Recombulator-X: A fast and user-friendly tool for estimating X chromosome recombination rates in forensic genetics

Genetic markers (especially short tandem repeats or STRs) located on the X chromosome are a valuable resource to solve complex kinship cases in forensic genetics in addition or alternatively to autosomal STRs. Groups of tightly linked markers are combined into haplotypes, thus increasing the discriminating power of tests. However, this approach requires precise knowledge of the recombination rates between adjacent markers. The International Society of Forensic Genetics recommends that recombination rate estimation on the X chromosome is performed from pedigree genetic data while taking into account the confounding effect of mutations. However, implementations that satisfy these requirements have several drawbacks: they were never publicly released, they are very slow and/or need cluster-level hardware and strong computational expertise to use. In order to address these key concerns we developed Recombulator-X, a new open-source Python tool. The most challenging issue, namely the running time, was addressed with dynamic programming techniques to greatly reduce the computational complexity of the algorithm. Compared to the previous methods, Recombulator-X reduces the estimation times from weeks or months to less than one hour for typical datasets. Moreover, the estimation process, including preprocessing, has been streamlined and packaged into a simple command-line tool that can be run on a normal PC. Where previous approaches were limited to small panels of STR markers (up to 15), our tool can handle greater numbers (up to 100) of mixed STR and non-STR markers. In conclusion, Recombulator-X makes the estimation process much simpler, faster and accessible to researchers without a computational background, hopefully spurring increased adoption of best practices.Author summary: The X-chromosome is unique in the human genome. In males, the single copy of the X-chromosome is transmitted as a single unbroken DNA chunk to the females of the next generation, while in females the two chromosomal copies recombine and one of them is passed to both male and female descendants. Given this peculiar inheritance mode, X-chromosomal genetic markers are crucial for kinship analyses involving, for instance, half-sisters or deficiency paternity cases. In this situation, the recombination rates between genetic markers along the X chromosome need to be known to perform unbiased kinship analysis in forensics, which would be otherwise flawed due to the independence assumption. However, available implementations of computational methods for the estimation of recombination rates are lacking: they are slow, cumbersome and not open source. Thanks to algorithmic improvements and other optimization techniques, we were able to drastically reduce running time, also allowing us to handle more markers than previously feasible. Moreover, we extended previous methods, that were limited to Short Tandem Repeats (STR) markers, to handle any type of polymorphisms. We released our complete implementation as a Python module named Recombulator-X, which is the first open-source software for the estimation of recombination rates between markers along the X-chromosome.