title: DNA copy number aberrations in intestinal-type gastric cancer revealed by array-based comparative genomic hybridization.
abstract: Genomic instability can be divided into 2 categories: chromosomal instability (CIN) and microsatellite instability (MSI). CIN has been linked to aneuploidy and chromosomal aberrations, and high-level loss of heterozygosity (LOH-H) has been suggested to be an indicator of CIN. High-level MSI (MSI-H), which results from nonfunctional mismatch repair, has previously been suggested to be mutually exclusive with CIN. Four MSI-H and three LOH-H primary gastric tumors of intestinal histology were used for copy number analysis by array-based comparative genomic hybridization (aCGH) with 13,000 cDNA targets. The MSI-H group showed fewer gains (0-12, average 4.5) and losses (0-10, average 2.5) per tumor as compared to the LOH-H group (9-15 gains, average 11.6 and 1-6 losses, average 4). Two MSI-H tumors did not show any copy number changes and one showed only gains of whole chromosomes. The most common alterations were gains of 20q (5/7 samples), 1q, 8, and 10p (3/7 samples) and losses of 1p and 5p (3/7 samples). The minimal amplified regions in 1q and 20q were localized to 1q21.1 approximately q21.2, 1q21.3, 20q11.2, 20q13.12, and 20q13.3 approximately qter. No copy number change was found to be specific for MSI-H or LOH-H. The results suggest that the LOH-H phenotype revealed by microsatellite analysis predicts reliably copy number abnormalities on aCGH and that a subset of MSI-H and all LOH-H tumors share the CIN phenotype.
authors.affiliation: Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital, POB 21, Haartmaninkatu 3, FI-00014, Helsinki, Finland. hanna.vauhkonen@helsinki.fi
authors.forename: Hanna
authors.initials: H
authors.lastname: Vauhkonen
authors.forename: Matti
authors.initials: M
authors.lastname: Vauhkonen
authors.forename: Antti
authors.initials: A
authors.lastname: Sajantila
authors.forename: Pentti
authors.initials: P
authors.lastname: Sipponen
authors.forename: Sakari
authors.initials: S
authors.lastname: Knuutila
mesh_terms: D000368:Aged; D000369:Aged, 80 and over; D043171:Chromosomal Instability; D004273:DNA, Neoplasm / Q000032:analysis; D005260:Female; D018628:Gene Dosage; D006801:Humans; D019656:Loss of Heterozygosity; D008297:Male; D018895:Microsatellite Repeats; D008875:Middle Aged; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D017422:Sequence Analysis, DNA; D013274:Stomach Neoplasms / Q000145:classification / Q000235:genetics*
chemical_list: D004273:DNA, Neoplasm