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.

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.

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.

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.

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%).

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.

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.

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.

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.

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.

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.

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.

Superconducting pair correlations in an amorphous insulating nanohoneycomb film.

The Cooper pairing mechanism that binds single electrons to form pairs in metals allows electrons to circumvent the exclusion principle and condense into a single superconducting or zero-resistance state. We present results from an amorphous bismuth film system patterned with a nanohoneycomb array of holes, which undergoes a thickness-tuned insulator-superconductor transition. The insulating films exhibit activated resistances and magnetoresistance oscillations dictated by the superconducting flux quantum h/2e. This 2e period is direct evidence indicating that Cooper pairing is also responsible for electrically insulating behavior.

Subgap density of states in superconductor-normal metal bilayers in the cooper limit.

We present transport and tunneling measurements of Pb-Ag bilayers with thicknesses, d(Pb) and d(Ag), that are much less than the superconducting coherence length. The transition temperature, T(c), and energy gap, Delta, in the tunneling density of states (DOS) decrease exponentially with d(Ag) at fixed d(Pb). Simultaneously, a DOS that increases linearly from the Fermi energy grows and introduces states within the gap. The integrated subgap DOS approaches 40% of the normal state value in the lowest T(c) film investigated (T(c) approximately 0.1 T(Pb)(c,bulk)). This behavior suggests that a growing fraction of quasiparticles decouple from the superconductor as T(c)-->0. The linear dependence is consistent with the quasiparticles becoming trapped on integrable trajectories in the metal layer.

Postpartum uterine involution in sheep: histoarchitecture and changes in endometrial gene expression.

After parturition, the uterus undergoes marked remodelling during involution; however, little is known of the hormonal, cellular and molecular mechanisms that regulate this process. The working hypothesis used in this study is that return of the ovine uterus to a non-pregnant state involves termination of a hormonal servomechanism that regulates endometrial gland morphogenesis and function during pregnancy. Suffolk ewes were ovariohysterectomized on postpartum days 1, 7, 14 or 28. Serum concentrations of oestradiol were high at parturition, declined to postpartum day 4, peaked on postpartum day 6, and then declined and remained low thereafter. Progesterone was undetectable in plasma from ewes post partum. Uterine wet mass and horn length decreased after postpartum day 1, but ovarian mass did not change. Residual placental cotyledons were present in the maternal caruncles on postpartum days 1 and 7 and were extruded by postpartum day 14 as plaques that were resorbed by postpartum day 28. The width of the total endometrium, stratum compactum, stratum spongiosum and myometrium, as well as endometrial gland density, decreased after parturition. Most apoptotic cells in the involuting uterus were large, vacuolated and located between the endometrial glandular epithelial cells on postpartum days 1 and 7. Immunofluorescence analyses identified both T and B cells within the glandular epithelium on postpartum day 1. Cell proliferation was detected in the luminal epithelium and glandular epithelium on postpartum days 1 and 7. On postpartum day 1, expression of oestrogen receptor alpha (ERalpha) was not detected in luminal epithelium and was low in glandular epithelium, but ERalpha was present in epithelia thereafter. Progesterone receptor (PR) protein was not detected in endometrial epithelia on postpartum day 1, but was detected in the glandular epithelium thereafter. Between postpartum days 1 and 7, ERalpha and PR protein increased substantially in the endometrial glandular epithelium. On postpartum days 1-28, abundant expression of oxytocin receptor mRNA was detected in endometrial luminal epithelium and superficial to the middle glandular epithelium. Prolactin receptor (PRLR) mRNA was detected in glandular epithelium on all postpartum days, whereas mRNA for uterine milk protein (UTMP), an index of secretory capacity of glandular epithelium, was present only on postpartum day 1. Collectively, these results indicate that uterine involution in ewes involves remodelling of both caruncular and intercaruncular areas of the uterine wall and termination of differentiated uterine gland functions characteristic of pregnancy.

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.