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This microscope has 4 lasers that with the use of a specialized array of filters can excite a wide variety of fluorochrome including the Cy5.5 (max excitation 680 nm, excited in this microscope with the 633 nm LASER, emission 680 nm) and Cy7 (excitation 749 nm, emission 790 nm).
To construct this specialized array, genomic segments fully covering these 18 chromosome regions with 3604 BAC genomic clones without gaps were mapped.
DNA from 40 Asian and 20 Caucasian non-small cell lung cancer (NSCLC) patients was analyzed using this specialized array to identify lung cancer-related genes either common or differential in these two ethnic groups.
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It provides a functional "synthetic genetic signature" for each state of the cell (i.e. genotype and environment) by surveying complex genetic libraries, and does not require specialized arrays of cDNAs/shRNAs, deletion strains, direct assessment of clonal growth or even a conditional phenotype.
The homogenous self-self hybridization image of reference DNA shown in the Additional file 3: Figure S1 (upper left panel) indicates the feasibility of our specialized array-CGH.
In conclusion, our specialized array-CGH results provide an invaluable database of specific chromosome regions about the gene copy number alterations common or differential in Caucasian and Asian lung cancer patients.
Changes in DNA methylation, microRNA expression or even protein phosphorylation states can be detected with specialized arrays.
Thousands of genes can be analyzed simultaneously with cDNA microarray and variants on this technique include specialized arrays that can detect SNPs and alternative splice variants (exon junction arrays) [ 38- 41].
As more genes are identified, it is likely that specialized arrays will be offered that are specific for a tissue type (eg mammary gland chip), physiologic process (eg apoptosis chip, angiogenesis chip, invasion chip) or class of genes (eg suppressor gene chip, oncogene chip).
Importantly, when performing focused aCGH with specialized arrays that do not cover the entire genome, or comprise probes with a disproportioned focus on specific genomic regions, even CNAs that affect a minor part of the genome can introduce a significant correlation between copy number and intensity, and can result in misinterpretations of how a given ratio level relate to copy number.
This work is a feasibility study which examines the use of SMASH with specialized coil array and data reception hardware to achieve previously unattainable accelerations.
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