Fully Automatic Quantification of Microarray Image Data

Abstract

DNA microarrays are now widely used to measure expression levels and DNA copy number in biological samples. Ratios of relative abundance of nucleic acids are derived from images of regular arrays of spots containing target genetic material to which fluorescently labeled samples are hybridized. Whereas there are a number of methods in use for the quantification of images, many of the software systems in wide use either encourage or require extensive human interaction at the level of individual spots on arrays. We present a fully automatic system for microarray image quantification. The system automatically locates both subarray grids and individual spots, requiring no user identification of any image coordinates. Ratios are computed based on explicit segmentation of each spot. On a typical image of 6000 spots, the entire process takes less than 20 sec. We present a quantitative assessment of performance on multiple replicates of genome-wide array-based comparative genomic hybridization experiments. By explicitly identifying the pixels in each spot, the system yields more accurate estimates of ratios than systems assuming spot circularity. The software, called UCSF Spot, runs on Windows platforms and is available free of charge for academic use.

Novel risk stratification of patients with neuroblastoma by genomic signature, which is independent of molecular signature

“…Hybridization was performed as previously reported (Pinkel et al, 1998). UCSF Spot and UCSF Sproc programs to analyse values for spotted clones (Jain et al, 2002) were used. All array-CGH data are available at NCBI Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) with accession number GSE 5784.…”

The lymphovascular embolus of inflammatory breast cancer exhibits a Notch 3 addiction

“…Gene expression profile studies and array comparative genomic hybridization Details of these methods (Jain et al, 2002;Krzywinski et al, 2004) are provided in Supplementary Information.…”

p53 suppression overwhelms DNA polymerase η deficiency in determining the cellular UV DNA damage response

“…2 μg of DNA was hybridized onto a BAC array by the staff at the Microarray Core, Comprehensive Cancer Center, University of California, San Francisco, according to published methods [40]. Data were analyzed using SPOT [62] and SPROC software. Chromosome gains and losses in normal and XP-V fibroblasts with or without p53 inhibition grown continuously for 20 passages.…”