Multiplexed measurements of gene signatures in different analytes using the Nanostring nCounter™ Assay System

This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

Research Data Management 'Green Shoots' Pilot Programme, Final Reports

This document contains the final reports of six Research Data Management Green Shoots projects run at Imperial College in 2014

Use of a mixed tissue RNA design for performance assessments on multiple microarray formats

The comparability and reliability of data generated using microarray technology would be enhanced by use of a common set of standards that allow accuracy, reproducibility and dynamic range assessments on multiple formats. We designed and tested a complex biological reagent for performance measurements on three commercial oligonucleotide array formats that differ in probe design and signal measurement methodology. The reagent is a set of two mixtures with different proportions of RNA for each of four rat tissues (brain, liver, kidney and testes). The design provides four known ratio measurements of >200 reference probes, which were chosen for their tissue-selectivity, dynamic range coverage and alignment to the same exemplar transcript sequence across all three platforms. The data generated from testing three biological replicates of the reagent at eight laboratories on three array formats provides a benchmark set for both laboratory and data processing performance assessments. Close agreement with target ratios adjusted for sample complexity was achieved on all platforms and low variance was observed among platforms, replicates and sites. The mixed tissue design produces a reagent with known gene expression changes within a complex sample and can serve as a paradigm for performance standards for microarrays that target other species

Heterozygous frameshift variants in HNRNPA2B1 cause early-onset oculopharyngeal muscular dystrophy

Missense variants in RNA-binding proteins (RBPs) underlie a spectrum of disease phenotypes, including amyotrophic lateral sclerosis, frontotemporal dementia, and inclusion body myopathy. Here, we present ten independent families with a severe, progressive muscular dystrophy, reminiscent of oculopharyngeal muscular dystrophy (OPMD) but of much earlier onset, caused by heterozygous frameshift variants in the RBP hnRNPA2/B1. All disease-causing frameshift mutations abolish the native stop codon and extend the reading frame, creating novel transcripts that escape nonsense-mediated decay and are translated to produce hnRNPA2/B1 protein with the same neomorphic C-terminal sequence. In contrast to previously reported disease-causing missense variants in HNRNPA2B1, these frameshift variants do not increase the propensity of hnRNPA2 protein to fibrillize. Rather, the frameshift variants have reduced affinity for the nuclear import receptor karyopherin β2, resulting in cytoplasmic accumulation of hnRNPA2 protein in cells and in animal models that recapitulate the human pathology. Thus, we expand the phenotypes associated with HNRNPA2B1 to include an early-onset form of OPMD caused by frameshift variants that alter its nucleocytoplasmic transport dynamics

THE EFFECT OF HYDROGEN ON PALLADIUM - METAL-OXIDE-SILICON CAPACITORS (INTERFACE STATES, CAPACITANCE, CONDUCTANCE, CHEMICAL SENSORS, DIFFUSION)

A palladium gate is used to inject hydrogen into a Pd-oxide-silicon capacitor by exposure to hydrogen gas. The hydrogen can be removed reversibly from the Pd-MOSCAP by exposure to oxygen at the measurement temperature. The admittance-frequency characteristics are measured at temperature in the ambient. Results are presented which demonstrate that hydrogen injected from the Pd can diffuse through a thermally grown oxide and into the silicon substrate. A change in the conductance is observed which is a result of the hydrogen injected to the oxide-silicon interface. A thermally oxidized n-type wafer with a boron implant extending 100nm below the oxide is used to demonstrate hydrogen diffusion into the silicon. Capacitance measurements in hydrogen reveal that the boron acceptors have been electrically deactivated. The effect is reversible by exchanging hydrogen and oxygen gases. The change in the conductance characteristics is analyzed using the conductance method. It is concluded that there is a change in the state density and the electron capture probability due to the hydrogen. Results are compared for samples of different fabrication techniques. The results are discussed in light of present models

THE EFFECT OF HYDROGEN ON PALLADIUM - METAL-OXIDE-SILICON CAPACITORS (INTERFACE STATES, CAPACITANCE, CONDUCTANCE, CHEMICAL SENSORS, DIFFUSION)

A palladium gate is used to inject hydrogen into a Pd-oxide-silicon capacitor by exposure to hydrogen gas. The hydrogen can be removed reversibly from the Pd-MOSCAP by exposure to oxygen at the measurement temperature. The admittance-frequency characteristics are measured at temperature in the ambient. Results are presented which demonstrate that hydrogen injected from the Pd can diffuse through a thermally grown oxide and into the silicon substrate. A change in the conductance is observed which is a result of the hydrogen injected to the oxide-silicon interface. A thermally oxidized n-type wafer with a boron implant extending 100nm below the oxide is used to demonstrate hydrogen diffusion into the silicon. Capacitance measurements in hydrogen reveal that the boron acceptors have been electrically deactivated. The effect is reversible by exchanging hydrogen and oxygen gases. The change in the conductance characteristics is analyzed using the conductance method. It is concluded that there is a change in the state density and the electron capture probability due to the hydrogen. Results are compared for samples of different fabrication techniques. The results are discussed in light of present models

Contribution à l'étude des epanchements pleuraux d'etiologie virale.

Diss. Nancy.OPLADEN-RUG0

In the wilderness,

Mode of access: Internet

Self-Assembly-Driven Bi2S3 Nanobelts Integrated a Silk-Fibroin-Based 3D-Printed Aerogel-Based Scaffold with a Dual-Network Structure for Photothermal Bone Cancer Therapy

: Multifunctional all-in-one biomaterial combining the therapeutic and regeneration functionalities for successive tumor therapy and tissue regeneration is in high demand in interdisciplinary research. In this study, a three-dimensional (3D) aerogel-based composite scaffold with a dual-network structure generated through self-assembly and photo-cross-linking with combined properties of photothermally triggered controlled anticancer drug release and photothermal cancer cell ablation was successfully fabricated. The fabrication of composites consists of self-assembly of a silk fibroin methacrylate (SF-MA) biopolymer incorporated with hydrothermally driven bismuth sulfide (Bi2S3) methacrylate nanobelts, followed by a photo-cross-linking-assisted 3D-printing process. The developed scaffolds presented hierarchically organized porosity and excellent photothermal conversion thanks to the strong near-infrared (NIR) photon absorption of incorporated Bi2S3 nanobelts inside the scaffold matrix. The heat generated in the scaffold mediated by laser irradiation has not only triggered controlled and prolonged release of the anticancer drug but also significantly ablated the bone cancer cells adhered on the scaffold. In addition, the developed 3D composite scaffolds have demonstrated excellent biodegradability for organic and inorganic network constituents at different media, enabling them as potential implants to be replaced by de novo tissue. In combination of chemotherapy and photothermal therapy, the multifunctional 3D-printed composite aerogel scaffold is expected to be an excellent implantable material in bone tissue engineering (BTE) for successive cancer therapy and tissue regeneration

Development of a microarray platform for FFPET profiling: application to the classification of human tumors

Abstract Background mRNA profiling has become an important tool for developing and validating prognostic assays predictive of disease treatment response and outcome. Archives of annotated formalin-fixed paraffin-embedded tissues (FFPET) are available as a potential source for retrospective studies. Methods are needed to profile these FFPET samples that are linked to clinical outcomes to generate hypotheses that could lead to classifiers for clinical applications. Methods We developed a two-color microarray-based profiling platform by optimizing target amplification, experimental design, quality control, and microarray content and applied it to the profiling of FFPET samples. We profiled a set of 50 fresh frozen (FF) breast cancer samples and assigned class labels according to the signature and method by van 't Veer et al 1 and then profiled 50 matched FFPET samples to test how well the FFPET data predicted the class labels. We also compared the sorting power of classifiers derived from FFPET sample data with classifiers derived from data from matched FF samples. Results When a classifier developed with matched FF samples was applied to FFPET data to assign samples to either "good" or "poor" outcome class labels, the classifier was able to assign the FFPET samples to the correct class label with an average error rate = 12% to 16%, respectively, with an Odds Ratio = 36.4 to 60.4, respectively. A classifier derived from FFPET data was able to predict the class label in FFPET samples (leave-one-out cross validation) with an error rate of ~14% (p-value = 3.7 × 10-7). When applied to the matched FF samples, the FFPET-derived classifier was able to assign FF samples to the correct class labels with 96% accuracy. The single misclassification was attributed to poor sample quality, as measured by qPCR on total RNA, which emphasizes the need for sample quality control before profiling. Conclusion We have optimized a platform for expression analyses and have shown that our profiling platform is able to accurately sort FFPET samples into class labels derived from FF classifiers. Furthermore, using this platform, a classifier derived from FFPET samples can reliably provide the same sorting power as a classifier derived from matched FF samples. We anticipate that these techniques could be used to generate hypotheses from archives of FFPET samples, and thus may lead to prognostic and predictive classifiers that could be used, for example, to segregate patients for clinical trial enrollment or to guide patient treatment.</p