Estimating the rate of gene conversion on human chromosome 21.
There is a growing recognition that gene conversion can be an important factor in shaping fine-scale patterns of linkage disequilibrium in the human genome. We devised simple multilocus summary statistics for estimating gene-conversion rates from genomewide polymorphism data sets. In addition to being computationally feasible for very large data sets, these summaries were designed to yield robust estimates of gene-conversion rates in the presence of variation in crossing-over rates. Using our summaries, we analyzed 21,840 biallelic single-nucleotide polymorphisms (SNPs) on human chromosome 21. Our results indicate that models including both crossing over and gene conversion fit the overall short-range data (0-5 kb) of chromosome 21 much better than do models including crossing over alone. The estimated ratio of gene-conversion rate to crossing-over rate has a range of 1.6-9.4, depending on the assumed conversion tract length (in the range of 500-50 bp). Removal of the 5,696 SNPs that occur in known mutational hotspots (CpG sites) did not significantly change our conclusions, suggesting that recurrent mutations alone cannot explain our data.
Padhukasahasram
Badri
B
Program in Molecular and Computational Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-1340, USA. padhukas@usc.edu
Marjoram
Paul
P
Nordborg
Magnus
M
D002869:Chromosome Aberrations; D002891:Chromosomes, Human, Pair 21 / Q000235:genetics / Q000648:ultrastructure*; D018899:CpG Islands; D003434:Crossing Over, Genetic; D004252:DNA Mutational Analysis; D019992:Databases as Topic; D005785:Gene Conversion; D006801:Humans; D016013:Likelihood Functions; D015810:Linkage Disequilibrium; D008957:Models, Genetic; D009154:Mutation; D011110:Polymorphism, Genetic; D020641:Polymorphism, Single Nucleotide; D013223:Statistics as Topic