This application note describes a method for performing copy number analysis of archived FFPE tumor samples using Agilent Oligo Array CGH. The method uses Kreatech’s Universal Linkage System (ULS™) technology, a non-enzymatic direct labeling methodology, that can be used with degraded FFPE tissue-derived DNA. The method also features a simple, single-step sample preparation procedure, which reduces the cost of sample preparation. In addition, the method employs a novel labeling strategy that significantly improves the labeling efficiency of samples. Finally, the method is validated using a variety of FFPE tissue samples, and the results demonstrate that the method is capable of producing high-quality copy number data.
This document details a protocol for performing Copy Number Analysis on archival Formalin-Fixed Paraffin-Embedded (FFPE) tumor samples using Agilent's Oligo Array CGH platform. It addresses the challenges of analyzing degraded DNA from FFPE tissues, which often yield noisy data due to fragmentation and damage. The note introduces a non-enzymatic direct labeling method based on Kreatech's Universal Linkage System (ULS) technology.
| Spatial Resolution | ~35 kb |
|---|---|
| Labeling Time | 30 minutes |
| Hybridization Time | 40 hours |
The protocol uses Kreatech's Universal Linkage System (ULS) technology, a non-enzymatic direct labeling methodology.
Compared to enzymatic labeling, the ULS method is independent of fragment length, four times faster, contains fewer steps, and is easier to automate.