Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Characterization of an electron spin qubit in a Si/SiGe quantum dot

The works presented in this thesiswere supported in part by ArmyResearch Office (W911NF-12-0607), the Dutch Foundation for Fundamental Research on Matter (FOM) and a European Research Council (ERC) Synergy grant; development and maintenance of the growth facilities used for fabricating samples is supported byDOE(DE-FG02-03ER46028). This research utilized NSF-supported shared facilities at the University of Wisconsin-Madison. Work at the Ames Laboratory was supported by the Department of Energy-Basic Energy Sciences under Contract No. DE-AC02-07CH11358. Erika Kawakami was supported by a fellowship from the Nakajima Foundation.QCD/Vandersypen La

Impact of Classical Control Electronics on Qubit Fidelity

Quantum processors rely on classical electronic controllers to manipulate and read out the state of quantum bits (qubits). As the performance of the quantum processor improves, nonidealities in the classical controller can become the performance bottleneck for the whole quantum computer. To prevent such limitation, this paper presents a systematic study of the impact of the classical electrical signals on the qubit fidelity. All operations, i.e., single-qubit rotations, two-qubit gates, and readout, are considered, in the presence of errors in the control electronics, such as static, dynamic, systematic, and random errors. Although the presented study could be extended to any qubit technology, it currently focuses on single-electron spin qubits, because of several advantages, such as purely electrical control and long coherence times, and for their potential for large-scale integration. As a result of this study, detailed electrical specifications for the classical control electronics for a given qubit fidelity can be derived. We also discuss how qubit fidelity is affected by the limited performance of the general-purpose room-temperature equipment typically employed to control the few qubits available today. Ultimately, we show that tailor-made electronic controllers can achieve significantly lower power, cost, and size, as required to support the scaling up of quantum computers.OLD QCD/Charbon LabQuTechGeneralQCD/Veldhorst LabQCD/Vandersypen LabQN/Vandersypen LabElectronics(OLD)Applied Quantum Architecture

A programmable two-qubit quantum processor in silicon

Now that it is possible to achieve measurement and control fidelities for individual quantum bits (qubits) above the threshold for fault tolerance, attention is moving towards the difficult task of scaling up the number of physical qubits to the large numbers that are needed for fault-tolerant quantum computing. In this context, quantum-dot-based spin qubits could have substantial advantages over other types of qubit owing to their potential for all-electrical operation and ability to be integrated at high density onto an industrial platform. Initialization, readout and single- and two-qubit gates have been demonstrated in various quantum-dot-based qubit representations. However, as seen with small-scale demonstrations of quantum computers using other types of qubit, combining these elements leads to challenges related to qubit crosstalk, state leakage, calibration and control hardware. Here we overcome these challenges by using carefully designed control techniques to demonstrate a programmable two-qubit quantum processor in a silicon device that can perform the Deutsch-Josza algorithm and the Grover search algorithm - canonical examples of quantum algorithms that outperform their classical analogues. We characterize the entanglement in our processor by using quantum-state tomography of Bell states, measuring state fidelities of 85-89 per cent and concurrences of 73-82 per cent. These results pave the way for larger-scale quantum computers that use spins confined to quantum dots.Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.QCD/Vandersypen LabQuTechQN/Quantum TransportQCD/Veldhorst LabQN/Vandersypen La