Physical and genetic map of 5q31: use of fluorescence in situ hybridization data to identify errors in the CEPH database

Abstract

Chromosome 5, band q31, contains the genes responsible for a number of interesting genetic and malignant diseases, as well as many cloned genes. To prepare a high-resolution map of this region, eight anonymous DNA markers were mapped by combining genetic data derived from linkage analysis, with physical data obtained using two-color fluorescent in situ hybridization (FISH). Probe order was determined by FISH on metaphase cells, supplemented with interphase analysis, while genetic distance and likely order were determined by multipoint linkage analysis using genotype data from Centre d’Etude de Polymorphisme Humain (CEPH) pedigrees. Discrepancies between the genetic and physical maps suggested that there was a high rate of genotyping errors in the CEPH data for these markers, and prompted a statistical analysis to identify these errors. By assuming a known physical order (as determined by FISH) it was possible to identify markers which had the greatest degree of error. The average typing error was estimated at 1.8%, but several markers had much higher error rates; a 14% error rate was predicted for one locus, which was subsequently confirmed by retyping. The analysis led to the preparation of a revised map spanning 24.5 cM of 5q31. This study illustrates the power of FISH to determine physical order over a wide genomic distance, and demonstrates how order can be used as an adjunct to linkage analysis, particularly in the identification of genotyping errors.