Measurement of DNA copy number at microsatellite loci using quantitative PCR analysis

• Published in: Cancer research (Chicago, Ill.) Vol. 60; no. 19; pp. 5405 - 5409
• Main Authors: GINZINGER, David G, GODFREY, Tony E, NIGRO, Janice, MOORE, Dan H, SUZUKI, Seiji, PALLAVICINI, Maria G, GRAY, Joe W, JENSEN, Ronald H
• Format: Journal Article
• Language: English
• Published: Philadelphia, PA American Association for Cancer Research 01-10-2000
• Subjects: Animals; Biological and medical sciences; Biotechnology; chromosome 2; copy number; DNA, Neoplasm - analysis; DNA, Neoplasm - genetics; Female; Fundamental and applied biological sciences. Psychology; Gene Dosage; Genes, Tumor Suppressor - genetics; Genetic engineering; Genetic technics; Humans; Leukemia, Myeloid - etiology; Leukemia, Myeloid - genetics; Leukemia, Radiation-Induced - genetics; Male; Methods. Procedures. Technologies; Mice; Mice, Inbred Strains; Mice, Knockout; Microsatellite Repeats - genetics; Modification of gene expression level; Neoplasm Proteins - genetics; Nucleic Acid Amplification Techniques; Ovarian Neoplasms - genetics; Polymerase Chain Reaction - methods; Prognosis; Reproducibility of Results; Survival Analysis; Trans-Activators - genetics; ZNF217 gene; Human; Methodology; Nucleotide sequence; Copy number; Rodentia; Biological marker; Chromosome 2; In vitro; Polymerase chain reaction; Tissue; Vertebrata; Gene amplification; Mammalia; Gene; Comparative genomic hybridization; Investigation method; Mouse; Animal; Microsatellite DNA; DNA; Established cell line; Onc gene; Quantitative analysis
• ISSN: 0008-5472; 1538-7445

This report describes the development and validation of quantitative microsatellite analysis (QuMA) for rapid measurement of relative DNA sequence copy number. In QuMA, the copy number of a test locus relative to a pooled reference is assessed using quantitative, real-time PCR amplification of loci carrying simple sequence repeats. Use of simple sequence repeats is advantageous because of the large numbers that are mapped precisely. In addition, all markers are informative because QuMA does not require that they be polymorphic. The utility of QuMA is demonstrated in assessment of the extent of deletions of chromosome 2 in leukemias arising in radiation-sensitive inbred SJL mice and in analysis of the association of increased copy number of the putative oncogene ZNF217 with reduced survival duration in ovarian cancer patients.