Resolving the resolution of array CGH.
Many recent technologies have been designed to supplant conventional metaphase CGH technology with the goal of refining the description of segmental copy number status throughout the genome. However, the emergence of new technologies has led to confusion as to how to describe adequately the capabilities of each array platform. The design of a CGH array can incorporate a uniform or a highly variable element distribution. This can lead to bias in the reporting of average or median resolutions, making it difficult to provide a fair comparison of platforms. In this report, we propose a new definition of resolution for array CGH technology, termed "functional resolution," that incorporates the uniformity of element spacing on the array, as well as the sensitivity of each platform to single-copy alterations. Calculation of these metrics is automated through the development of a Java-based application, "ResCalc," which is applicable to any array CGH platform.
Coe
Bradley P
BP
British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, Canada V5Z 1L3. bcoe@bccrc.ca
Ylstra
Bauke
B
Carvalho
Beatriz
B
Meijer
Gerrit A
GA
Macaulay
Calum
C
Lam
Wan L
WL
D018628:Gene Dosage; D015894:Genome, Human; D006801:Humans; D019656:Loss of Heterozygosity; D009693:Nucleic Acid Hybridization / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012680:Sensitivity and Specificity; D013673:Technology Assessment, Biomedical / Q000379:methods*