There are more than 7000 described rare genetic disorders; however, the molecular basis underlying approximately half of these disorders is unknown, and the majority are currently untreatable. Stature and growth abnormalities are a common clinical feature of many rare disorders including: Floating-Harbor syndrome (FHS), a short stature syndrome characterized by delayed osseous maturation, language deficits, and unique dysmorphic facial features; Weaver syndrome, an overgrowth syndrome characterized by advanced osseous maturation, developmental delay, and macrocephaly; and Sotos syndrome with cutis laxa, an overgrowth syndrome with marked tissue laxity in addition to the typical Sotos characteristics of developmental delay, macrocephaly, and a unique facial gestalt. The genetic basis underlying these three rare stature conditions were unknown at the outset of this study. We utilized high-throughput exome sequencing approaches to investigate the molecular etiology of these rare disorders and identified truncating mutations in the final exon of SRCAP as the genetic cause underlying FHS, missense mutations in EZH2 in Weaver syndrome, and novel mutations in the Sotos syndrome gene NSD1 in Sotos syndrome with cutis laxa. Next, we investigated the spectrum of SRCAP mutations in FHS and established the clustering of truncating SRCAP mutations in the final exon as being highly suggestive of a non-haploinsufficiency mutational mechanism in FHS. Finally, global methylation array analysis identified a unique methylation ‘epi-signature’ in FHS individuals, providing further insight into FHS disease mechanism and a diagnostic signature. These studies have delineated the molecular etiology of these three rare stature/growth disorders, furthered our understanding of the associated clinical spectrum, and provided biological insight into disease pathogenesis.

Indiana University-Purdue University Indianapolis (IUPUI)

Indiana University-Purdue University Indianapolis (IUPUI) / The rapid innovations in biotechnology have led to an exponential growth of data and electronically accessible scientific literature. In this enormous scientific data, knowledge can be exploited, and novel discoveries can be made. In my dissertation, I have focused on the novel molecular mechanism and therapeutic discoveries from big data for complex diseases. It is very evident today that complex diseases have many factors including genetics and environmental effects. The discovery of these factors is challenging and critical in personalized medicine. The increasing cost and time to develop new drugs poses a new challenge in effectively treating complex diseases. In this dissertation, we want to demonstrate that the use of existing data and literature as a potential resource for discovering novel therapies and in repositioning existing drugs. The key to identifying novel knowledge is in integrating information from decades of research across the different scientific disciplines to uncover interactions that are not explicitly stated. This puts critical information at the fingertips of researchers and clinicians who can take advantage of this newly acquired knowledge to make informed decisions. This dissertation utilizes computational biology methods to identify and integrate existing scientific data and literature resources in the discovery of novel molecular targets and drugs that can be repurposed. In chapters 1 of my dissertation, I extensively sifted through scientific literature and identified a novel interaction between Vitamin A and CYP19A1 that could lead to a potential increase in the production of estrogens. Further in chapter 2 by exploring a microarray dataset from an estradiol gene sensitivity study I was able to identify a potential novel anti-estrogenic indication for the commonly used urinary analgesic, phenazopyridine. Both discoveries were experimentally validated in the laboratory. In chapter 3 of my dissertation, through the use of a manually curated corpus and machine learning algorithms, I identified and extracted genes that are essential for cell survival. These results brighten the reality that novel knowledge with potential clinical applications can be discovered from existing data and literature by integrating information across various scientific disciplines.

Thesis (PhD)-- Stellenbosch University, 2014. / ENGLISH ABSTRACT: Ventricular arrhythmias are the most important cause of sudden cardiac death (SCD) among adults living in industrialised nations. Genetic factors have substantial effects in determining population-based risk for SCD and may also account for inter-individual variability in susceptibility. Great progress has been made in identifying genes underlying various Mendelian disorders associated with inherited arrhythmia susceptibility. The most well studied familial arrhythmia syndrome is the congenital long QT syndrome (LQTS) caused by mutations in genes encoding subunits of myocardial ion channels. Not all mutation carriers have equal risk for experiencing the clinical manifestations of disease (i.e. syncope, sudden death). This observation has raised the possibility that additional genetic factors may modify the risk of LQTS manifestations. This study establishes the genetic aetiology of LQTS in South Africa and Denmark through the identification and characterisation of LQTS-causative mutations in five previously identified genes, as well as examining possible novel genetic causes of LQTS in a cohort comprising Danish and British probands. We have functionally characterised several of the mutations identified in this study and examined other cardiac phenotypes that may be explained by variants causing repolarisation disorders. / AFRIKAANSE OPSOMMING: Ventrikulêre aritmie bly die enkele belangrikste oorsaak van skielike hart dood (SCD) onder volwassenes wat in geïndustrialiseerde lande woon. Genetiese faktore het aansienlike gevolge in die bepaling van bevolking-gebaseerde risiko vir SCD en kan ook verantwoordelik wees vir die inter-individuele variasie in vatbaarheid. Groot vordering is gemaak in die identifisering van gene onderliggende verskeie Mendeliese siektes wat verband hou met geërf aritmie vatbaarheid. Die mees goed bestudeerde familie aritmie sindroom is die aangebore lang QT-sindroom (LQTS) wat veroorsaak word deur mutasies in gene kode subeenhede van miokardiale ioonkanale. Nie alle mutasie draers het 'n gelyke risiko vir die ervaring van die kliniese manifestasies van die siekte (dws sinkopee, skielike dood). Hierdie waarneming het die moontlikheid genoem dat genetiese faktore anders as die primêre siekte-verwante mutasie kan die risiko van LQTS manifestasies verander. Hierdie studie stel die genetiese oorsake van LQTS in Suid-Afrika en Denemarke deur die identifisering en karakterisering van LQTS-veroorsakende mutasies in vyf voorheen geïdentifiseer gene, asook die behandeling van moontlike nuwe genetiese oorsake van LQTS in 'n groep wat bestaan uit van die Deense en die Britse probands. Ons het funksioneel gekenmerk verskeie van die mutasies wat in hierdie studie ondersoek en ander kardiovaskulêre fenotipes wat deur variante veroorsaak repolarisasie versteurings verduidelik word. / South African National Research Foundation / Harry and Doris Crossley Foundation / Danish Strategic Research Foundation.

The purpose of this hermeneutic phenomenological study was to understand the essence of the lived experience of women after having an abnormal prenatal ultrasound. One hundred years ago, health disciplines had limited therapies for prenatal and neonatal disorders. During this period, the eugenics movement influenced leaders to involuntarily sterilize individuals who were sought to be "unfit" to prevent disorders in offspring. ... One of these contemporary reproductive genetic technologies is the use of ultrasound and serum bio-medical markers for detection of congenital, chromosome, and genetic disorders. When ultrasounds reveal abnormal findings, the perceived perfect pregnancy vanishes and gives way to feelings of shock, disbelief, fear, guilt, loss, and threats to self and their unborn baby. Twelve women who had an abnormal ultrasound were interviewed within the context of their cultural values and beliefs. The method of van Manen's hermeneutic phenomenology illuminated the meaning for these women in their life worlds. ... They endured this experience through their own coping mechanisms, but often felt uncertainty and emotional turmoil until the birth. The women also sought comfort through their cultural values, beliefs, and traditions. In coping with the risks found on this abnormal ultrasound, women often selected silence or blocking perceived threats. With these coping methods, they were alone in their suffering. ... Health providers, in not recognizing these women's misunderstandings and emotional fears, abandoned them in their psychosocial and cultural needs. The significance reveals that nurses and health providers need to infuse human caring ways of being, knowing, and doing within advanced technological environments. / by Jeanne Chatham Gottlieb. / Thesis (Ph.D.)--Florida Atlantic University, 2013. / Includes bibliography. / Mode of access: World Wide Web. / System requirements: Adobe Reader.

Les variants du nombre de copies (CNV) offre un cadre riche pour étudier les mécanismes neurobiologiques qui sous tendent la vulnérabilité aux troubles neuropsychiatriques. Notamment, les délétions du 16p11.2 et 22q11.2 sont parmi les facteurs génétiques les plus fréquents associés au trouble du spectre de l’autisme (TSA) et à la schizophrénie (SCZ). À l’heure actuelle, les perturbations fonctionnelles cérébrales qui sous-tendent cette vulnérabilité cognitive restent mécomprises. Récemment, l’analyse par gradient du connectome humain a révélé une réorganisation le long de l’axe dominant sensorimoteur à transmodal dans le TSA et la SCZ. Dans cette étude, nous avons cherché à étendre cette approche analytique aux porteurs d’une délétion du 16p11.2 et du 22q11.2 conférant un risque élevé pour de mêmes conditions. À cette fin, nous avons utilisé les données d’imagerie par résonance magnétique au repos combinant les données de deux cohortes génétiques, pour un total de 180 sujets incluant 61 porteurs. Par le biais d’un paradigme cas-contrôle, nous rapportons la première évidence d’une compression du gradient fonctionnel sensorimoteur à transmodal chez les porteurs de telles délétions. En dernier lieu, nous présentons une étude exploratoire d’association endophénotype-phénome dans la population générale du UK Biobank. Nous démontrons que la ressemblance aux profils de compression corticale des délétions est reliée à plusieurs traits humains complexes, en concordance avec les dimensions cliniques impactées par ces mêmes CNV. / Copy number variants (CNVs) present a unique opportunity to study the neural mechanisms underlying vulnerability to neuropsychiatric disorders. Notably, deletions of the 16p11.2 and 22q11.2 region are among the most common genetic variations associated with autism spectrum disorder (ASD) and schizophrenia (SCZ). However, brain functional disruptions underlying this cognitive vulnerability remains unclear. Recent gradient analysis framework developed to study parsimonious connectome dimensions at the system-level have reported disruptions along the overarching sensorimotor-to-transmodal gradient in ASD and SCZ. In this study, we sought to extend this gradient approach to carriers of a deletion at the 16p11.2 and 22q11.2 region. To achieve this, we pooled resting-state functional magnetic resonance imaging data from a total of 180 subjects, including 61 carriers, distributed among two genetic cohorts. By the means of a case-control study design, we provide the first evidence of a compressed cortical functional gradient in CNV carriers compared to healthy controls. Finally, we provide an exploratory endophenotype-phenome association study in the general UK Biobank population. We demonstrate that resemblance to 16p11.2 and 22q11.2 deletion profiles of cortical compression is related to several complex human traits, in concordance with clinical dimensions known to be impacted by the same CNV.

The topic of cleft lip and/or palate is widely researched in literature. However no research to date has focused on mothers' experiences raising twins when one twin is born with a cleft lip and/or palate. This qualitative study aims to explore the unigue experiences of these mothers. The epistemological foundations of this study are postmodern, social constructionist and systemic. In accordance with a gualitative methodology data was collected in the form of the participants' personal written stories. This was done from a post-modern paradigm, from a systemic perspective. Themes that were extracted from the stories according to thematic content analysis, not only reflect the experiences of mothers raising twins when one twin is born with a cleft lip and/or palate, they also provide an in-depth understanding of these mothers' experiences and unique situations. Recommendations for future research are offered. / Psychology / M.A. (Clinical Psychology)

18q- is a chromosomal deletion disorder caused by missing genetic material from the long arm of the 18th chromosome. The extensive impairments associated with 18qmay be a significant source of stress to parents. Research on families of handicapped children suggests that these families experience additional stress related to challenges such as increased caregiving demands, changes in social support systems, and financial burdens related to medical needs and decreased income. Changes in the family environment are also implicated in families coping with a disabled child. Some studies reveal highly cohesive environments within these families, while others reveal decreased levels of expressiveness and cohesion and increases in conflict. The present study compared variables of parenting stress and family environment in families of children with and without disabilities. Group 1 consisted of 24 primary caregivers of children with 18q-. Group 2 consisted of 32 primary caregivers of children with DS. Group 3 consisted of 32 primary caregivers of typically developing children. A one-way, between groups multivariate analysis of variance (MANOVA) was conducted to investigate differences in parenting stress on three subscales of the Parenting Stress Index. A significant difference between groups was found. Post hoc pairwise comparisons indicated that the DS group reported statistically significantly more stress than the Control group on both the Isolation and Spouse subscales. The 18q- group was not found to be statistically significantly different from either the Control or DS group on any of the three PSI subscales. A one-way, between groups multivariate analysis of variance (MANOVA) was also conducted to investigate differences in family environment on three subscales of the Family Environment Scale. A significant difference between groups was found. Post hoc pairwise comparisons indicated that the DS group showed statistically significantly less amounts of cohesion in the family environment than both the 18q- and Control groups. The 18q- group showed similar levels of cohesion to the Control group. There were no significant differences between groups on the other two FES subscales. Findings from the study provide important information about the role of family environment and parenting stress in families of children with disabilities. Limitations of the study and implications for future research and practice are discussed. / text

The topic of cleft lip and/or palate is widely researched in literature. However no research to date has focused on mothers' experiences raising twins when one twin is born with a cleft lip and/or palate. This qualitative study aims to explore the unigue experiences of these mothers. The epistemological foundations of this study are postmodern, social constructionist and systemic. In accordance with a gualitative methodology data was collected in the form of the participants' personal written stories. This was done from a post-modern paradigm, from a systemic perspective. Themes that were extracted from the stories according to thematic content analysis, not only reflect the experiences of mothers raising twins when one twin is born with a cleft lip and/or palate, they also provide an in-depth understanding of these mothers' experiences and unique situations. Recommendations for future research are offered. / Psychology / M.A. (Clinical Psychology)

Indiana University-Purdue University Indianapolis (IUPUI) / Human induced pluripotent stem (iPS) cells have the unique ability to differentiate into 200 or so somatic cell types that make up the adult human being. The use of human iPS cells to study development and disease is a highly exciting and interdependent field that holds great promise in understanding and elucidating mechanisms behind cellular differentiation with future applications in drug screening and cell replacement studies for complex and currently incurable cellular degenerative disorders. The recent advent of iPS cell technology allows for the generation of patient-specific cell lines that enable us to model the progression of a disease phenotype in a human in vitro model. Differentiation of iPS cells toward the affected cell type provides an unlimited source of diseased cells for examination, and to further study the developmental progression of the disease in vitro, also called the “disease-in-a-dish” model. In this study, efforts were undertaken to recapitulate the differentiation of distinct retinal cell affected in two highly prevalent retinal diseases, Usher syndrome and glaucoma. Using a line of Type III Usher Syndrome patient derived iPS cells efforts were undertaken to develop such an approach as an effective in vitro model for studies of Usher Syndrome, the most commonly inherited disorder affecting both vision and hearing. Using existing lines of iPS cells, studies were also aimed at differentiation and characterization of the more complex retinal cell types, retinal ganglion cells (RGCs) and astrocytes, the cell types affected in glaucoma, a severe neurodegenerative disease of the retina leading to eventual irreversible blindness. Using a previously described protocol, the iPS cells were directed to differentiate toward a retinal fate through a step-wise process that proceeds through all of the major stages of neuroretinal development. The differentiation process was monitored for a period of 70 days for the differentiation of retinal cell types and 150 days for astrocyte development. The different stages of differentiation and the individually derived somatic cell types were characterized by the expression of developmentally associated transcription factors specific to each cell type. Further approaches were undertaken to characterize the morphological differences between RGCs and other neuroretinal cell types derived in the process. The results of this study successfully demonstrated that Usher syndrome patient derived iPS cells differentiated to the affected photoreceptors of Usher syndrome along with other mature retinal cell types, chronologically analogous to the development of the cell types in a mature human retina. This study also established a robust method for the in vitro derivation of RGCs and astrocytes from human iPS cells and provided novel methodologies and evidence to characterize these individual somatic cell types. Overall, this study provides a unique insight into the application of human pluripotent stem cell biology by establishing a novel platform for future studies of in vitro disease modeling of the retinal degenerative diseases: Usher syndrome and glaucoma. In downstream applications of this study, the disease relevant cell types derived from human iPS cells can be used as tools to further study disease progression, drug screening and cell replacement strategies.