An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Measurement of the ttbar Production Cross Section in ppbar Collisions at sqrt{s} = 1.96 TeV using Kinematic Characteristics of Lepton + Jets Events

We present a measurement of the top quark pair ttbar production cross section in ppbar collisions at a center-of-mass energy of 1.96 TeV using 230 pb**{-1} of data collected by the DO detector at the Fermilab Tevatron Collider. We select events with one charged lepton (electron or muon), large missing transverse energy, and at least four jets, and extract the ttbar content of the sample based on the kinematic characteristics of the events. For a top quark mass of 175 GeV, we measure sigma(ttbar) = 6.7 {+1.4-1.3} (stat) {+1.6- 1.1} (syst) +/-0.4 (lumi) pb, in good agreement with the standard model prediction.Comment: submitted to Phys.Rev.Let

Measurement of the ttbar Production Cross Section in ppbar Collisions at sqrt(s)=1.96 TeV using Lepton + Jets Events with Lifetime b-tagging

We present a measurement of the top quark pair ($t\bar{t}$) production cross section ($\sigma_{t\bar{t}}$) in $p\bar{p}$ collisions at $\sqrt{s}=1.96$ TeV using 230 pb$^{-1}$ of data collected by the D0 experiment at the Fermilab Tevatron Collider. We select events with one charged lepton (electron or muon), missing transverse energy, and jets in the final state. We employ lifetime-based b-jet identification techniques to further enhance the $t\bar{t}$ purity of the selected sample. For a top quark mass of 175 GeV, we measure $\sigma_{t\bar{t}}=8.6^{+1.6}_{-1.5}(stat.+syst.)\pm 0.6(lumi.)$ pb, in agreement with the standard model expectation.Comment: 7 pages, 2 figures, 3 tables Submitted to Phys.Rev.Let

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as TMPRSS2, RET, FGFR3, ALK, and ESR1 in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy

Search for single top quark production in ppbar collisions at sqrt(s)=1.96 TeV

We present a search for electroweak production of single top quarks in the s-channel and t-channel using neural networks for signal-background separation. We have analyzed 230 pb$^{-1}$ of data collected with the D0 detector at the Fermilab Tevatron Collider at a center-of-mass energy of 1.96 TeV and find no evidence for a single top quark signal. The resulting 95% confidence level upper limits on the single top quark production cross sections are 6.4 pb in the s-channel and 5.0 pb in the t-channel.Comment: 9 pages, 4 figure

Measurement of the WW production cross section in p anti-p collisions at s**(1/2) = 1.96 TeV

We present a measurement of the W boson pair-production cross section in p anti-p collisions at a center-of-mass energy of sqrt{s}=1.96 TeV. The data, collected with the Run II DO detector, correspond to an integrated luminosity of 224-252 pb^-1 depending on the final state (ee, emu or mumu). We observe 25 candidates with a background expectation of 8.1+/-0.6(stat)+/-0.6(syst)+/-0.5(lum) events. The probability for an upward fluctuation of the background to produce the observed signal is 2.3x10^-7, equivalent to 5.2 standard deviations.The measurement yields a cross section of 13.8+4.3/-3.8(stat)+1.2/-0.9(syst)+/-0.9(lum) pb, in agreement with predictions from the standard model.Comment: submitted to PR

Measurement of the Lambda^0_b lifetime in the decay Lambda^0_b -> J/psi Lambda^0 with the D0 Detector

We present measurements of the Lambda^0_b lifetime in the exclusive decay channel Lambda^0_{b}->J/psi Lambda^0, with J/psi to mu+ mu- and Lambda^0 to p pi-, the B^0 lifetime in the decay B^0 -> J/psi K^0_S with J/psi to mu+ mu- and K^0_S to pi+ pi-, and the ratio of these lifetimes. The analysis is based on approximately 250 pb^{-1} of data recorded with the D0 detector in pp(bar) collisions at sqrt{s}=1.96 TeV. The Lambda^0_b lifetime is determined to be tau(Lambda^0_b) = 1.22 +0.22/-0.18 (stat) +/- 0.04 (syst) ps, the B^0 lifetime tau(B^0) = 1.40 +0.11/-0.10 (stat) +/- 0.03 (syst) ps, and the ratio tau(Lambda^0_b)/tau(B^0) = 0.87 +0.17/-0.14 (stat) +/- 0.03 (syst). In contrast with previous measurements using semileptonic decays, this is the first determination of the Lambda^0_b lifetime based on a fully reconstructed decay channel.Comment: 7 pages, 4 figures, Submitted to Physical Review Letters, v2: Added FNAL Pub-numbe