STATISTICAL-METHODS FOR GENE MAP CONSTRUCTION BY FLUORESCENCE IN-SITUHYBRIDIZATION

Fluorescence in situ hybridization (FISH) provides an efficient and po werful technique for ordering loci both on metaphase chromosomes and i n less condensed interphase chromatin. Two-color metaphase FISH can be used to order pairs of loci relative to the centromere; two- and thre e-color interphase FISH can be used to accurately order trios of loci spaced within I Mb relative to one another. Loci separated by a distan ce >1-2 Mb exhibit chromatin loops that often give rise to a statistic ally significant but incorrect order. We derive Bayesian methods for s electing the best locus order based on microscopic evaluation for each of these types of FISH mapping data. We then describe how the results from several two- and three-locus analyses can be combined to evaluat e the approximate posterior probability of a given multilocus order wi thin the limits of the technology utilized. These methods directly add ress the question of interest: What is the probability that the inferr ed two-, three-, or multilocus order actually is correct? We illustrat e our analysis methods by applying them to previously described FISH m apping data of 14 markers in the BRCA1 region on chromosome 17q12-q21. We also propose design strategies to order a group of closely spaced (<1 Mb) loci, two and three loci at a time, using a bisection strategy for two-color FISH data and a trisection strategy for three-color FIS H data. These strategies have the best worst-case performance for orde ring a new locus relative to a group of ordered loci and are nearly op timal for ordering a group of loci of unknown order. These, in conjunc tion with physical mapping strategies, provide efficient and reliable methods for gene map construction by FISH.