Bias–Variance Tradeoffs in Recombination Rate Estimation

Bias-Variance Tradeoffs in Recombination Rate Estimation.

In 2013, we and coauthors published a paper characterizing rates of recombination within the 2.1-megabase garnet-scalloped (g-sd) region of the Drosophila melanogaster X chromosome. To extract the signal of recombination in our high-throughput sequence data, we adopted a nonparametric smoothing procedure, reducing variance at the cost of biasing individual recombination rates. In doing so, we s...

Estimation of recombination rate and detection of recombination hotspots from dense single-nucleotide polymorphism trio data.

RECENT studies employing single-sperm haplotyping ( Jeffreys and Neumann 2002), pedigrees (Visser et al. 2005), and population studies using dense genetic marker data (Crawford et al. 2004; McVean et al. 2004; Myers et al. 2005) have shown that there is a large amount of local variation in recombination rate in the human genome. Methods to estimate fine-scale recombination rates from population...

Estimation of the in vivo recombination rate for a plant RNA 3 virus 4 5

On the Recombination Rate Estimation in the Presence of Population Substructure

As recombination events are not uniformly distributed along the human genome, the estimation of fine-scale recombination maps, e.g. HapMap Project, has been one of the major research endeavors over the last couple of years. For simulation studies, these estimates provide realistic reference scenarios to design future study and to develop novel methodology. To achieve a feasible framework for th...

Estimation of the in vivo recombination rate for a plant RNA virus.

Phylogenomic evidence suggested that recombination is an important evolutionary force for potyviruses, one of the larger families of plant RNA viruses. However, mixed-genotype potyvirus infections are marked by low levels of cellular coinfection, precluding template switching and recombination events between virus genotypes during genomic RNA replication. To reconcile these conflicting observat...