High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays.
Author(s): Wang Y, Carlton VE, Karlin-Neumann G, Sapolsky R, Zhang L, Moorhead M, Wang ZC, Richardson AL, Warren R, Walther A, Bondy M, Sahin A, Krahe R, Tuna M, Thompson PA, Spellman PT, Gray JW, Mills GB, Faham M
Publication: BMC Med Genomics, 2009, Vol. 2, Page 8
PubMed ID: 19228381 PubMed Review Paper? No
Suggested by: ISBER
Purpose of Paper
The purpose of this paper was to determine the effects of using archival formalin-fixed paraffin embedded (FFPE) specimens on copy number and genotype determination.
Conclusion of Paper
While all frozen specimens yielded high quality copy number determination, only 76% of FFPE specimens yielded high quality copy number determination. The percentage of FFPE specimens producing high quality data was dependent on cohort with some cohorts producing high quality data from all specimens. While copy numbers generally were in agreement between FFPE and frozen specimens, some differences were identified, but the authors were unclear if they reflected tumor heterogeneity or were an artifact of fixation. The genotype call rate was slightly higher using frozen specimens than FFPE specimens and using normal tissue than tumor tissue. The average genotype concordance between matched frozen and FFPE normal specimens was 99.99%, and the genotype concordance between frozen and FFPE tumor specimens was 99.90%.
Studies
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Study Purpose
The purpose of this study was to determine the effects of using FFPE rather than frozen specimens for copy number and genotype determination. Specimens were from 7 different cohorts including normal and tumor tissue from breast, colorectal, liver, bladder and kidney. The FFPE blocks had been stored 0.5-28 years before analysis. No details of specimen processing or DNA extraction were provided.
Summary of Findings:
All frozen specimens yielded high quality copy number determination (two-point relative standard error, 2p-RSE of <0.18), but only 88% of FFPE specimens yielded passable acceptable copy number data, and 76% of FFPE specimens produced high quality copy number determination. The percentage of FFPE specimens producing high quality data was dependent on cohort with some cohortss producing high quality data from all specimens. While copy numbers generally were in agreement between FFPE and frozen specimens, some differences were identified, but the authors were unclear if they reflected tumor heterogeneity or were an artifact of fixation. The authors report that copy numbers observed with molecular inversion probes (MIP) generally agreed with those observed previously with Bacterial artificial chromosome (BAC) arrays. 96.4% of FFPE specimens and all frozen specimens had genotype call rates of more than 85%, and the average call rate from FFPE specimens was only slightly lower than that from frozen specimens (97.5% versus 98.7%). The genotype call rate was also slightly higher for normal tissue than for tumor tissue. The average genotype concordance between matched frozen and FFPE normal specimens was 99.99%, and between frozen and FFPE tumor specimens the average genotype concordance was 99.90%.
Biospecimens
Preservative Types
- Formalin
- Frozen
Diagnoses:
- Neoplastic - Carcinoma
- Normal
- Not specified
Platform:
Analyte Technology Platform DNA DNA microarray DNA CGH Pre-analytical Factors:
Classification Pre-analytical Factor Value(s) Biospecimen Preservation Type of fixation/preservation Formalin (buffered)
Frozen