THE EFFECTS OF GENOTYPING ERRORS AND INTERFERENCE ON ESTIMATION OF GENETIC-DISTANCE

Analysis of linkage data has typically been carried out assuming genot yping errors are absent. Recent studies have shown, however, that the impact of ignoring genotyping errors can be great, especially in dense marker maps [Buetow, Am J Hum Genet 1991;49:985-994; Lincoln and Land er, Genomics 1992;14:604-610]. Because most organisms exhibit positive chiasma interference, we use the chi(2) model [Foss et al., Genetics 1993;144:681-691] to examine the role interference plays in the estima tion of genetic distance in the presence of genotyping errors. For sim plicity, we confine our analyses to samples of 1,000 fully informative gametes. Our results support previous findings that ignoring errors i nflates distance estimates. The larger the error rate, the greater the inflation. For a given error rate, the relative error in estimated ge netic distance is greatest when interference is known to be weak or ab sent. An approximation to relative error which quantifies the relation to distance, error rate, and interference is provided. Robustness of estimation to error misspecification is also investigated. When the as sumed error rate is too low, distance is overestimated while interfere nce is underestimated. The situation is reversed when too large an err or rate is assumed (interference is overestimated, and distance undere stimated). Unfortunately, the joint estimation of distance and interfe rence is not very robust to error misspecification.