An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. RESULTS: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. CONCLUSIONS: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups

Modelling human choices: MADeM and decision‑making

Research supported by FAPESP 2015/50122-0 and DFG-GRTK 1740/2. RP and AR are also part of the Research, Innovation and Dissemination Center for Neuromathematics FAPESP grant (2013/07699-0). RP is supported by a FAPESP scholarship (2013/25667-8). ACR is partially supported by a CNPq fellowship (grant 306251/2014-0)

Observation of the B0 → ρ0ρ0 decay from an amplitude analysis of B0 → (π+π−)(π+π−) decays

Proton–proton collision data recorded in 2011 and 2012 by the LHCb experiment, corresponding to an integrated luminosity of 3.0 fb−1 , are analysed to search for the charmless B0→ρ0ρ0 decay. More than 600 B0→(π+π−)(π+π−) signal decays are selected and used to perform an amplitude analysis, under the assumption of no CP violation in the decay, from which the B0→ρ0ρ0 decay is observed for the first time with 7.1 standard deviations significance. The fraction of B0→ρ0ρ0 decays yielding a longitudinally polarised final state is measured to be fL=0.745−0.058+0.048(stat)±0.034(syst) . The B0→ρ0ρ0 branching fraction, using the B0→ϕK⁎(892)0 decay as reference, is also reported as B(B0→ρ0ρ0)=(0.94±0.17(stat)±0.09(syst)±0.06(BF))×10−6

Observation of the decay B0s→ψ(2S)K+π−

The decay B¯s0→ψ(2S)K+π− is observed using a data set corresponding to an integrated luminosity of 3.0 fb−1 collected by the LHCb experiment in pp collisions at centre-of-mass energies of 7 and 8 TeV. The branching fraction relative to the B0→ψ(2S)K+π− decay mode is measured to be B(B¯s0→ψ(2S)K+π−)B(B0→ψ(2S)K+π−)=5.38±0.36(stat)±0.22(syst)±0.31(fs/fd)%, where fs/fd indicates the uncertainty due to the ratio of probabilities for a b quark to hadronise into a Bs0 or B0 meson. Using an amplitude analysis, the fraction of decays proceeding via an intermediate K⁎(892)0 meson is measured to be 0.645±0.049(stat)±0.049(syst) and its longitudinal polarisation fraction is 0.524±0.056(stat)±0.029(syst) . The relative branching fraction for this component is determined to be B(B¯s0→ψ(2S)K⁎(892)0)B(B0→ψ(2S)K⁎(892)0)=5.58±0.57(stat)±0.40(syst)±0.32(fs/fd)%. In addition, the mass splitting between the Bs0 and B0 mesons is measured as M(Bs0)−M(B0)=87.45±0.44(stat)±0.09(syst) MeV/c2

Measurement of CP violation parameters and polarisation fractions in Bs0→J/ψK‾∗0 {\mathrm{B}}_{\mathrm{s}}^0\to \mathrm{J}/\psi {\overline{\mathrm{K}}}^{\ast 0} decays

The first measurement of ${C\!P}$ asymmetries in the decay ${B_s^0\to J/\psi \overline{K}^{*}(892)^{0}}$ and an updated measurement of its branching fraction and polarisation fractions are presented. The results are obtained using data corresponding to an integrated luminosity of $3.0\,fb^{-1}$ of proton-proton collisions recorded with the LHCb detector at centre-of-mass energies of $7$ and $8\,\mathrm{TeV}$. Together with constraints from ${B^0\to J/\psi \rho^0}$, the results are used to constrain additional contributions due to penguin diagrams in the ${C\!P}$-violating phase ${{\phi}_{s}}$, measured through ${B_s^0}$ decays to charmonium.The first measurement of CP asymmetries in the decay ${B}_s^0\to J/\psi {\overline{\mathrm{K}}}^{\ast }{(892)}^0$ and an updated measurement of its branching fraction and polarisation fractions are presented. The results are obtained using data corresponding to an integrated luminosity of 3.0 fb^{−}^{1} of proton-proton collisions recorded with the LHCb detector at centre-of-mass energies of 7 and 8 TeV. Together with constraints from B$^{0}$ → J/ψ ρ$^{0}$, the results are used to constrain additional contributions due to penguin diagrams in the CP -violating phase ϕ$_{s}$ , measured through B$_{s}^{0}$ decays to charmonium.The first measurement of ${C\!P}$ asymmetries in the decay ${B_s^0\to J/\psi \overline{K}^{*}(892)^{0}}$ and an updated measurement of its branching fraction and polarisation fractions are presented. The results are obtained using data corresponding to an integrated luminosity of $3.0\,fb^{-1}$ of proton-proton collisions recorded with the LHCb detector at centre-of-mass energies of $7$ and $8\,\mathrm{TeV}$. Together with constraints from ${B^0\to J/\psi \rho^0}$, the results are used to constrain additional contributions due to penguin diagrams in the ${C\!P}$-violating phase ${{\phi}_{s}}$, measured through ${B_s^0}$ decays to charmonium