1 2.0 array
Custom BAC array