Aligning tumor mutational burden (TMB) quantification across diagnostic platforms: phase II of the Friends of Cancer Research TMB Harmonization Project.

BACKGROUND: Tumor mutational burden (TMB) measurements aid in identifying patients who are likely to benefit from immunotherapy; however, there is empirical variability across panel assays and factors contributing to this variability have not been comprehensively investigated. Identifying sources of variability can help facilitate comparability across different panel assays, which may aid in broader adoption of panel assays and development of clinical applications. MATERIALS AND METHODS: Twenty-nine tumor samples and 10 human-derived cell lines were processed and distributed to 16 laboratories; each used their own bioinformatics pipelines to calculate TMB and compare to whole exome results. Additionally, theoretical positive percent agreement (PPA) and negative percent agreement (NPA) of TMB were estimated. The impact of filtering pathogenic and germline variants on TMB estimates was assessed. Calibration curves specific to each panel assay were developed to facilitate translation of panel TMB values to whole exome sequencing (WES) TMB values. RESULTS: Panel sizes >667 Kb are necessary to maintain adequate PPA and NPA for calling TMB high versus TMB low across the range of cut-offs used in practice. Failure to filter out pathogenic variants when estimating panel TMB resulted in overestimating TMB relative to WES for all assays. Filtering out potential germline variants at >0% population minor allele frequency resulted in the strongest correlation to WES TMB. Application of a calibration approach derived from The Cancer Genome Atlas data, tailored to each panel assay, reduced the spread of panel TMB values around the WES TMB as reflected in lower root mean squared error (RMSE) for 26/29 (90%) of the clinical samples. CONCLUSIONS: Estimation of TMB varies across different panels, with panel size, gene content, and bioinformatics pipelines contributing to empirical variability. Statistical calibration can achieve more consistent results across panels and allows for comparison of TMB values across various panel assays. To promote reproducibility and comparability across assays, a software tool was developed and made publicly available.

AC signal characterization for optimization of a CMOS single-electron pump.

Pumping single electrons at a set rate is being widely pursued as an electrical current standard. Semiconductor charge pumps have been pursued in a variety of modes, including single gate ratchet, a variety of 2-gate ratchet pumps, and 2-gate turnstiles. Whether pumping with one or two AC signals, lower error rates can result from better knowledge of the properties of the AC signal at the device. In this work, we operated a CMOS single-electron pump with a 2-gate ratchet style measurement and used the results to characterize and optimize our two AC signals. Fitting this data at various frequencies revealed both a difference in signal path length and attenuation between our two AC lines. Using this data, we corrected for the difference in signal path length and attenuation by applying an offset in both the phase and the amplitude at the signal generator. Operating the device as a turnstile while using the optimized parameters determined from the 2-gate ratchet measurement led to much flatter, more robust charge pumping plateaus. This method was useful in tuning our device up for optimal charge pumping, and may prove useful to the semiconductor quantum dot community to determine signal attenuation and path differences at the device.

Developing Single Layer MOS Quantum Dots for Diagnostic Qubits.

The design, fabrication and characterization of single metal gate layer, metal-oxide-semiconductor (MOS) quantum dot devices robust against dielectric breakdown are presented as prototypes for future diagnostic qubits. These devices were developed as a preliminary solution to a longer term goal of a qubit platform for intercomparison between materials or for in-line diagnostics, and to provide a testbed for establishing classical measurements predictive of coherence performance. For this stage, we seek a robust MOS design that is compatible with wafer and chip architectures, that has a reduced process overhead and is sufficiently capable of challenging and advancing our measurement capabilities. In this report, we present our initial batch of silicon MOS devices using a single gate layer, which have not exhibited any failures with gate voltage excursions > 10 V, but do exhibit the reduced electrostatic control expected of a single gate layer design. We observe quantum dot formation, capacitive charge sensing between channels, and reasonable effective electron temperatures that enable spin qubit studies. The costs and benefits of the trade-off between device performance and fabrication efficiency will be discussed, as well as opportunities for future improvements.

Alternatives to aluminum gates for silicon quantum devices: defects and strain.

Gate-defined quantum dots (QD) benefit from the use of small grain size metals for gate materials because it aids in shrinking the device dimensions. However, it is not clear what differences arise with respect to process-induced defect densities and inhomogeneous strain. Here, we present measurements of fixed charge, Q f , interface trap density, D it , the intrinsic film stress, σ, and the coefficient of thermal expansion, α as a function of forming gas anneal temperature for Al, Ti/Pd, and Ti/Pt gates. We show D it is minimal at an anneal temperature of 350 °C for all materials but Ti/Pd and Ti/Pt have higher Q f and D it compared to Al. In addition, σ and α increase with anneal temperature for all three metals with α larger than the bulk value. These results indicate that there is a tradeoff between minimizing defects and minimizing the impact of strain in quantum device fabrication.

Field evolution of coexisting superconducting and magnetic orders in CeCoIn5.

We present nuclear magnetic resonance (NMR) measurements on the three distinct In sites of CeCoIn5 with a magnetic field applied in the [100] direction. We identify the microscopic nature of the long range magnetic order (LRO) stabilized at low temperatures in fields above 10.2 T while still in the superconducting (SC) state. We infer that the ordered moment is oriented along the c axis and map its field evolution. The study of the field dependence of the NMR shift for the different In sites indicates that the LRO likely coexists with a modulated SC phase, possibly that predicted by Fulde, Ferrell, Larkin, and Ovchinnikov. Furthermore, we discern a field region dominated by strong spin fluctuations where static LRO is absent and propose a revised phase diagram.

A Reusable, Low-profile, Cryogenic Wire Seal.

We describe the design of a reusable Indium wire seal which has a small profile and is leak tight to better than 1x10(-10) std. cc/sec. from room temperature down to approximately mK. The pressure necessary to deform the Indium wire o-ring is provided by a screw-cap mating to threads on the outside of the cylindrical volume to be sealed.

The effect of strain on tunnel barrier height in silicon quantum devices.

Semiconductor quantum dot (QD) devices experience a modulation of the band structure at the edge of lithographically defined gates due to mechanical strain. This modulation can play a prominent role in the device behavior at low temperatures, where QD devices operate. Here, we develop an electrical measurement of strain based on the I(V) characteristics of tunnel junctions defined by aluminum and titanium gates. We measure relative differences in the tunnel barrier height due to strain consistent with experimentally measured coefficients of thermal expansion (α) that differ from the bulk values. Our results show that the bulk parameters commonly used for simulating strain in QD devices incorrectly capture the impact of strain. The method presented here provides a path forward towards exploring different gate materials and fabrication processes in silicon QDs in order to optimize strain.

Reduction of charge offset drift using plasma oxidized aluminum in SETs.

Aluminum oxide ([Formula: see text])-based single-electron transistors (SETs) fabricated in ultra-high vacuum (UHV) chambers using in situ plasma oxidation show excellent stabilities over more than a week, enabling applications as tunnel barriers, capacitor dielectrics or gate insulators in close proximity to qubit devices. Historically, [Formula: see text]-based SETs exhibit time instabilities due to charge defect rearrangements and defects in [Formula: see text] often dominate the loss mechanisms in superconducting quantum computation. To characterize the charge offset stability of our [Formula: see text]-based devices, we fabricate SETs with sub-1 e charge sensitivity and utilize charge offset drift measurements (measuring voltage shifts in the SET control curve). The charge offset drift ([Formula: see text]) measured from the plasma oxidized [Formula: see text] SETs in this work is remarkably reduced (best [Formula: see text] over [Formula: see text] days and no observation of [Formula: see text] exceeding [Formula: see text]), compared to the results of conventionally fabricated [Formula: see text] tunnel barriers in previous studies (best [Formula: see text] over [Formula: see text] days and most [Formula: see text] within one day). We attribute this improvement primarily to using plasma oxidation, which forms the tunnel barrier with fewer two-level system (TLS) defects, and secondarily to fabricating the devices entirely within a UHV system.

Observation of giant positive magnetoresistance in a Cooper pair insulator.

Ultrathin amorphous Bi films, patterned with a nanohoneycomb array of holes, can exhibit an insulating phase with transport dominated by the incoherent motion of Cooper pairs (CP) of electrons between localized states. Here, we show that the magnetoresistance (MR) of this Cooper pair insulator (CPI) phase is positive and grows exponentially with decreasing temperature T, for T well below the pair formation temperature. It peaks at a field estimated to be sufficient to break the pairs and then decreases monotonically into a regime in which the film resistance assumes the T dependence appropriate for weakly localized single electron transport. We discuss how these results support proposals that the large MR peaks in other unpatterned, ultrathin film systems disclose a CPI phase and provide new insight into the CP localization.

Low-Resistance, High-Yield Electrical Contacts to Atom Scale Si:P Devices Using Palladium Silicide.

Scanning tunneling microscopy (STM) enables the fabrication of two-dimensional δ-doped structures in Si with atomistic precision, with applications from tunnel field-effect transistors to qubits. The combination of a very small contact area and the restrictive thermal budget necessary to maintain the integrity of the δ layer make developing a robust electrical contact method a significant challenge to realizing the potential of atomically precise devices. We demonstrate a method for electrical contact using Pd2Si formed at the temperature of silicon overgrowth (250 °C), minimizing the diffusive impact on the δ layer. We use the transfer length method to show our Pd2Si contacts have very high yield (99.7% +0.2% -1.5%) and low resistivity (272±41Ωµm) in contacting mesa-etched Si:P δ layers. We also present three terminal measurements of low contact resistance (<1 kΩ) to devices written by STM hydrogen depassivation lithography with similarly high yield (100% +0% -3.2%).

Effect of device design on charge offset drift in Si/SiO2 single electron devices.

We have measured the low-frequency time instability known as charge offset drift of Si/SiO2 single electron devices (SEDs) with and without an overall poly-Si top gate. We find that SEDs with a poly-Si top gate have significantly less charge offset drift, exhibiting fewer isolated jumps and a factor of two reduction in fluctuations about a stable mean value. The observed reduction can be accounted for by the electrostatic reduction in the mutual capacitance Cm between defects and the quantum dot, and increase in the total defect capacitance Cd due to the top gate. These results depart from the prominent interpretation that the level of charge offset drift in SEDs is determined by the intrinsic material properties, forcing consideration of the device design as well. We expect these results to be of importance in developing SEDs for applications from quantum information to metrology or wherever charge noise or integrability of devices is a challenge.

STM patterned nanowire measurements using photolithographically defined implants in Si(100).

Using photolithographically defined implant wires for electrical connections, we demonstrate measurement of a scanning tunneling microscope (STM) patterned nanoscale electronic device on Si(100). By eliminating onerous alignment and complex lithography techniques, this approach is accessible to researchers in smaller efforts who may not have access to tools like electron beam lithography. Electrical contact to the nanodevices is achieved by implanting patterned, degenerately doped wires in the substrate using photolithography and commercial low energy ion implantation. We bring several isolated, implanted wires to within the STM scanner's field of view where the STM can detect and smoothly draw contiguous patterns that directly overlap with implant lines for electrical connections. This overlapping provides a two-dimensional (2D) overlap interface with the 2D electron system, in contrast to many state-of-the-art methods that rely on contacting an exposed edge. After the STM pattern is phosphine dosed and overgrown with silicon, photolithography is then used again to align (≈ 160 µm)2 aluminum contact pads onto (≈ 200 µm)2 implanted areas at the ends of the wires. We present detailed results that optimize the spacing of neighboring wires while maintaining electrical isolation after heating to > 1200 °C, a step required for in situ Si surface preparation.

Quantifying atom-scale dopant movement and electrical activation in Si:P monolayers.

Advanced hydrogen lithography techniques and low-temperature epitaxial overgrowth enable the patterning of highly phosphorus-doped silicon (Si:P) monolayers (ML) with atomic precision. This approach to device fabrication has made Si:P monolayer systems a testbed for multiqubit quantum computing architectures and atomically precise 2-D superlattice designs whose behaviors are directly tied to the deterministic placement of single dopants. However, dopant segregation, diffusion, surface roughening, and defect formation during the encapsulation overgrowth introduce large uncertainties to the exact dopant placement and activation ratio. In this study, we develop a unique method by combining dopant segregation/diffusion models with sputter profiling simulation to monitor and control, at the atomic scale, dopant movement using room-temperature grown locking layers (LLs). We explore the impact of LL growth rate, thickness, rapid thermal annealing, surface accumulation, and growth front roughness on dopant confinement, local crystalline quality, and electrical activation within Si:P 2-D systems. We demonstrate that dopant movement can be more efficiently suppressed by increasing the LL growth rate than by increasing the LL thickness. We find that the dopant segregation length can be suppressed below a single Si lattice constant by increasing the LL growth rates at room temperature while maintaining epitaxy. Although dopant diffusivity within the LL is found to remain high (on the order of 10-17 cm2 s-1) even below the hydrogen desorption temperature, we demonstrate that exceptionally sharp dopant confinement with high electrical quality within Si:P monolayers can be achieved by combining a high LL growth rate with low-temperature LL rapid thermal annealing. The method developed in this study provides a key tool for 2-D fabrication techniques that require precise dopant placement to suppress, quantify, and predict a single dopant's movement at the atomic scale.

A new regime of Pauli-spin blockade.

Pauli-spin blockade (PSB) is a transport phenomenon in double quantum dots that allows for a type of spin to charge conversion often used to probe fundamental physics such as spin relaxation and singlet-triplet coupling. In this paper, we theoretically explore Pauli-spin blockade as a function of magnetic field B applied parallel to the substrate. In the well-studied low magnetic field regime, where PSB occurs in the forward (1, 1) → (0, 2) tunneling direction, we highlight some aspects of PSB that are not discussed in detail in existing literature, including the change in size of both bias triangles measured in the forward and reverse biasing directions as a function of B. At higher fields, we predict a crossover to "reverse PSB" in which current is blockaded in the reverse direction due to the occupation of a spin singlet as opposed to the traditional triplet blockade that occurs at low fields. The onset of reverse PSB coincides with the development of a tail like feature in the measured bias triangles and occurs when the Zeeman energy of the polarized triplet equals the exchange energy in the (0, 2) charge configuration. In Si quantum dots, these fields are experimentally accessible; thus, this work suggests a way to observe a crossover in magnetic field to qualitatively different behavior.

A quantitative study of bias triangles presented in chemical potential space.

We present measurements of bias triangles in several biasing configurations. Using a capacitive model and two fit parameters we are able to predict the shapes and locations of the bias triangles in all measurement configurations. Furthermore, analysis of the data using this model allows us to present data from all four possible bias configurations on a single plot in chemical potential space. This presentation allows comparison between different biasing directions to be made in a clean and straightforward manner. Our analysis and presentation will prove useful in demonstrations of Pauli-spin blockade where comparisons between different biasing directions are paramount. The long term stability of the CMOS compatible Si/SiO2 only architecture leads to the success of this analysis. We also propose a simple variation to this analysis that will extend its use to systems lacking the long term stability of these devices.

Interferon-tau (IFNtau) regulation of IFN-stimulated gene expression in cell lines lacking specific IFN-signaling components.

Interferon-tau (IFNtau) is a unique type I IFN secreted by the ruminant conceptus that acts in a paracrine manner on the endometrial epithelium to signal pregnancy recognition. In the ovine endometrium, IFNtau suppresses estrogen receptor alpha and oxytocin receptor gene expression, but increases or induces expression of IFN-simulated genes (ISGs), including signal transducer and activator of transcription-1 (STAT1), STAT2, ISG factor-3gamma (ISGF3gamma)/p48/IFN regulatory factor-9, and 2',5'-oligoadenylate synthetase (OAS). Human fibroblast cell lines lacking specific IFN signaling components were employed to determine the roles of STAT1, STAT2, and ISGF3gamma in the effects of IFNtau on ISG protein expression. Results indicated that STAT1alpha or STAT1beta is required for IFNtau effects on STAT2, ISGF3gamma, and OAS (40/46, 69/71, and 100 kDa). STAT2 is required for effects on STAT1, ISGF3gamma, and all OAS forms. ISGF3gamma is required for effects of IFNtau on STAT2 and 40/46- and 69/71-kDa OAS and plays a role in the effects of IFNtau on 100-kDa OAS and STAT1. Mutation of Tyr(701), but not Ser(727), of STAT1 abolished the effects of IFNtau on ISG expression. Mutation of the SH2 domain of STAT1 abolished the effects of IFNtau on all ISGs and reduced increases in 100-kDa OAS. These data illustrate the importance of transcription factors composed of STAT1, STAT2, and ISGF3gamma in the signaling pathway mediating the effects of IFNtau on ISG expression.

Interferon-tau activates multiple signal transducer and activator of transcription proteins and has complex effects on interferon-responsive gene transcription in ovine endometrial epithelial cells.

Interferon-tau (IFNtau), a type I IFN produced by sheep conceptus trophectoderm, is the signal for maternal recognition of pregnancy. Although it is clear that IFNtau suppresses transcription of the estrogen receptor alpha and oxytocin receptor genes and induces expression of various IFN-stimulated genes within the endometrial epithelium, little is known of the signal transduction pathway activated by the hormone. This study determined the effects of IFNtau on signal transducer and activator of transcription (STAT) activation, expression, DNA binding, and transcriptional activation using an ovine endometrial epithelial cell line. IFNtau induced persistent tyrosine phosphorylation and nuclear translocation of STAT1 and -2 (10 min to 48 h), but transient phosphorylation and nuclear translocation of STAT3, -5a/b, and -6 (10 to <60 min). IFNtau increased expression of STAT1 and -2, but not STAT3, -5a/b, and -6. IFN-stimulated gene factor-3 and STAT1 homodimers formed and bound an IFN-stimulated response element (ISRE) and gamma-activated sequence (GAS) element, respectively. IFNtau increased transcription of GAS-driven promoters at 3 h, but suppressed their activity at 24 h. In contrast, the activity of an ISRE-driven promoter was increased at 3 and 24 h. These results indicate that IFNtau activates multiple STATs and has differential effects on ISRE- and GAS-driven gene transcription.

Ovine IFN-tau modulates the expression of MHC antigens on murine cerebrovascular endothelial cells and inhibits replication of Theiler's virus.

Interferon-beta (IFN-beta) has been used successfully to treat patients with relapsing-remitting multiple sclerosis (MS). IFN-tau is a new class of type I IFN that is secreted by the trophoblast and is the signal for maternal recognition of pregnancy in sheep. IFN-tau has potent immunosuppressive and antiviral activities similar to other type I IFN but is less cytotoxic than IFN-alpha/beta. The current investigation concerns the effect of recombinant ovine IFN-tau (rOvIFN-tau) on the modulation of MHC class I and II expression on cloned mouse cerebrovascular endothelial (CVE) cells. IFN-tau induced tyrosine phosphorylation of Stat1 and upregulated the expression of MHC class I on CVE. One proposed action by which type I IFN reduce the relapse rate in MS is via interference with IFN-gamma-induced MHC class II expression. IFN-tau was shown to downregulate IFN-gamma-induced MHC class II expression on CVE and, hence, may be of potential therapeutic value in downregulating inflammation in the central nervous system (CNS). IFN-tau did not upregulate the expression of MHC class II on CVE. IFN-tau also inhibited the replication of Theiler's virus in CVE. These in vitro results suggest that IFN-tau may be of therapeutic value in the treatment of virus-induced demyelinating disease.

Subclavian and axillary involvement in temporal arteritis and polymyalgia rheumatica.

PURPOSE: We describe 10 female patients with temporal arteritis (TA) and/or polymyalgia rheumatica (PMR) who presented with upper-extremity ischemia. PATIENTS, METHODS, AND RESULTS: Arm claudication or Raynaud's phenomenon was the initial manifestation of the disease in four cases, appeared with classical symptoms in one case, or occurred during decreasing corticosteroid therapy in five cases. Temporal artery biopsy was performed in nine patients and showed typical giant-cell granulomatous arteritis in seven cases. Angiograms in all cases showed multiple bilateral smooth stenoses, or obliterations of postvertebral subclavian and/or axillary arteries, or both. Symptoms always improved with corticosteroid treatment and none of the patients required reconstructive surgery, although angiography performed after stabilization did not show revascularization of occluded vessels. CONCLUSION: We conclude that large-artery involvement in TA and PMR affects most commonly the subclavian and axillary arteries, with a female predominance comparable to that in Takayasu's arteritis. Both these disorders should be considered in elderly women with occlusive disease of the upper extremities. Although response to steroid therapy was sufficient in our series to avoid surgery, we believe it is preferable to recognize large-artery involvement as early as possible and recommend performance of ultrasonic Doppler examination when any sign of oncoming ischemia or stenosis is observed.