Interpreting Human Genetic Variation through Genomics and In Vivo Models

Improvements in genomic technology, both in the increased speed and reduced cost of sequencing, have expanded the appreciation of the abundance of human genetic variation. However the sheer amount of variation, as well as the varying type and genomic content of variation, poses a challenge in understanding the clinical consequence of a single mutation. This work uses several methodologies to interpret the observed variation in the human genome, and presents novel strategies for the prediction of allele pathogenicity.

Using the zebrafish model system as an in vivo assay of allele function, we identified a novel driver of Bardet-Biedl Syndrome (BBS) in CEP76. A combination of targeted sequencing of 785 cilia-associated genes in a cohort of BBS patients and subsequent in vivo functional assays recapitulating the human phenotype gave strong evidence for the role of CEP76 mutations in the pathology of an affected family. This portion of the work demonstrated the necessity of functional testing in validating disease-associated mutations, and added to the catalogue of known BBS disease genes.

Further study into the role of copy-number variations (CNVs) in a cohort of BBS patients showed the significant contribution of CNVs to disease pathology. Using high-density array comparative genomic hybridization (aCGH) we were able to identify pathogenic CNVs as small as several hundred bp. Dissection of constituent gene and in vivo experiments investigating epistatic interactions between affected genes allowed for an appreciation of several paradigms by which CNVs can contribute to disease. This study revealed that the contribution of CNVs to disease in BBS patients is much higher than previously expected, and demonstrated the necessity of consideration of CNV contribution in future (and retrospective) investigations of human genetic disease.

Finally, we used a combination of comparative genomics and in vivo complementation assays to identify second-site compensatory modification of pathogenic alleles. These pathogenic alleles, which are found compensated in other species (termed compensated pathogenic deviations [CPDs]), represent a significant fraction (from 3 – 10%) of human disease-associated alleles. In silico pathogenicity prediction algorithms, a valuable method of allele prioritization, often misrepresent these alleles as benign, leading to omission of possibly informative variants in studies of human genetic disease. We created a mathematical model that was able to predict CPDs and putative compensatory sites, and functionally showed in vivo that second-site mutation can mitigate the pathogenicity of disease alleles. Additionally, we made publically available an in silico module for the prediction of CPDs and modifier sites.

These studies have advanced the ability to interpret the pathogenicity of multiple types of human variation, as well as made available tools for others to do so as well.

Screening for Sexual Trauma, Intimate Partner Violence and Mental Health Symptoms among HIV Positive South African Women

Background: The psychological sequelae of sexual trauma and physical intimate partner violence (IPV) exposure can lead to poor HIV care outcomes, including poor treatment adherence. This study aimed to estimate the prevalence of and factors associated with mental health symptoms and trauma among HIV positive women. Additionally, the study aimed to assess the feasibility and acceptability of screening for trauma and mental health symptoms among HIV positive South African women. Finally, the study aimed to elicit healthcare workers’ perceptions related to sexual trauma and the provision of care and services for HIV positive women with trauma histories.

Methods: The study utilized a mixed-methods approach that included a cross-sectional survey of 70 HIV positive women recruited through referral sampling and key informant interviews with seven healthcare workers (HCWs). A study-screening instrument consisting of 24 items from standard measures was used to screen women for sexual trauma, physical intimate partner violence (IPV), depression and PTSD. Sexual trauma and IPV were assessed across the lifetime, while depression and PTSD were current assessments. Logistic regression models were used to explore the relationship between trauma exposure and mental health symptoms, while controlling for age and education. Interview transcripts were coded and analyzed for emergent themes on HCWs perceptions on sexual trauma and HIV care.

Results: Among participants, 51% had sexual trauma experience and 75% had intimate partner violence (IPV) experience. Among participants, 36% met screening criteria for major depression; among those with traumatic experiences (n=57), 70% met screening criteria for post-traumatic stress disorder (PTSD). Compared to having no sexual trauma or IPV exposure, having both sexual trauma and IPV was significantly associated with higher odds of depression (OR = 8.11; 95% CI 1.48-44.34), while having either IPV or sexual trauma individually was not significantly associated with increased odds of depression. Compared to having either IPV or sexual trauma, having both sexual trauma and IPV was not significantly associated with PTSD. Responses from participants’ feedback on screening process suggest that screening was feasible and acceptable to participants. Some of the health care workers (HCWs) did not perceive dealing with trauma to be part of their duties, but instead viewed social workers or psychologists as the appropriate health cadre to provide care related to trauma and mental health.

Conclusions: High levels of sexual trauma, IPV and mental health distress were reported among HIV positive women in this setting. Screening for trauma and mental health symptoms was acceptable to the participants, but several challenges were encountered in implementing screening. Given the potential impact of trauma and mental health on HIV care engagement, interventions to address trauma and its psychological sequelae are needed.

Prostate cancer screening

Universal screening for prostate cancer (Pca) using prostate-specific antigen-based testing is not recommended, as the potential harms of screening (overdiagnosis and overtreatment) outweigh potential benefits. The case for Pca screening requires a paradigm shift, which emphasizes the risks of screening over the risks of undetected cancer. Physicians are encouraged to use shared decision making with patients who express an interest in Pca screening, taking into account both the patient's screening preferences and individual risk profile. New models of care informed by the Patient Protection and Affordable Care Act are intended to assist clinicians in providing recommended preventive services. © 2014 Elsevier Inc.

Neural Network Evidence for the Coupling of Presaccadic Visual Remapping to Predictive Eye Position Updating.

As we look around a scene, we perceive it as continuous and stable even though each saccadic eye movement changes the visual input to the retinas. How the brain achieves this perceptual stabilization is unknown, but a major hypothesis is that it relies on presaccadic remapping, a process in which neurons shift their visual sensitivity to a new location in the scene just before each saccade. This hypothesis is difficult to test in vivo because complete, selective inactivation of remapping is currently intractable. We tested it in silico with a hierarchical, sheet-based neural network model of the visual and oculomotor system. The model generated saccadic commands to move a video camera abruptly. Visual input from the camera and internal copies of the saccadic movement commands, or corollary discharge, converged at a map-level simulation of the frontal eye field (FEF), a primate brain area known to receive such inputs. FEF output was combined with eye position signals to yield a suitable coordinate frame for guiding arm movements of a robot. Our operational definition of perceptual stability was "useful stability," quantified as continuously accurate pointing to a visual object despite camera saccades. During training, the emergence of useful stability was correlated tightly with the emergence of presaccadic remapping in the FEF. Remapping depended on corollary discharge but its timing was synchronized to the updating of eye position. When coupled to predictive eye position signals, remapping served to stabilize the target representation for continuously accurate pointing. Graded inactivations of pathways in the model replicated, and helped to interpret, previous in vivo experiments. The results support the hypothesis that visual stability requires presaccadic remapping, provide explanations for the function and timing of remapping, and offer testable hypotheses for in vivo studies. We conclude that remapping allows for seamless coordinate frame transformations and quick actions despite visual afferent lags. With visual remapping in place for behavior, it may be exploited for perceptual continuity.