title: FACADE: a fast and sensitive algorithm for the segmentation and calling of high resolution array CGH data.
abstract: The availability of high resolution array comparative genomic hybridization (CGH) platforms has led to increasing complexities in data analysis. Specifically, defining contiguous regions of alterations or segmentation can be computationally intensive and popular algorithms can take hours to days for the processing of arrays comprised of hundreds of thousands to millions of elements. Additionally, tumors tend to demonstrate subtle copy number alterations due to heterogeneity, ploidy and hybridization effects. Thus, there is a need for fast, sensitive array CGH segmentation and alteration calling algorithms. Here, we describe Fast Algorithm for Calling After Detection of Edges (FACADE), a highly sensitive and easy to use algorithm designed to rapidly segment and call high resolution array data.
authors.affiliation: Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada. bcoe@bccrc.ca
authors.forename: Bradley P
authors.initials: BP
authors.lastname: Coe
authors.forename: Raj
authors.initials: R
authors.lastname: Chari
authors.forename: Calum
authors.initials: C
authors.lastname: MacAulay
authors.forename: Wan L
authors.initials: WL
authors.lastname: Lam
mesh_terms: D000465:Algorithms; D045744:Cell Line, Tumor; D055028:Comparative Genomic Hybridization / Q000379:methods*; D003198:Computer Simulation; D006801:Humans; D009369:Neoplasms / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis