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Series GSE3264

Query DataSets for GSE3264

Status

Public on Dec 19, 2005

Title

Oligonucleotide-based arrayCGH

Organisms

Homo sapiens; Mus musculus

Experiment type

Genome variation profiling by array
Genome variation profiling by genome tiling array

Summary

Array-based comparative genomic hybridisation is a high-resolution method for measuring chromosomal copy number changes. Here we present a validated protocol using in-house spotted oligonucleotide libraries for array CGH. This oligo array CGH platform yields reproducible results and is capable of detecting single copy gains, multi-copy amplifications as well as homozygous and heterozygous deletions as small as 100 kb with high resolution. A human oligonucleotide library was printed on amine binding slides. Arrays were hybridised using a hybstation and analysed using BleuFuse feature extraction software, with over 95% of spots passing quality control. The protocol allows as little as 300 ng of input DNA without the need for amplification or target reduction and a 90% reduction of Cot1-DNA without compromising quality. High quality results have also been obtained with DNA from archival tissue. Finally, in addition to human oligo arrays, we have applied the protocol successfully to mouse oligo arrays. We believe that this oligo-based platform using “off-the-shelf” oligo-libraries provides an easy accessible alternative to BAC arrays for CGH, which is cost-effective, available at high resolution and easily implemented for any sequenced organism without compromising the quality of the results.
Keywords: comparative genomic hybridization, oligonucleotide,

Overall design

16 human and 2 mouse samples are analyzed on oligonucleotide arrays and some of them also on BAC arrays. Replicates are included in the series so that the total number of hybridizations is 30. Corresponding figure numbers: 1A/C: GSM73557, 1B/D: GSM75163, 2: GSM74521, 3: GSM73557, GSM75164, GSM75165, GSM75166, 4A: GSM75169, 4C: GSM75170, 5A: GSM75171, 6A: GSM75199, 6B: GSM75205, 7A: GSM75209, 7B: GSM75175, GSM75174.

Contributor(s)

van den IJssel P, Tijssen M, Chin S, Eijk PP, Carvalho B, Hopmans E, Holstege H, Jonkers J, Meijer GA, Caldas C, Ylstra B

Citation(s)

16361265

Submission date

Sep 08, 2005

Last update date

Aug 08, 2013

Contact name

Daoud Sie

E-mail(s)

d.sie@vumc.nl