Full-genome next-generation sequencing of hepatitis C virus to assess the accuracy of genotyping by the commercial assay LiPA and the prevalence of resistance-associated substitutions in a Belgian cohort

Funding Information: This work and KTC were supported by grants from the Fonds voor Wetenschappelijk Onderzoek Vlaanderen (FWO) ( G069214 , G0B2317N , 1S38819N ). LC acknowledges FWO travel grant for a research visit at University of Oxford ( V431117N ). The authors thank the staff in Oxford in their support of the laboratory work and the donation of the probes used for enrichment of HCV. Publisher Copyright: © 2022 Elsevier B.V.Background: Although most currently used regimens for Hepatitis C virus (HCV) infections can be initiated without prior knowledge of genotype and subtype, genotyping is still useful to identify patients who might benefit from a personalized treatment due to resistance to direct-acting antivirals (DAA). Objectives: To assess the utility of full-genome next-generation sequencing (FG-NGS) for HCV genotyping. Study design: 138 HCV plasma samples previously genotyped by VERSANT HCV Genotype Assay (LiPA) were subjected to FG-NGS and phylogenetically genotyped Genome Detective. Consensuses were analysed by HCV-GLUE for resistance-associated substitutions (RASs) and their impact on treatment response was investigated. Results: 102/138 (73.9%) samples were sequenced to a genome coverage and depth of >90% of the HCV open reading frame covered by >100 reads/site. Concordant genotype and subtype results were assigned in 97.1% and 79.4% of samples, respectively. FG-NGS resolved the subtype of 13.7% samples that had ambiguous calls by LiPA and identified one dual infection and one recombinant strain. At least one RAS was found for the HCV genes NS3, NS5A, and NS5B in 2.91%, 36.98% and 27.3% samples, respectively. Irrespective of the observed RAS, all patients responded well to DAA treatment, except for HCV1b-infected patients treated with Zepatier (33.3% failure rate (5/15)). Conclusion: While LiPA and FG-NGS showed overall good concordance, FG-NGS improved specificity for subtypes, recombinant and mixed infections. FG-NGS enabled the detection of RAS, but its predictive value for treatment outcome in DAA-naïve patients remains uncertain. With additional refinements, FG-NGS may be the way forward for HCV genotyping.publishersversionpublishe

Search for associated Higgs boson production using like charge dilepton events in p(p)over-bar collisions at root s=1.96 TeV

We present a search for associated Higgs boson production in the process p (p) over bar -> W/ZH -> l(+/-)l'(+/-) + X in ee, e mu, and mu mu final states. The search is based on data collected by the D0 experiment at the Fermilab Tevatron Collider at root s = 1.96 TeV corresponding to 5.3 fb(-1) of integrated luminosity. We require two isolated leptons (electrons or muons) with the same electric charge and additional kinematic requirements. No significant excess above background is observed, and we set 95% C. L. observed (expected) upper limits on ratio of the production cross section to the standard model prediction of 6.4 (7.3) for a Higgs boson mass of 165 GeV and 13.5 (19.8) for a mass of 115 GeV

Study of Zγ events and limits on anomalous ZZγ and Zγγ couplings in pp̄ collisions at s=1.96TeV

We present a measurement of the Zγ production cross section and limits on anomalous ZZγ and Zγγ couplings for form-factor scales of Λ=750 and 1000 GeV. The measurement is based on 138 (152) candidates in the eeγ (μμγ) final state using 320(290)pb-1 of pp̄ collisions at s=1.96TeV. The 95% C.L. limits on real and imaginary parts of individual anomalous couplings are |h10,30Z|<0.23, |h20,40Z|<0.020, |h10,30γ|<0.23, and |h20,40γ|<0.019 for Λ=1000GeV. © 2005 The American Physical Society

Evaluation of Clear Cell, Papillary, and Chromophobe Renal Cell Carcinoma Metastasis Sites and Association with Survival

Importance: There exists considerable biological and clinical variability between histologic variants of metastatic renal cell carcinoma (mRCC). Data reporting on patterns of metastasis in histologic variants of mRCC are sparse. Objective: To characterize sites of metastasis and their association with survival across the 3 most common histologic variants of mRCC: clear cell (ccRCC), papillary (pRCC), and chromophobe (chrRCC). Design, Setting, and Participants: In this multicenter, international cohort study, the International mRCC Database Consortium (IMDC) database was used to identify consecutive patients starting systemic therapy for mRCC between 2002 and 2019. Patients with mixed histologic subtype were excluded. Statistical analysis was performed from February to June 2020. Exposures: Data regarding histologic subtype and sites of metastatic involvement at the time of first systemic therapy initiation were collected. Main Outcomes and Measures: The primary outcomes were prevalence of metastatic site involvement and overall survival (OS) from time of systemic therapy initiation. Patients with multiple sites of metastatic involvement were included in analyses of all groups to which they had metastases. Results: A total of 10105 patients were eligible for analysis. Median (interquartile range) age at diagnosis was 60 (53-67) years, 7310 (72.4%) were men and 8526 (84.5%) underwent nephrectomy. Of these, 9252 (92%) had ccRCC, 667 (7%) had pRCC, and 186 (2%) had chrRCC. The median number of sites of metastasis was 2 (range, 0-7). In ccRCC, the most common sites of metastasis were lung (70%; 6189 of 8804 patients [448 missing]), lymph nodes (45%; 3874 of 8655 patients [597 missing]), bone (32%; 2847 of 8817 patients [435 missing]), liver (18%; 1560 of 8804 [448 missing]), and adrenal gland (10%; 678 of 6673 patients [2579 missing]). Sites of metastasis varied between subtypes. Lung, adrenal, brain, and pancreatic metastases were more frequent in ccRCC, lymph node involvement was more common in pRCC, and liver metastases were more frequent in chrRCC. Median OS for ccRCC varied by site of metastatic involvement, ranging between 16 months (95% CI, 13.7-18.8 months) for the pleura and 50 months (95% CI, 41.1-55.5 months) for the pancreas. Compared with ccRCC, patients with pRCC tended to have lower OS, regardless of metastatic site. Conclusions and Relevance: Sites of metastatic involvement differ according to histologic subtype in mRCC and are associated with OS. These data highlight the clinical and biological variability between histologic subtypes of mRCC. Patterns of metastatic spread may reflect differences in underlying disease biology. Further work to investigate differences in immune, molecular, and genetic profiles between metastatic sites and histologic subtypes is encouraged

Precise measurement of the top quark mass in the dilepton channel at D0

We measure the top quark mass (mt) in ppbar collisions at a center of mass energy of 1.96 TeV using dilepton ttbar->W+bW-bbar->l+nubl-nubarbbar events, where l denotes an electron, a muon, or a tau that decays leptonically. The data correspond to an integrated luminosity of 5.4 fb-1 collected with the D0 detector at the Fermilab Tevatron Collider. We obtain mt = 174.0 +- 1.8(stat) +- 2.4(syst) GeV, which is in agreement with the current world average mt = 173.3 +- 1.1 GeV. This is currently the most precise measurement of mt in the dilepton channel.Comment: 7 pages, 4 figure

A search for charged massive long-lived particles

We report on a search for charged massive long-lived particles (CMLLPs), based on 5.2 fb$^{-1}$ of integrated luminosity collected with the D0 detector at the Fermilab Tevatron $p\bar{p}$ collider. We search for events in which one or more particles are reconstructed as muons but have speed and ionization energy loss $(dE/dx)$ inconsistent with muons produced in beam collisions. CMLLPs are predicted in several theories of physics beyond the standard model. We exclude pair-produced long-lived gaugino-like charginos below 267 GeV and higgsino-like charginos below 217 GeV at 95% C.L., as well as long-lived scalar top quarks with mass below 285 GeV.Comment: submitted to Phys. Rev. Letter

Search for single vector-like quarks in ppbar collisions at sqrt(s) = 1.96 TeV

We present a search for hypothetical vector-like quarks in ppbar collisions at sqrt(s) = 1.96 TeV. The data were collected by the D0 detector at the Fermilab Tevatron Collider and correspond to an integrated luminosity of 5.4 fb^(-1). We select events with a final state composed of a W or Z boson and a jet consistent with a heavy object decay. We observe no significant excess in comparison to the background prediction and set limits on production cross sections for vector-like quarks decaying to W+jet and Z+jet. These are the most stringent mass limits for electroweak single vector-like quark production at hadron colliders.Comment: submitted to Phys. Rev. Let

Measurement of the top quark pair production cross section in the lepton+jets channel in proton-antiproton collisions at s\sqrt{s}=1.96 TeV

We present a measurement of the inclusive top quark pair production cross section in \ppbar collisions at (\sqrt{s}=1.96) TeV utilizing data corresponding to an integrated luminosity of \lumi\ collected with the D0 detector at the Fermilab Tevatron Collider. We consider final states containing one high-$p_{T}$ isolated electron or muon and at least two jets, and we perform three analyses: one exploiting specific kinematic features of \ttbar events, the second using $b$-jet identification, and the third using both techniques to separate \ttbar\ signal from background. In the third case, we determine simultaneously the $t\bar{t}$ cross section and the ratio of the production rates of $W$+heavy flavor jets and $W$+light flavor jets, which reduces the impact of the systematic uncertainties related to the background estimation. Assuming a top quark mass of 172.5 GeV, we obtain $\sigma_{t\bar{t}} = 7.78^{+0.77}_{-0.64}$ pb. This result agrees with predictions of the standard model.Comment: 19 pages, 6 figures, submitted to Phys. Rev.

Journal Staff

We present the first measurements of the differential cross section d sigma/dp(T)(gamma) for the production of an isolated photon in association with at least two b-quark jets. The measurements consider photons with rapidities vertical bar y(gamma)vertical bar &lt; 1.0 and transverse momenta 30 &lt; p(T)(gamma) &lt; 200 GeV. The b-quark jets are required to have p(T)(jet) &gt; 15 GeVand vertical bar y(jet)vertical bar &lt; 1.5. The ratio of differential production cross sections for gamma + 2 b-jets to gamma + b-jet as a function of p(T)(gamma) is also presented. The results are based on the proton-antiproton collision data at root s = 1.96 TeV collected with the D0 detector at the Fermilab Tevatron Collider. The measured cross sections and their ratios are compared to the next- to- leading order perturbative QCD calculations as well as predictions based on the k(T)- factorization approach and those from the sherpa and pythia Monte Carlo event generators

Direct measurement of the mass difference between top and antitop quarks

We present a direct measurement of the mass difference between top and antitop quarks (dm) in lepton+jets top-antitop final states using the "matrix element" method. The purity of the lepton+jets sample is enhanced for top-antitop events by identifying at least one of the jet as originating from a b quark. The analyzed data correspond to 3.6 fb-1 of proton-antiproton collisions at 1.96 TeV acquired by D0 in Run II of the Fermilab Tevatron Collider. The combination of the e+jets and mu+jets channels yields dm = 0.8 +/- 1.8 (stat) +/- 0.5 (syst) GeV, which is in agreement with the standard model expectation of no mass difference.Comment: submitted to Phys. Rev.