Copy number and loss of heterozygosity detected by SNP array of formalin-fixed tissues using whole-genome amplification.

Author(s): Stokes A, Drozdov I, Guerra E, Ouzounis CA, Warnakulasuriya S, Gleeson MJ, McGurk M, Tavassoli M, Odell EW

Publication: PLoS One, 2011, Vol. 6, Page e24503

PubMed ID: 21966361 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   The purpose of this study was to determine the effects of WGA of DNA from FFPE normal and dysplastic oral epithelium on copy number and LOH determination using SNP microarrays. Specimens were stored 3-12 years prior to DNA extraction and experimentation.

   Summary of Findings:

   Call rates were similar for unamplified and WGA DNA from FFPE specimens (90.1% and 89.8%, respectively), but these rates decreased to 84.1% and 82.8%, respectively, when only SNPs on fragments less than 350 bp were considered. Homozygous and heterozygous call rates were similar for WGA and unamplified DNA. 56.1% of the SNPs that failed using WGA DNA also failed using unamplified DNA, but there were 2.3% less failed calls for the homozygous AA SNPs using WGA DNA indicating a bias in amplification. 76.5% of SNPs produced calls using WGA and unamplified DNA with an 82.4% concordance in calls between the two types. When copy number changes were identified using both WGA and unamplified DNA, the direction was concordant 99.5% of the time, but 50.25% of the copy number changes identified using unamplified DNA were not identified using WGA DNA with more amplifications missed than deletions. Further, 36.4% of copy number changes identified using WGA DNA were not found using unamplified DNA. 73.5% of LOH instances found in unamplified DNA were not found using WGA DNA, and 74.49% of identified LOH instances using WGA DNA were not found with unamplified DNA. Chromosomal location was not found to have any effects on LOH.

   Biospecimens

   • Tissue - Oral Cavity

   Preservative Types

   • Formalin

   Diagnoses:

   • Normal
   • Other diagnoses

   Platform:

   Analyte	Technology Platform
   DNA	Array CGH
   DNA	DNA microarray
   DNA	Whole genome amplification
   DNA	SNP assay

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Preaquisition	Diagnosis/ patient condition	Dysplastic
   Whole genome amplification Specific	Nucleic acid amplification	None Amplified with OmniPlex

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