A Unifying Framework for Evaluating the Predictive Power of Genetic Variants Based on the Level of Heritability Explained

An increasing number of genetic variants have been identified for many complex diseases. However, it is controversial whether risk prediction based on genomic profiles will be useful clinically. Appropriate statistical measures to evaluate the performance of genetic risk prediction models are required. Previous studies have mainly focused on the use of the area under the receiver operating characteristic (ROC) curve, or AUC, to judge the predictive value of genetic tests. However, AUC has its limitations and should be complemented by other measures. In this study, we develop a novel unifying statistical framework that connects a large variety of predictive indices together. We showed that, given the overall disease probability and the level of variance in total liability (or heritability) explained by the genetic variants, we can estimate analytically a large variety of prediction metrics, for example the AUC, the mean risk difference between cases and non-cases, the net reclassification improvement (ability to reclassify people into high- and low-risk categories), the proportion of cases explained by a specific percentile of population at the highest risk, the variance of predicted risks, and the risk at any percentile. We also demonstrate how to construct graphs to visualize the performance of risk models, such as the ROC curve, the density of risks, and the predictiveness curve (disease risk plotted against risk percentile). The results from simulations match very well with our theoretical estimates. Finally we apply the methodology to nine complex diseases, evaluating the predictive power of genetic tests based on known susceptibility variants for each trait

A Genome-Wide Screening and SNPs-to-Genes Approach to Identify Novel Genetic Risk Factors Associated with Frontotemporal Dementia

Frontotemporal dementia (FTD) is the second most prevalent form of early onset dementia after Alzheimer’s disease (AD). We performed a case-control association study in an Italian FTD cohort (n = 530) followed by the novel SNPs-to-genes approach and functional annotation analysis. We identified two novel potential loci for FTD. Suggestive SNPs reached p-values ~10-7 and OR > 2.5 (2p16.3) and 1.5 (17q25.3). Suggestive alleles at 17q25.3 identified a disease-associated haplotype causing decreased expression of -cis genes such as RFNG and AATK involved in neuronal genesis and differentiation, and axon outgrowth, respectively. We replicated this locus through the SNPs-to-genes approach. Our functional annotation analysis indicated significant enrichment for functions of the brain (neuronal genesis, differentiation and maturation), the synapse (neurotransmission and synapse plasticity), and elements of the immune system, the latter supporting our recent international FTD-GWAS. This is the largest genome-wide study in Italian FTD to date. Although our results are not conclusive, we set the basis for future replication studies and identification of susceptible molecular mechanisms involved in FTD pathogenesis

The EBLM project-VII. Spin-orbit alignment for the circumbinary planet host EBLM J0608-59 A/TOI-1338 A

A dozen short-period detached binaries are known to host transiting circumbinary planets. In all circumbinary systems so far, the planetary and binary orbits are aligned within a couple of degrees. However, the obliquity of the primary star, which is an important tracer of their formation, evolution, and tidal history, has only been measured in one circumbinary system until now. EBLM J0608-59/TOI-1338 is a low-mass eclipsing binary system with a recently discovered circumbinary planet identified by TESS. Here, we perform high-resolution spectroscopy during primary eclipse to measure the projected stellar obliquity of the primary component. The obliquity is low, and thus the primary star is aligned with the binary and planetary orbits with a projected spin-orbit angle $\beta = 2.8 \pm 17.1$ deg. The rotation period of $18.1 \pm 1.6$ days implied by our measurement of $v\sin{i_\star}$ suggests that the primary has not yet pseudo-synchronized with the binary orbit, but is consistent with gyrochronology and weak tidal interaction with the binary companion. Our result, combined with the known coplanarity of the binary and planet orbits, is suggestive of formation from a single disc. Finally, we considered whether the spectrum of the faint secondary star could affect our measurements. We show through simulations that the effect is negligible for our system, but can lead to strong biases in $v\sin{i_\star}$ and $\beta$ for higher flux ratios. We encourage future studies in eclipse spectroscopy test the assumption of a dark secondary for flux ratios $\gtrsim 1$ ppt

Three newly discovered sub-Jupiter-mass planets: WASP-69b and WASP-84b transit active K dwarfs and WASP-70Ab transits the evolved primary of a G4+K3 binary

We report the discovery of the transiting exoplanets WASP-69b, WASP-70Ab and WASP-84b, each of which orbits a bright star (V ∼ 10). WASP-69b is a bloated Saturn-mass planet (0.26 MJup, 1.06 RJup) in a 3.868-d period around an active, ∼1-Gyr, mid-K dwarf. ROSAT detected X-rays 60±27 arcsec from WASP-69. If the star is the source then the planet could be undergoing mass-loss at a rate of ∼1012 g s−1. This is one to two orders of magnitude higher than the evaporation rate estimated for HD 209458b and HD 189733b, both of which have exhibited anomalously large Lyman α absorption during transit. WASP-70Ab is a sub-Jupiter-mass planet (0.59 MJup, 1.16 RJup) in a 3.713-d orbit around the primary of a spatially resolved, 9–10-Gyr, G4+K3 binary, with a separation of 3.3 arcsec (≥800 au). WASP-84b is a sub-Jupiter-mass planet (0.69 MJup, 0.94 RJup) in an 8.523-d orbit around an active, ∼1-Gyr, early-K dwarf. Of the transiting planets discovered from the ground to date, WASP-84b has the third-longest period. For the active stars WASP-69 and WASP-84, we pre-whitened the radial velocities using a low-order harmonic series. We found that this reduced the residual scatter more than did the oft-used method of pre-whitening with a fit between residual radial velocity and bisector span. The system parameters were essentially unaffected by pre-whitening

Second malignancies in the context of lenalidomide treatment: an analysis of 2732 myeloma patients enrolled to the Myeloma XI trial.

We have carried out the largest randomised trial to date of newly diagnosed myeloma patients, in which lenalidomide has been used as an induction and maintenance treatment option and here report its impact on second primary malignancy (SPM) incidence and pathology. After review, 104 SPMs were confirmed in 96 of 2732 trial patients. The cumulative incidence of SPM was 0.7% (95% confidence interval (CI) 0.4-1.0%), 2.3% (95% CI 1.6-2.7%) and 3.8% (95% CI 2.9-4.6%) at 1, 2 and 3 years, respectively. Patients receiving maintenance lenalidomide had a significantly higher SPM incidence overall (P=0.011). Age is a risk factor with the highest SPM incidence observed in transplant non-eligible patients aged >74 years receiving lenalidomide maintenance. The 3-year cumulative incidence in this group was 17.3% (95% CI 8.2-26.4%), compared with 6.5% (95% CI 0.2-12.9%) in observation only patients (P=0.049). There was a low overall incidence of haematological SPM (0.5%). The higher SPM incidence in patients receiving lenalidomide maintenance therapy, especially in advanced age, warrants ongoing monitoring although the benefit on survival is likely to outweigh risk

Monoclonal gammopathy of undetermined significance and bone health outcomes: a systematic review and exploratory meta-analysis

Monoclonal gammopathy of undetermined significance (MGUS) is a common condition in the elderly. A number of studies have investigated the relationship between MGUS and bone health outcomes including bone mineral density (BMD), osteoporosis and fractures, but no meta-analysis exists. We conducted a systematic review and exploratory meta-analysis comparing bone health outcomes in patients with MGUS. Two independent authors searched PubMed and Scopus from inception until 19 October 2016. A meta-analysis of cross-sectional and longitudinal studies investigating fractures and BMD was conducted. Standardised mean differences (SMD) ± 95% confidence intervals (CIs) were calculated for BMD, and risk ratios (RRs) were calculated for prevalent and incident fractures. Of 174 initial hits, 10 studies of moderate methodological quality were eligible, including 8711 individuals with MGUS vs. 52,865 controls. Compared to controls, subjects with MGUS showed significantly lower values for radial cortical volumetric BMD (1 study; SMD = -5.45, 95% CI: -7.24 to -3.66), but not at the lumbar spine, femoral neck or hip. The incidence of fractures was higher in people with MGUS (n = 7466) vs. controls (n = 52,304) (RR = 1.36, 95% CI 1.28-1.44, I 2 = 0%) over a median of 12.5-year follow-up. The incidence of vertebral fractures was particularly elevated (RR = 2.50, 95% CI 1.53-4.06) although limited to two studies. In conclusion, although with limitations, our preliminary meta-analysis suggests that patients with MGUS are at higher risk of fractures despite evidence for differences in BMD being equivocal. Future longitudinal research is required to confirm our findings and determine if fracture prevention interventions are warranted in people with MGUS

Search for CP violation in D0 and D+ decays

A high statistics sample of photoproduced charm particles from the FOCUS (E831) experiment at Fermilab has been used to search for CP violation in the Cabibbo suppressed decay modes D+ to K-K+pi+, D0 to K-K+ and D0 to pi-pi+. We have measured the following CP asymmetry parameters: A_CP(K-K+pi+) = +0.006 +/- 0.011 +/- 0.005, A_CP(K-K+) = -0.001 +/- 0.022 +/- 0.015 and A_CP(pi-pi+) = +0.048 +/- 0.039 +/- 0.025 where the first error is statistical and the second error is systematic. These asymmetries are consistent with zero with smaller errors than previous measurements.Comment: 12 pages, 4 figure