Application of droplet digital PCR in minimal residual disease monitoring of rare fusion transcripts and mutations in haematological malignancies.

Leukaemia of various subtypes are driven by distinct chromosomal rearrangement or genetic abnormalities. The leukaemogenic fusion transcripts or genetic mutations serve as molecular markers for minimal residual disease (MRD) monitoring. The current study evaluated the applicability of several droplet digital PCR assays for the detection of these targets at RNA and DNA levels (atypical BCR::ABL1 e19a2, e23a2ins52, e13a2ins74, rare types of CBFB::MYH11 (G and I), PCM1::JAK2, KMT2A::ELL2, PICALM::MLLT10 fusion transcripts and CEBPA frame-shift and insertion/duplication mutations) with high sensitivity. The analytical performances were assessed by the limit of blanks, limit of detection, limit of quantification and linear regression. Our data demonstrated serial MRD monitoring for patients at molecular level could become "digitalized", which was deemed important to guide clinicians in treatment decision for better patient care.

Ion Migration Studies in Exfoliated 2D Molybdenum Oxide via Ionic Liquid Gating for Neuromorphic Device Applications.

The formation of an electric double layer in ionic liquid (IL) can electrostatically induce charge carriers and/or intercalate ions in and out of the lattice which can trigger a large change of the electronic, optical, and magnetic properties of materials and even modify the crystal structure. We present a systematic study of ionic liquid gating of exfoliated 2D molybdenum trioxide (MoO3) devices and correlate the resultant electrical properties to the electrochemical doping via ion migration during the IL biasing process. A nearly 9 orders of magnitude modulation of the MoO3 conductivity is obtained for the two types of ionic liquids that are investigated. In addition, notably rapid on/off switching was realized through a lithium-containing ionic liquid whereas much slower modulation was induced via oxygen extraction/intercalation. Time of flight-secondary ion mass spectrometry confirms the Li intercalation. Density functional theory (DFT) calculations have been carried out to examine the underlying metallization mechanism. Results of short-pulse tests show the potential of these MoO3 devices as neuromorphic computing elements due to their synaptic plasticity.

Role of Electrical Double Layer Structure in Ionic Liquid Gated Devices.

Ionic liquid gating of transition metal oxides has enabled new states (magnetic, electronic, metal-insulator), providing fundamental insights into the physics of strongly correlated oxides. However, despite much research activity, little is known about the correlation of the structure of the liquids in contact with the transition metal oxide surface, its evolution with the applied electric potential, and its correlation with the measured electronic properties of the oxide. Here, we investigate the structure of an ionic liquid at a semiconducting oxide interface during the operation of a thin film transistor where the electrical double layer gates the device using experiment and theory. We show that the transition between the ON and OFF states of the amorphous indium gallium zinc oxide transistor is accompanied by a densification and preferential spatial orientation of counterions at the oxide channel surface. This process occurs in three distinct steps, corresponding to ion orientations, and consequently, regimes of different electrical conductivity. The reason for this can be found in the surface charge densities on the oxide surface when different ion arrangements are present. Overall, the field-effect gating process is elucidated in terms of the interfacial ionic liquid structure, and this provides unprecedented insight into the working of a liquid gated transistor linking the nanoscopic structure to the functional properties. This knowledge will enable both new ionic liquid design as well as advanced device concepts.

High performance top-gated multilayer WSe2 field effect transistors.

In this paper, high performance top-gated WSe2 field effect transistor (FET) devices are demonstrated via a two-step remote plasma assisted ALD process. High-quality, low-leakage aluminum oxide (Al2O3) gate dielectric layers are deposited onto the WSe2 channel using a remote plasma assisted ALD process with an ultrathin (∼1 nm) titanium buffer layer. The first few nanometers (∼2 nm) of the Al2O3 dielectric film is deposited at relatively low temperature (i.e. 50 °C) and remainder of the film is deposited at 150 °C to ensure the conformal coating of Al2O3 on the WSe2 surface. Additionally, an ultra-thin titanium buffer layer is introduced at the WSe2 channel surface prior to ALD process to mitigate oxygen plasma induced doping effects. Excellent device characteristics with current on-off ratio in excess of 106 and a field effect mobility as high as 70.1 cm2 V-1 s-1 are achieved in a few-layer WSe2 FET device with a 30 nm Al2O3 top-gate dielectric. With further investigation and careful optimization, this method can play an important role for the realization of high performance top gated FETs for future optoelectronic device applications.

Reversible Control of Interfacial Magnetism through Ionic-Liquid-Assisted Polarization Switching.

The ability to control magnetism of materials via electric field enables a myriad of technological innovations in information storage, sensing, and computing. We use ionic-liquid-assisted ferroelectric switching to demonstrate reversible modulation of interfacial magnetism in a multiferroic heterostructure composed of ferromagnetic (FM) La0.8Sr0.2MnO3 and ferroelectric (FE) PbZr0.2Ti0.8O3. It is shown that ionic liquids can be used to persistently and reversibly switch a large area of a FE film. This is a prerequisite for polarized neutron reflectometry (PNR) studies that are conducted to directly probe magnetoelectric coupling of the FE polarization to the interfacial magnetization.

Target fluorescence in-situ hybridization (Target FISH) for plasma cell enrichment in myeloma.

BACKGROUND: Cytogenetic abnormalities are important prognostic markers in plasma cell myeloma (PCM) and detection is routinely performed by interphase fluorescence in-situ hybridization (FISH) with a panel of probes after enrichment of the plasma cells in the bone marrow specimen. Cell sorting by immunomagnetic beads and concurrent labeling of the cytoplasmic immunoglobulin are the usual enrichment methods. We present an alternative method of plasma cell enrichment termed Target FISH, which is an automated system that combines the images of May-Grünwald- Giemsa (MGG) staining and FISH study on the same plasma cell for analysis. RESULTS: Our experience of Target FISH on 40 PCM patients was described. Briefly, plasma cells were MGG stained, image captured, de-stained, FISH probe hybridized and finally relocated for simultaneous analysis of morphology and FISH signal pattern. The FISH probe panel was TP53/CEP17, t(4;14) IGH/FGFR3, t(14;16) IGH/MAF and CKS1B(1q21)/CDKN2C(P18). Gain of 1q21 was the most common abnormality detected in 18 patients (45 %), to be followed by t(4;14) IGH/FGFR3 detected in 11 patients (27.5 %). Of note, 10 patients showed coexistence of both t(4;14) and 1q21 gain. Two patients showed del(17p)/TP53, one in association with t(4;14) and 1q gain while the other was stand alone. None of this patient cohort showed t(14;16) IGH/MAF. Using the critical binomial function, the normal cutoff FISH positive value for del(17p)/TP53 was 3.4 %, t(4;14) IGH/FGFR3 was 6.8 %, t(14;16) IGH/MAF was 5.6 % and +1q21 was 5.7 %. CONCLUSIONS: The equipment cost notwithstanding, when compared with cell sorting, the total reagent cost was around 10 % lower in Target FISH. The total processing time was longer for Target FISH but manual fluorescence microscopy was no longer necessary. The main advantage of Target FISH was the complete certainty that the cytogenetic abnormality was detected in the cells of interest, and hence a more stringent analytical cutoff value might be considered. Optimization of the cell collection and slide preparation process upfront was required to accrue adequate target cells on each slide for analysis. Our experience suggested that Target FISH was applicable as a routine method of plasma cell enrichment in clinical diagnostic laboratories.

Dynamic defect correlations dominate activated electronic transport in SrTiO3.

Strontium titanate (SrTiO3, STO) is a critically important material for the study of emergent electronic phases in complex oxides, as well as for the development of applications based on their heterostructures. Despite the large body of knowledge on STO, there are still many uncertainties regarding the role of defects in the properties of STO, including their influence on ferroelectricity in bulk STO and ferromagnetism in STO-based heterostructures. We present a detailed analysis of the decay of persistent photoconductivity in STO single crystals with defect concentrations that are relatively low but significantly affect their electronic properties. The results show that photo-activated electron transport cannot be described by a superposition of the properties due to independent point defects as current models suggest but is, instead, governed by defect complexes that interact through dynamic correlations. These results emphasize the importance of defect correlations for activated electronic transport properties of semiconducting and insulating perovskite oxides.

Detection of Germline Mutation in Hereditary Breast and/or Ovarian Cancers by Next-Generation Sequencing on a Four-Gene Panel.

Mutation in BRCA1/BRCA2 genes accounts for 20% of familial breast cancers, 5% to 10% of which may be due to other less penetrant genes which are still incompletely studied. Herein, a four-gene panel was used to examine the prevalence of BRCA1, BRCA2, TP53, and PTEN in hereditary breast and ovarian cancers in Southern Chinese population. In this cohort, 948 high-risk breast and/or ovarian patients were recruited for genetic screening by next-generation sequencing (NGS). The performance of our NGS pipeline was evaluated with 80 Sanger-validated known mutations and eight negative cases. With appropriate bioinformatics analysis pipeline, the detection sensitivity of NGS is comparable with Sanger sequencing. The prevalence of BRCA1/BRCA2 germline mutations was 9.4% in our Chinese cohort, of which 48.8% of the mutations arose from hotspot mutations. With the use of a tailor-made algorithm, HomopolymerQZ, more mutations were detected compared with single mutation detection algorithm. The frequencies of PTEN and TP53 were 0.21% and 0.53%, respectively, in the Southern Chinese patients with breast and/or ovarian cancers. High-throughput NGS approach allows the incorporation of control cohort that provides an ethnicity-specific data for polymorphic variants. Our data suggest that hotspot mutations screening such as SNaPshot could be an effective preliminary screening alternative adopted in a standard clinical laboratory without NGS setup.

Epitaxial Growth of Intermetallic MnPt Films on Oxides and Large Exchange Bias.

High-quality epitaxial growth of inter-metallic MnPt films on oxides is achieved, with potential for multiferroic heterostructure applications. Antisite-stabilized spin-flipping induces ferromagnetism in MnPt films, although it is robustly antiferromagnetic in bulk. Moreover, highly ordered antiferromagnetic MnPt films exhibit superiorly large exchange coupling with a ferromagnetic layer.

Strain Doping: Reversible Single-Axis Control of a Complex Oxide Lattice via Helium Implantation.

We report on the use of helium ion implantation to independently control the out-of-plane lattice constant in epitaxial La(0.7)Sr(0.3)MnO(3) thin films without changing the in-plane lattice constants. The process is reversible by a vacuum anneal. Resistance and magnetization measurements show that even a small increase in the out-of-plane lattice constant of less than 1% can shift the metal-insulator transition and Curie temperatures by more than 100 °C. Unlike conventional epitaxy-based strain tuning methods which are constrained not only by the Poisson effect but by the limited set of available substrates, the present study shows that strain can be independently and continuously controlled along a single axis. This permits novel control over orbital populations through Jahn-Teller effects, as shown by Monte Carlo simulations on a double-exchange model. The ability to reversibly control a single lattice parameter substantially broadens the phase space for experimental exploration of predictive models and leads to new possibilities for control over materials' functional properties.

Evaluation of 2 real-time PCR assays for in vitro diagnostic use in the rapid and multiplex detection of EGFR gene mutations in NSCLC.

Activating mutations of the epidermal growth factor receptor (EGFR) gene in non-small cell lung cancer predict for a favorable clinical response to tyrosine kinase inhibitor therapy. Although Sanger sequencing is a conventional method to detect EGFR gene mutations, multiplex real-time allele-specific polymerase chain reaction (PCR) systems are increasingly used in the routine molecular diagnostic setting. We aim to evaluate 2 proprietary real-time PCR assays (cobas and therascreen) against Sanger sequencing in the detection of EGFR gene mutations. The overall concordance rate between cobas and therascreen assays with Sanger sequencing was 89% and 88%, respectively, and increased to 96% and 98%, respectively, if the mutations not covered were excluded. The cobas assay showed a superior coverage of exon 20 mutations, but L861Q was not targeted. The nature of specimen, DNA integrity, and tumor cell content are factors that affect the assay performance. DNA extracted from cell block and clot of pleural fluid gave rise to 1 invalid call and 1 false-negative result by the cobas assay and 1 missed T790M mutation and 1 false-negative result by the therascreen assay. Both assays are around 5 times more expensive compared with Sanger sequencing in terms of reagent cost. We conclude that both assays prove to be a rapid, simple, and validated method in detecting the most common and clinically significant EGFR gene mutations in non-small cell lung cancer. Although less convenient compared with real-time PCR assays, Sanger sequencing is cheaper in terms of reagent cost and allows the detection of rare or novel EGFR gene mutations.