Association analyses of the MAS-QTL data set using grammar, principal components and Bayesian network methodologies

<p>Abstract</p> <p>Background</p> <p>It has been shown that if genetic relationships among individuals are not taken into account for genome wide association studies, this may lead to false positives. To address this problem, we used Genome-wide Rapid Association using Mixed Model and Regression and principal component stratification analyses. To account for linkage disequilibrium among the significant markers, principal components loadings obtained from top markers can be included as covariates. Estimation of Bayesian networks may also be useful to investigate linkage disequilibrium among SNPs and their relation with environmental variables.</p> <p>For the quantitative trait we first estimated residuals while taking polygenic effects into account. We then used a single SNP approach to detect the most significant SNPs based on the residuals and applied principal component regression to take linkage disequilibrium among these SNPs into account. For the categorical trait we used principal component stratification methodology to account for background effects. For correction of linkage disequilibrium we used principal component logit regression. Bayesian networks were estimated to investigate relationship among SNPs.</p> <p>Results</p> <p>Using the Genome-wide Rapid Association using Mixed Model and Regression and principal component stratification approach we detected around 100 significant SNPs for the quantitative trait (p<0.05 with 1000 permutations) and 109 significant (p<0.0006 with local FDR correction) SNPs for the categorical trait. With additional principal component regression we reduced the list to 16 and 50 SNPs for the quantitative and categorical trait, respectively.</p> <p>Conclusions</p> <p>GRAMMAR could efficiently incorporate the information regarding random genetic effects. Principal component stratification should be cautiously used with stringent multiple hypothesis testing correction to correct for ancestral stratification and association analyses for binary traits when there are systematic genetic effects such as half sib family structures. Bayesian networks are useful to investigate relationships among SNPs and environmental variables.</p

Studies of the Decay B+- -> D_CP K+-

We report studies of the decay B+- -> D_CP K+-, where D_CP denotes neutral D mesons that decay to CP eigenstates. The analysis is based on a 29.1/fb data sample of collected at the \Upsilon(4S) resonance with the Belle detector at the KEKB asymmetric e+ e- storage ring. Ratios of branching fractions of Cabibbo-suppressed to Cabibbo-favored processes involving D_CP are determined to be B(B- -> D_1 K-)/B(B- -> D_1 pi-)=0.125 +- 0.036 +- 0.010 and B(B- -> D_2 K-)/B(B- -> D_2 pi-)=0.119 +- 0.028 +- 0.006, where indices 1 and 2 represent the CP=+1 and CP=-1 eigenstates of the D0 - anti D0 system, respectively. We also extract the partial rate asymmetries for B+- -> D_CP K+-, finding A_1 = 0.29 +- 0.26 +- 0.05 and A_2 = -0.22 +- 0.24 +- 0.04.Comment: 10 pages, 2 figures, submitted to Physical Review Letter

Improved measurements of branching fractions for B -> K pi and B -> pi pi decays

We report improved measurements of branching fractions for B -> K pi and B -> pi pi decays based on a data sample of 449 million B Bbar pairs collected at the Upsilon(4S) resonance with the Belle detector at the KEKB e^+e^- collider. We also calculate the ratios of partial widths for the decays B -> K pi and pi pi, namely R_c = 1.08 +- 0.06 +- 0.08 and R_n = 1.08 +-0.08 +0.09-0.08, where the first and second errors are statistical and systematical, respectively. These ratios are sensitive to enhanced electroweak penguin contributions from new physics; the new measurements are, however, consistent with Standard Model expectations.Comment: 6 pages, 1 figur

Observation of Ds+K- and evidence for D-s(+)pi(-) final states in neutral B decays

We report the first observation of a B meson decay that is not accessible by a direct spectator process. The channel (B) over bar (0)-->Ds+K- is found in a sample of 85x10(6) B (B) over bar events, collected with the Belle detector at KEKB, with a branching fraction B((B) over bar (0)-->Ds+K-)=(4.6(-1.1)(+1.2)+/-1.3)x10(-5). We also obtain evidence for the B-0-->D(s)(+)pi(-) decay with branching fraction B(B-0-->D(s)(+)pi(-))=(2.4(-0.8)(+1.0)+/-0.7)x10(-5). This value may be used to extract a model-dependent value of \V-ub\

Evidence for direct CP violation in B-0 -> K+pi(-) decays

We report evidence for direct CP violation in the decay B-0-->K(+)pi(-) with 253 fb(-1) of data collected with the Belle detector at the KEKB e(+)e(-) collider. Using 275x10(6) B(B) over bar pairs we observe a B-->K(+/-)pi(-/+) signal with 2140+/-53 events. The measured CP violating asymmetry is A(CP)(K(+)pi(-))=-0.101+/-0.025(stat)+/-0.005(syst), corresponding to a significance of 3.9sigma including systematics. We also search for CP violation in the decays B+-->K(+)pi(0) and B+-->pi(+)pi(0). The measured CP violating asymmetries are A(CP)(K(+)pi(0))=0.04+/-0.05(stat)+/-0.02(syst) and A(CP)(pi(+)pi(0))=-0.02+/-0.10(stat)+/-0.01(syst), corresponding to the intervals -0.05< A(CP)(K(+)pi(0))<0.13 and -0.18< A(CP)(pi(+)pi(0))<0.14 at 90% confidence level

Observation of the radiative decay D-0 ->phi gamma

We report the observation of the decay D-0-->phigamma with a statistical significance of 5.4sigma in 78.1 fb(-1) of data collected by the Belle experiment at the KEKB e(+)e(-) collider. This is the first observation of a flavor-changing radiative decay of a charmed meson. The Cabibbo- and color-suppressed decays D-0-->phipi(0), phieta are also observed for the first time. We measure branching fractions B(D-0-->phigamma)=[2.60(-0.61)(+0.70)(stat)(-0.17)(+0.15)(syst)]x10(-5), B(D-0-->phipi(0))=[8.01+/-0.26(stat)+/-0.47(syst)]x10(-4), and B(D-0-->phieta)=[1.48+/-0.47(stat)+/-0.09(syst)]x10(-4)

Observation of a charmoniumlike state produced in association with a J/psi in e(+)e(-) annihilation at root s approximate to 10.6 GeV

We report the first observation of a charmoniumlike state recoiling from the J/psi in the inclusive process e(+)e(-)-> J/psi+anything at a mass of (3.943 +/- 0.006 +/- 0.006) GeV/c(2). We also observe the decay of this state into (DD)-D-* and determine its intrinsic width to be less than 52 MeV/c(2) at the 90% C.L. These results are obtained from a 357 fb(-1) data sample collected with the Belle detector near the Upsilon(4S) resonance, at the KEKB asymmetric-energy e(+)e(-) collider