BackgroundCopy number variation is an important dimension of genetic diversity and has implications in development and disease. As an important model organism, the mouse is a prime candidate for copy number variant (CNV) characterization, but this has yet to be completed for a large sample size. Here we report CNV analysis of publicly available, high-density microarray data files for 351 mouse tail samples, including 290 mice that had not been characterized for CNVs previously.ResultsWe found 9634 putative autosomal CNVs across the samples affecting 6.87 % of the mouse reference genome. We find significant differences in the degree of CNV uniqueness (single sample occurrence) and the nature of CNV-gene overlap between wild-caught mice and classical laboratory strains. CNV-gene overlap was associated with lipid metabolism, pheromone response and olfaction compared to immunity, carbohydrate metabolism and amino-acid metabolism for wild-caught mice and classical laboratory strains, respectively. Using two subspecies of wild-caught Mus musculus, we identified putative CNVs unique to those subspecies and show this diversity is better captured by wild-derived laboratory strains than by the classical laboratory strains. A total of 9 genic copy number variable regions (CNVRs) were selected for experimental confirmation by droplet digital PCR (ddPCR).ConclusionThe analysis we present is a comprehensive, genome-wide analysis of CNVs in Mus musculus, which increases the number of known variants in the species and will accelerate the identification of novel variants in future studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1713-z) contains supplementary material, which is available to authorized users.

Objective:To determine if cochlear implantation without removal of inner ear schwannomas (IES) is an effective treatment option for Neurofibromatosis 2 (NF2) patients. To determine how the presence of an intracochlear schwannoma might impact cochlear implant (CI) outcomes and programming parameters.Study Design:Retrospective chart review.Setting:Tertiary center for cochlear and auditory brainstem implantation.Patients:Of 10 NF2 patients with IES, 8 are reported with no previous tumor removal on the implanted ear.Interventions:Cochlear implant without tumor removal.Main Outcome Measures:Performance outcomes with CI at least 1-year post intervention. Programming parameters, including impedances, for patients with IES.Results:All patients had full insertion of the electrode arrays with round window approaches. Performance outcomes ranged from 0 to 100% for Bamford-Kowal-Bench sentences. Impedance measurements for active electrodes for patients with IES were comparable to those measured in patients without vestibular schwannoma (VS). Only patients who had radiation treatment before receiving their implant had elevated threshold requirements for CI programming compared with CI recipients without VS.Conclusion:Cochlear implantation without tumor removal is an effective option for treating NF2 patients with IES. The presence of an intracochlear tumor did not have an impact on CI performance or programming requirements compared with patients without VS; however, previous treatment with radiation may be related to elevated current requirements in the CI settings.

§Guy's and St. Thomas' NHS Foundation Trust, London; and jjOticon Medical, UK Objectives: To investigate the combined effect of changing pulse shape and grounding configuration to manage facial nerve stimulation (FNS) in cochlear implant (CI) recipients. Patients: Three adult CI recipients with severe FNS were offered a replacement implant when standard stimulation strategies and programming adjustments did not resolve symptoms. Our hypothesis was that the facial nerve was less likely to be activated when using anodic pulses with ''mixed-mode'' intra-cochlear and extra-cochlear current return. Intervention: All patients were reimplanted with an implant that uses a pseudo-monophasic anodic pulse shape, with mixed-mode grounding (stimulus mixed-mode anodic)-the Neuro Zti CI (Oticon Medical). This device also allows measurements of neural function and loudness with monopolar, symmetric biphasic pulses (stimulus MB), the clinical standard used by most CIs as a comparison. Main Outcome Measures: The combined effect of pulse shape and grounding configuration on FNS was monitored during surgery. Following CI activation, FNS symptoms and performance with the Neuro Zti implant were compared with outcomes before reimplantation. Results: FNS could only be recorded using stimulus MB for all patients. In clinical use, all patients reported reduced FNS and showed an improvement in Bamford-Kowal-Bench sentences recognition compared with immediately before reimplantation. Bamford-Kowal-Bench scores with a male speaker were lower compared with measurements taken before the onset of severe FNS for patients 1 and 2. Conclusions: In patients where CI auditory performance was severely limited by FNS, charge-balanced pseudo-monophasic stimulation mode with a mixed-mode grounding configuration limited FNS and improved loudness percept compared with standard biphasic stimulation with monopolar grounding.