Meta-analysis of Gene-Level Associations for Rare Variants Based on Single-Variant Statistics

Meta-analysis of genome-wide association studies (GWASs) has led to the discoveries of many common variants associated with complex human diseases. There is a growing recognition that identifying “causal” rare variants also requires large-scale meta-analysis. The fact that association tests with rare variants are performed at the gene level rather than at the variant level poses unprecedented challenges in the meta-analysis. First, different studies may adopt different gene-level tests, so the results are not compatible. Second, gene-level tests require multivariate statistics (i.e., components of the test statistic and their covariance matrix), which are difficult to obtain. To overcome these challenges, we propose to perform gene-level tests for rare variants by combining the results of single-variant analysis (i.e., p values of association tests and effect estimates) from participating studies. This simple strategy is possible because of an insight that multivariate statistics can be recovered from single-variant statistics, together with the correlation matrix of the single-variant test statistics, which can be estimated from one of the participating studies or from a publicly available database. We show both theoretically and numerically that the proposed meta-analysis approach provides accurate control of the type I error and is as powerful as joint analysis of individual participant data. This approach accommodates any disease phenotype and any study design and produces all commonly used gene-level tests. An application to the GWAS summary results of the Genetic Investigation of ANthropometric Traits (GIANT) consortium reveals rare and low-frequency variants associated with human height. The relevant software is freely available.     

Female‐borne cues affecting Psyttalia concolor (Hymenoptera: Braconidae) male behavior during courtship and mating

Knowledge of the mechanisms that regulate courtship and mating behavior in Psyttalia concolor (Szépligeti)–a koinobiont endophagous solitary parasitoid of the olive fruit fly, Bactrocera oleae (Rossi), and of other fruit flies–is essential to its mass rearing and management. Augmentative releases of P. concolor for olive fruit fly control started in the Mediterranean areas in the 1950s and still continue with limited success. We determined the influence of visual and chemical cues on courtship and mating behavior of this braconid and the possible effect of the mating status of males and females in the perception of these cues. Our results suggest that integration of visual and chemical stimuli are fundamental for mate location and courtship. Indeed, the optimal response of the male was achieved when physical and chemical cues were simultaneously presented and vision and olfaction worked synergistically.     

Hereditary Angioedema Attacks Resolve Faster and Are Shorter after Early Icatibant Treatment

Background

Attacks of hereditary angioedema (HAE) are unpredictable and, if affecting the upper airway, can be lethal. Icatibant is used for physician- or patient self-administered symptomatic treatment of HAE attacks in adults. Its mode of action includes disruption of the bradykinin pathway via blockade of the bradykinin B₂ receptor. Early treatment is believed to shorten attack duration and prevent severe outcomes; however, evidence to support these benefits is lacking.

Objective

To examine the impact of timing of icatibant administration on the duration and resolution of HAE type I and II attacks.

Methods

The Icatibant Outcome Survey is an international, prospective, observational study for patients treated with icatibant. Data on timings and outcomes of icatibant treatment for HAE attacks were collected between July 2009–February 2012. A mixed-model of repeated measures was performed for 426 attacks in 136 HAE type I and II patients.

Results

Attack duration was significantly shorter in patients treated <1 hour of attack onset compared with those treated ≥1 hour (6.1 hours versus 16.8 hours [p<0.001]). Similar significant effects were observed for <2 hours versus ≥2 hours (7.2 hours versus 20.2 hours [p<0.001]) and <5 hours versus ≥5 hours (8.0 hours versus 23.5 hours [p<0.001]). Treatment within 1 hour of attack onset also significantly reduced time to attack resolution (5.8 hours versus 8.8 hours [p<0.05]). Self-administrators were more likely to treat early and experience shorter attacks than those treated by a healthcare professional.

Conclusion

Early blockade of the bradykinin B₂ receptor with icatibant, particularly within the first hour of attack onset, significantly reduced attack duration and time to attack resolution.     

Mixed Modeling of Meta-Analysis P-Values (MixMAP) Suggests Multiple Novel Gene Loci for Low Density Lipoprotein Cholesterol

Informing missing heritability for complex disease will likely require leveraging information across multiple SNPs within a gene region simultaneously to characterize gene and locus-level contributions to disease phenotypes. To this aim, we introduce a novel strategy, termed Mixed modeling of Meta-Analysis P-values (MixMAP), that draws on a principled statistical modeling framework and the vast array of summary data now available from genetic association studies, to test formally for locus level association. The primary inputs to this approach are: (a) single SNP level p-values for tests of association; and (b) the mapping of SNPs to genomic regions. The output of MixMAP is comprised of locus level estimates and tests of association. In application of MixMAP to summary data from the Global Lipids Gene Consortium, we suggest twelve new loci (PKN, FN1, UGT1A1, PPARG, DMDGH, PPARD, CDK6, VPS13B, GAD2, GAB2, APOH and NPC1) for low-density lipoprotein cholesterol (LDL-C), a causal risk factor for cardiovascular disease and we also demonstrate the potential utility of MixMAP in small data settings. Overall, MixMAP offers novel and complementary information as compared to SNP-based analysis approaches and is straightforward to implement with existing open-source statistical software tools.     

Severe progressive scoliosis in an adult female possibly secondary thoracic surgery in childhood treated with scoliosis specific Schroth physiotherapy: Case presentation

Background

Scoliosis is a complex three-dimensional (3D) spinal deformity. Acquired scoliosis in early childhood may progress into adulthood and pose an increased risk of health problems and reduction in quality of life. In Canada, patients with scoliosis are not referred for physiotherapeutic scoliosis-specific exercises (PSSE) despite the fact that Schroth physiotherapy, a scoliosis-specific 3D posture training and exercise program, can be effective in reducing pain and improving scoliosis curves, vital capacity, and overall quality of life in scoliosis patients. This case presentation shows that indeed adult curve progression can be stopped and even reversed with scoliosis specific Schroth physiotherapy (SSSPT) in an adult patient with scoliosis.

Methods

This is a retrospective case presentation involving a 23-year-old female scoliosis patient who began an outpatient Schroth physiotherapy exercise program and was initially monitored monthly and then annually for improvement in measurements of angle of trunk rotation (ATR) and chest expansion and improvement in vital capacity measured with incentive spirometry. Photos were taken to document body image periodically throughout Schroth physiotherapy treatment. Additionally, the patient completed SRS-22 quality of life questionnaires every 2 years to evaluate daily function, pain, self-imagine, mental health, and scoliosis management satisfaction.

Results

Within one month of beginning SSSPT, the patient reported no more back pain and within 2 months, reported improved breathing. The patient also benefitted from improved chest expansion, reduced scoliosis curve angles (measured in Cobb degrees), increased vital capacity, decreased ATR, and higher SRS-22 scores. She became more active and resumed all athletic activity within 8 months of beginning Schroth physiotherapy.

Conclusions

Adult scoliosis patients are not routinely referred for PSSE in Canada, even though Schroth physiotherapy, a form of PSSE, is shown to be effective in this case presentation. The patient in this case presentation was successfully treated with Schroth physiotherapy. Long-term comprehensive Schroth physiotherapy, to help correct and maintain proper posture in all aspects of daily living, should be part of scoliosis management for adult scoliosis patients in Canada to stop and reverse curve progression and to improve overall quality of life.

     

Effective gene flow in a historically fragmented area at the southern edge of silver fir (<Emphasis Type="Italic">Abies alba</Emphasis> Mill.) distribution

Fragmented populations at the edges of a species’ distribution can be highly exposed to the loss of genetic variation, unless sufficient gene flow maintains their genetic connectivity. Gene movements leading to successful establishment of external gametes (i.e. effective gene flow) into fragmented populations can solely be assessed by investigating the origin of natural regeneration. This study is focused on studying gene flow patterns in two silver fir stands in Central Apennines, where the species has a highly fragmented distribution. By using nuclear and chloroplast microsatellite markers, we investigated genetic variation, fine-scale spatial genetic structure, effective gene flow rates and large-scale connectivity characterizing both stands. Similar levels of genetic variation and low genetic differentiation between stands (F _ST = 0.005) and across generations were found, coupled with low inbreeding and weak to absent SGS in the adult cohort (Sp < 0.003). On the other hand, substantial differences between the two stands in terms of gene flow rates were observed. Irrespective of the parentage approach used, higher gene flow rates were found in the stand located at the upper silver fir altitudinal limit, especially for seed-mediated gene flow (0.79 in the upper stand vs. 0.48 in the lower stand). Conversely, the lower stand was characterized by a higher reproductive dominance of local adults. Our findings suggest that, despite similar levels of genetic variation and generally high gene flow rates, different processes may be acting on the two stands, reflecting varying ecological conditions.     

Operating room scheduling and rescheduling: a rolling horizon approach

In this work we consider the problem of selecting a set of patients among a given waiting list of elective patients and assigning them to a set of available operating room blocks. We assume a block scheduling strategy in which the number and the length of available blocks are given. As each block is related to a specific day, by assigning a patient to a block his/her surgery date is fixed, as well. Each patient is characterized by a recommended maximum waiting time and an uncertain surgery duration. In practical applications, new patients enter the waiting list continuously. Patient selection and assignment is performed by surgery departments on a short-term, usually a week, regular base. We propose a so-called rolling horizon approach for the patient selection and assignment. At each iteration short-term patient assignment is decided. However, in a look-ahead perspective, a longer planning horizon is considered when looking for the patient selection. The mid-term assignment over the next \(n\) weeks is generated by solving an ILP problem, minimizing a penalty function based on total waiting time and tardiness of patients. The approach is iteratively applied by shifting ahead the mid-term planning horizon. When applying the first week solution, unpredictable extensions of surgeries may disrupt the schedule. Such disruptions are recovered in the next iteration: the mid-term solution is rescheduled limiting the number of variations from the previously computed plan. Besides, the approach allows to deal with new patient arrivals. To keep limited the number of disruptions due to uncertain surgery duration, we propose also a robust formulation of the ILP problem. The deterministic and the robust formulation based frameworks are compared over a set of instances, including different stochastic realization of surgery times.     

Pathologic Evaluation of Type 2 Porcine Reproductive and Respiratory Syndrome Virus Infection at the Maternal-Fetal Interface of Late Gestation Pregnant Gilts

The pathogenesis of fetal death caused by porcine reproductive and respiratory syndrome virus (PRRSV) remains unclear. The objective of this study was to improve our understanding of the pathogenesis by assessing potential relationships between specific histopathological lesions and PRRSV RNA concentration in the fetuses and the maternal-fetal interface. Pregnant gilts were inoculated with PRRSV (n = 114) or sham inoculated (n = 19) at 85±1 days of gestation. Dams and their litters were humanely euthanized and necropsied 21 days later. PRRSV RNA concentration was measured by qRT-PCR in the maternal-fetal interface and fetal thymus (n = 1391). Presence of fetal lesions was positively related to PRRSV RNA concentration in the maternal-fetal interface and fetal thymus (P<0.05 for both), but not to the distribution or severity of vasculitis, or the severity of endometrial inflammation. The presence of fetal and umbilical lesions was associated with greater odds of meconium staining (P<0.05 for both). The distribution and severity of vasculitis in endometrium were not significantly related to PRRSV RNA concentration in maternal-fetal interface or fetal thymus. Endometrial inflammation severity was positively related to distribution and severity of vasculitis in endometrium (P<0.001 for both). Conclusions from this study suggest that type 2 PRRSV infection in pregnant gilts induces significant histopathological lesions at maternal-fetal interface, but they are not associated with presence of PRRSV in the maternal-fetal interface at 21 days post infection. Conversely, fetal pathological lesions are associated with presence of PRRSV in the maternal-fetal interface and fetal thymus, and meconium staining is significantly associated with the presence of both fetal and umbilical lesions observed 21 days post infection.