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Optimized amplification and fluorescent labeling of small cell samples for genomic array‐CGH
Author(s) -
Knijnenburg Jeroen,
van der Burg Marja,
Tanke Hans J.,
Szuhai Károly
Publication year - 2007
Publication title -
cytometry part a
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.316
H-Index - 90
eISSN - 1552-4930
pISSN - 1552-4922
DOI - 10.1002/cyto.a.20412
Subject(s) - comparative genomic hybridization , genome , copy number analysis , genomic dna , biology , computational biology , dna , copy number variation , genetics , gene
Background: Whole genome amplification (WGA) is usually needed in the genetic analysis of samples containing a low number of cells. In genome‐wide analysis of DNA copy numbers by array comparative genomic hybridization (array‐CGH) it is very important that the genome is evenly represented throughout the amplified product. All currently available WGA techniques are generating some degree of bias. Methods: A way to compensate for this is using a reference sample which is similarly amplified, as the introduced amplification bias will be leveled out. Additionally, direct labeling of the amplified DNA is performed to bypass the currently widely applied random primed labeling, which involves an additional amplification of the product and is introducing extra bias. Results: In this article it is shown that equal processing of the test and reference sample is indeed crucial to generate an optimal array‐CGH profile of amplified DNA samples. Also presented here is that the labeling method may significantly effect the array‐CGH result, it is shown that with direct chemical labeling using platinum derivates (ULS labeling) optimal array‐CGH results are obtained. Conclusions: We show that an optimized WGA strategy for both test and reference sample in combination with direct chemical labeling results in a reliable array‐CGH profile of samples as low as a 30 cell equivalent. © 2007 International Society for Analytical Cytology