Analysis of sequence variation in the three fibroblast growth factor receptor genes and estimation of mutation frequency at the achondroplasia base in pools of human sperm

The amount of sequence variation present in a genomic region is affected by many factors. One of the largest influences is mutation rate. In the absence of selection, there should be a direct relationship between mutation rate and the amount of variation present. This relationship allowed us to use the amount of variation as a surrogate measure of mutation rate. We chose to study genes that have a strong likelihood of having a high mutation rate in at least portions of their genomic regions, the Fibroblast Growth Factor Receptor (FGFR) genes. FGFR2 and FGFR3 have very frequent spontaneous disease-causing mutations. The mutation rate at certain nucleotides of these genes has been estimated, based on birth frequencies, to be 35-fold to 175-fold increased compared to the background rate in the human genome.; We sequenced FGFR2, FGFR3, and FGFR4 in 36 individuals and one chimpanzee. The overall amount of variation and divergence in these genes is not significantly different, nor is it different from other genes in the human genome. This may suggest the high mutation rate at certain nucleotides does not extend to other bases in the genomic sequence. However, there may be evidence for a selective sweep in at least portions of FGFR2 and FGFR3, in the form of an excess proportion of rare variation. This may have reduced the overall amount of variation in these regions, however it is unlikely to account for a 35-fold decrease.; As another method of studying variation in FGFR3, we developed assays to detect the two most common mutations that cause achondroplasia, as well as a synonymous change in the neighboring nucleotide, in pools of human sperm. These assays are capable of detecting a single mutant sperm in a background of 1000 wild-type sperm. Our results were consistent with the observed ratio of common and less frequent spontaneous mutations at the achondroplasia nucleotide. We also found the mutant frequency at the neighboring nucleotide to be nearly as high as at the common achondroplasia nucleotide. These assays require more optimization. However, the results demonstrate the potential for direct estimation of mutation frequencies in human sperm.