Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference.

Restriction site-associated DNA sequencing (RADseq) provides researchers with the ability to record genetic polymorphism across thousands of loci for nonmodel organisms, potentially revolutionizing the field of molecular ecology. However, as with other genotyping methods, RADseq is prone to a number of sources of error that may have consequential effects for population genetic inferences, and these have received only limited attention in terms of the estimation and reporting of genotyping error rates. Here we use individual sample replicates, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome. We then use sample replicates to (i) optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci; and (ii) quantify error rates for loci, alleles and single-nucleotide polymorphisms. As an empirical example, we use a double-digest RAD data set of a nonmodel plant species, Berberis alpina, collected from high-altitude mountains in Mexico.

De novo undifferentiated pleomorphic sarcoma arising from a renal allograft: A case report

To the best of our knowledge, this is the first report of an undifferentiated pleomorphic sarcoma arising from a renal graft. Transplantectomy was performed in a 47-year old woman presenting to the emergency room because of general weakness. Preoperative workup revealed a 5.5 cm malignant mass of the graft which was not present on routine ultrasound performed 12 months earlier. Following transplantectomy, local recurrence developed despite complete tumor resection and interruption of immunosuppression. Despite radiation therapy, the outcome was ultimately fatal. Genetic analysis revealed that the tumor had arisen from donor tissue. Annual ultrasound surveillance might not be enough effective to screen for these rare high grade neoplasms.