title: A versatile statistical analysis algorithm to detect genome copy number variation.
abstract: We have developed a versatile statistical analysis algorithm for the detection of genomic aberrations in human cancer cell lines. The algorithm analyzes genomic data obtained from a variety of array technologies, such as oligonucleotide array, bacterial artificial chromosome array, or array-based comparative genomic hybridization, that operate by hybridizing with genomic material obtained from cancer and normal cells and allow detection of regions of the genome with altered copy number. The number of probes (i.e., resolution), the amount of uncharacterized noise per probe, and the severity of chromosomal aberrations per chromosomal region may vary with the underlying technology, biological sample, and sample preparation. Constrained by these uncertainties, our algorithm aims at robustness by using a priorless maximum a posteriori estimator and at efficiency by a dynamic programming implementation. We illustrate these characteristics of our algorithm by applying it to data obtained from representational oligonucleotide microarray analysis and array-based comparative genomic hybridization technology as well as to synthetic data obtained from an artificial model whose properties can be varied computationally. The algorithm can combine data from multiple sources and thus facilitate the discovery of genes and markers important in cancer, as well as the discovery of loci important in inherited genetic disease.
authors.affiliation: Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012, USA.
authors.forename: Raoul-Sam
authors.initials: RS
authors.lastname: Daruwala
authors.forename: Archisman
authors.initials: A
authors.lastname: Rudra
authors.forename: Harry
authors.initials: H
authors.lastname: Ostrer
authors.forename: Robert
authors.initials: R
authors.lastname: Lucito
authors.forename: Michael
authors.initials: M
authors.lastname: Wigler
authors.forename: Bud
authors.initials: B
authors.lastname: Mishra
mesh_terms: D000465:Algorithms; D001499:Bayes Theorem; D001943:Breast Neoplasms / Q000235:genetics; D045744:Cell Line, Tumor; D002869:Chromosome Aberrations; D003627:Data Interpretation, Statistical; D005260:Female; D018628:Gene Dosage; D015894:Genome, Human; D006801:Humans; D008297:Male; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000706:statistics & numerical data; D011471:Prostatic Neoplasms / Q000235:genetics