title: Computational BAC clone contig assembly for comprehensive genome analysis.
abstract: Comparative genomic hybridization (CGH) has proved to be a powerful tool for the detection of genome copy number changes in human cancers and in other diseases caused by segmental aneusomies. Array versions of CGH allow the definition of these aberrations, with resolution determined by the size and distribution of the array elements. Resolution approaching 100 kb can be achieved by use of arrays comprising bacterial artificial chromosomes (BACs) distributed contiguously across regions of interest. We describe here a computer program that automatically assembles contigs of minimally overlapping BAC clones, using information about BAC end-sequences and the normal genome DNA sequence. We demonstrate the characteristics of contigs assembled and annotated by use of this approach for regions of recurrent abnormality in human ovarian and breast cancers at chromosome bands 3q25-q27 and 8q24 and chromosome arm 20q. We also show illustrative analyses of regions of amplification in these regions in breast and ovarian tumor cell lines by use of array CGH with arrays comprising contiguous BACs.
authors.affiliation: Department of Laboratory Medicine and UCSF Comprehensive Cancer Center, University of California San Francisco, USA.
authors.forename: Anna
authors.initials: A
authors.lastname: Lapuk
authors.forename: Stanislav
authors.initials: S
authors.lastname: Volik
authors.forename: Robert
authors.initials: R
authors.lastname: Vincent
authors.forename: Koei
authors.initials: K
authors.lastname: Chin
authors.forename: Wen-Lin
authors.initials: WL
authors.lastname: Kuo
authors.forename: Pieter
authors.initials: P
authors.lastname: de Jong
authors.forename: Colin
authors.initials: C
authors.lastname: Collins
authors.forename: Joe W
authors.initials: JW
authors.lastname: Gray
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics / Q000473:pathology; D045744:Cell Line, Tumor; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics*; D002890:Chromosomes, Human, Pair 20 / Q000235:genetics; D002893:Chromosomes, Human, Pair 3 / Q000235:genetics; D019295:Computational Biology / Q000379:methods / Q000639:trends*; D020451:Contig Mapping / Q000379:methods* / Q000639:trends*; D004273:DNA, Neoplasm / Q000235:genetics; D005260:Female; D052138:Genes, Neoplasm / Q000235:genetics; D015894:Genome, Human; D006801:Humans; D009693:Nucleic Acid Hybridization; D010051:Ovarian Neoplasms / Q000235:genetics / Q000473:pathology; D012984:Software
chemical_list: D004273:DNA, Neoplasm