FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data

We have developed FusionSeq to identify fusion transcripts from paired-end RNA-sequencing. FusionSeq includes filters to remove spurious candidate fusions with artifacts, such as misalignment or random pairing of transcript fragments, and it ranks candidates according to several statistics. It also has a module to identify exact sequences at breakpoint junctions. FusionSeq detected known and novel fusions in a specially sequenced calibration data set, including eight cancers with and without known rearrangements

Fludarabine, cytarabine, granulocyte colony-stimulating factor, and idarubicin with gemtuzumab ozogamicin improves event-free survival in younger patients with newly diagnosed aml and overall survival in patients with npm1 and flt3 mutations

Purpose To determine the optimal induction chemotherapy regimen for younger adults with newly diagnosed AML without known adverse risk cytogenetics. Patients and Methods One thousand thirty-three patients were randomly assigned to intensified (fludarabine, cytarabine, granulocyte colony-stimulating factor, and idarubicin [FLAG-Ida]) or standard (daunorubicin and Ara-C [DA]) induction chemotherapy, with one or two doses of gemtuzumab ozogamicin (GO). The primary end point was overall survival (OS). Results There was no difference in remission rate after two courses between FLAG-Ida + GO and DA + GO (complete remission [CR] + CR with incomplete hematologic recovery 93% v 91%) or in day 60 mortality (4.3% v 4.6%). There was no difference in OS (66% v 63%; P = .41); however, the risk of relapse was lower with FLAG-Ida + GO (24% v 41%; P < .001) and 3-year event-free survival was higher (57% v 45%; P < .001). In patients with an NPM1 mutation (30%), 3-year OS was significantly higher with FLAG-Ida + GO (82% v 64%; P = .005). NPM1 measurable residual disease (MRD) clearance was also greater, with 88% versus 77% becoming MRD-negative in peripheral blood after cycle 2 (P = .02). Three-year OS was also higher in patients with a FLT3 mutation (64% v 54%; P = .047). Fewer transplants were performed in patients receiving FLAG-Ida + GO (238 v 278; P = .02). There was no difference in outcome according to the number of GO doses, although NPM1 MRD clearance was higher with two doses in the DA arm. Patients with core binding factor AML treated with DA and one dose of GO had a 3-year OS of 96% with no survival benefit from FLAG-Ida + GO. Conclusion Overall, FLAG-Ida + GO significantly reduced relapse without improving OS. However, exploratory analyses show that patients with NPM1 and FLT3 mutations had substantial improvements in OS. By contrast, in patients with core binding factor AML, outcomes were excellent with DA + GO with no FLAG-Ida benefit

Molecular screening for new fusion genes in cancer

Gene fusions arising from translocations make an important contribution to the development of cancer. A new study uses high-throughput sequencing to characterize such fusions at an unprecedented level of resolution

Multimode Resistive Switching in Single ZnO Nanoisland System

Resistive memory has attracted a great deal of attention as an alternative to contemporary flash memory. Here we demonstrate an interesting phenomenon that multimode resistive switching, i.e. threshold-like, self-rectifying and ordinary bipolar switching, can be observed in one self-assembled single-crystalline ZnO nanoisland with base diameter and height ranging around 30 and 40 nm on Si at different levels of current compliance. Current-voltage characteristics, conductive atomic force microscopy (C-AFM), and piezoresponse force microscopy results show that the threshold-like and self-rectifying types of switching are controlled by the movement of oxygen vacancies in ZnO nanoisland between the C-AFM tip and Si substrate while ordinary bipolar switching is controlled by formation and rupture of conducting nano-filaments. Threshold-like switching leads to a very small switching power density of 1 × 10(3) W/cm(2)

Targeted education ApproaCH to improve Peritoneal Dialysis Outcomes (TEACH-PD) : a feasibility study

Background: There is substantial variation in peritonitis rates across peritoneal dialysis (PD) units globally. This may, in part, be related to the wide variability in the content and delivery of training for PD nurse trainers and patients. Aim: The aim of this study was to test the feasibility of implementing the Targeted Education ApproaCH to improve Peritoneal Dialysis Outcomes (TEACH-PD) curriculum in real clinical practice settings. Methods: This study used mixed methods including questionnaires and semi-structured interviews (pretraining and post-training) with nurse trainers and patients to test the acceptability and usability of the PD training modules implemented in two PD units over 6 months. Quantitative data from the questionnaires were analysed descriptively. Interviews were analysed using thematic analysis. Results: Ten PD trainers and 14 incident PD patients were included. Mean training duration to complete the modules were 10.9 h (range 6–17) and 24.9 h (range 15–35), for PD trainers and patients, respectively. None of the PD patients experienced PD-related complications at 30 days follow-up. Three (21%) patients were transferred to haemodialysis due to non-PD–related complications. Ten trainers and 14 PD patients participated in the interviews. Four themes were identified including use of adult learning principles (trainers), comprehension of online modules (trainers), time to complete the modules (trainers) and patient usability of the manuals (patient). Conclusion: This TEACH-PD study has demonstrated feasibility of implementation in a real clinical setting. The outcomes of this study have informed refinement of the TEACH-PD modules prior to rigorous evaluation of its efficacy and cost-effectiveness in a large-scale study

High-resolution identification of balanced and complex chromosomal rearrangements by 4C technology.

Balanced chromosomal rearrangements can cause disease, but techniques for their rapid and accurate identification are missing. Here we demonstrate that chromatin conformation capture on chip (4C) technology can be used to screen large genomic regions for balanced and complex inversions and translocations at high resolution. The 4C technique can be used to detect breakpoints also in repetitive DNA sequences as it uniquely relies on capturing genomic fragments across the breakpoint. Using 4C, we uncovered LMO3 as a potentially leukemogenic translocation partner of TRB@. We developed multiplex 4C to simultaneously screen for translocation partners of multiple selected loci. We identified unsuspected translocations and complex rearrangements. Furthermore, using 4C we detected translocations even in small subpopulations of cells. This strategy opens avenues for the rapid fine-mapping of cytogenetically identified translocations and inversions, and the efficient screening for balanced rearrangements near candidate loci, even when rearrangements exist only in subpopulations of cells.