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Vanderbilt University
1.
Davis, Mary Feller.
Parkinson Disease Loci in the Mid-Western Amish.
Degree: MS, Interdisciplinary Studies: Applied Statistics, 2013, Vanderbilt University
URL: http://hdl.handle.net/1803/11436 
► Previous evidence has shown that Parkinson disease (PD) has a heritable component, but only a small proportion of the total genetic contribution to PD has…
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▼ Previous evidence has shown that Parkinson disease (PD) has a heritable component, but only a small proportion of the total genetic contribution to PD has been identified. Genetic heterogeneity complicates the verification of proposed PD genes and the identification of new PD susceptibility genes. Our approach to overcome the problem of heterogeneity is to study a population isolate, the mid-western Amish communities of Indiana and Ohio. We performed genome-wide association and linkage analyses on 798 individuals (31 with PD), who are part of a 4,998 member pedigree. Through these analyses, we identified a region on chromosome 5q31.3 that shows evidence of association (p-value < 1 x 10-4) and linkage (multipoint HLOD = 3.77). We also found further evidence of linkage on chromosomes 6 and 10 (multipoint HLOD 4.02 and 4.35 respectively). These data suggest that locus heterogeneity, even within the Amish, may be more extensive than previously appreciated.
Advisors/Committee Members: Jonathan L. Haines (committee member), Scott Williams (committee member), Marylyn Ritchie (committee member).
Subjects/Keywords: parkinson disease; Amish; genetics; linkage; association
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APA (6th Edition):
Davis, M. F. (2013). Parkinson Disease Loci in the Mid-Western Amish. (Thesis). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/11436
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Davis, Mary Feller. “Parkinson Disease Loci in the Mid-Western Amish.” 2013. Thesis, Vanderbilt University. Accessed March 07, 2021.
http://hdl.handle.net/1803/11436.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Davis, Mary Feller. “Parkinson Disease Loci in the Mid-Western Amish.” 2013. Web. 07 Mar 2021.
Vancouver:
Davis MF. Parkinson Disease Loci in the Mid-Western Amish. [Internet] [Thesis]. Vanderbilt University; 2013. [cited 2021 Mar 07].
Available from: http://hdl.handle.net/1803/11436.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Davis MF. Parkinson Disease Loci in the Mid-Western Amish. [Thesis]. Vanderbilt University; 2013. Available from: http://hdl.handle.net/1803/11436
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Vanderbilt University
2.
Gandhi, Vishal V.
Investigating mitochondrial deoxyribonucleotide metabolism and its role in a family of genetic diseases.
Degree: PhD, Human Genetics, 2011, Vanderbilt University
URL: http://hdl.handle.net/1803/14867
► Abnormal regulation of mitochondrial deoxyribonucleoside triphosphate pools can lead to mitochondrial DNA depletion syndromes, a set of genetic diseases associated with depletion of mitochondrial DNA.…
(more)
▼ Abnormal regulation of mitochondrial deoxyribonucleoside triphosphate pools can lead to mitochondrial DNA depletion syndromes, a set of genetic diseases associated with depletion of mitochondrial DNA. Besides mitochondrial DNA depletion syndromes, improper maintenance of mitochondrial deoxyribonucleoside triphosphate pools and mitochondrial DNA have also been implicated in a host of other human pathologies. The unifying objective of this dissertation was to enhance our knowledge of the regulation of mitochondrial deoxyribonucleoside triphosphate pools. The first step was to investigate the characteristics of mitochondrial and cytoplasmic deoxyribonucleoside triphosphate levels. I calculated mitochondrial and cytoplasmic deoxyribonucleoside triphosphate concentrations from previously published data. Cytoplasmic and mitochondrial deoxyribonucleoside triphosphates are strongly correlated in normal cells but not in transformed cells. Following up this discovery with analysis of gene expression, I discovered that, consistent with the trends in deoxyribonucleoside triphosphate concentrations in cells, genes coding for enzymes that maintain cytoplasmic and mitochondrial deoxyribonucleoside triphosphates have correlated expression across normal tissues but not across transformed tissues. To further understand the influence of cytoplasmic deoxyribonucleoside triphosphates on mitochondrial deoxyribonucleoside triphosphates, I simulated the metabolism of mitochondrial deoxyribonucleosides with a computational model. Cytoplasmic deoxyribonucleotides have a substantial and indispensable contribution to mitochondrial deoxyribonucleoside triphosphates in most circumstances. My results further show that import from the cytoplasm would need to occur at either deoxyribonucleoside diphosphate or triphosphate levels.
Advisors/Committee Members: Emmanuele DiBenedetto (committee member), David Samuels (committee member), Scott Williams (committee member), Todd Hulgan (committee member), Tricia Thornton-Wells (Committee Chair).
Subjects/Keywords: depletion; dNTP; mitochondria; nucleotide; mtDNA
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APA (6th Edition):
Gandhi, V. V. (2011). Investigating mitochondrial deoxyribonucleotide metabolism and its role in a family of genetic diseases. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/14867
Chicago Manual of Style (16th Edition):
Gandhi, Vishal V. “Investigating mitochondrial deoxyribonucleotide metabolism and its role in a family of genetic diseases.” 2011. Doctoral Dissertation, Vanderbilt University. Accessed March 07, 2021.
http://hdl.handle.net/1803/14867.
MLA Handbook (7th Edition):
Gandhi, Vishal V. “Investigating mitochondrial deoxyribonucleotide metabolism and its role in a family of genetic diseases.” 2011. Web. 07 Mar 2021.
Vancouver:
Gandhi VV. Investigating mitochondrial deoxyribonucleotide metabolism and its role in a family of genetic diseases. [Internet] [Doctoral dissertation]. Vanderbilt University; 2011. [cited 2021 Mar 07].
Available from: http://hdl.handle.net/1803/14867.
Council of Science Editors:
Gandhi VV. Investigating mitochondrial deoxyribonucleotide metabolism and its role in a family of genetic diseases. [Doctoral Dissertation]. Vanderbilt University; 2011. Available from: http://hdl.handle.net/1803/14867
Vanderbilt University
3.
Jones, Carissa Christine.
Examining the role of genetics in lung cancer survival and risk in African Americans.
Degree: PhD, Human Genetics, 2017, Vanderbilt University
URL: http://hdl.handle.net/1803/13799
► Lung cancer is a leading cause of cancer in the United States and accounts for more deaths than prostate, breast, and colorectal cancers combined. Genetic…
(more)
▼ Lung cancer is a leading cause of cancer in the United States and accounts for more deaths than prostate, breast, and colorectal cancers combined. Genetic variation has been known to play a role in lung cancer survival and risk. Furthermore, a racial disparity exists in lung cancer risk and survival such that African American males have increased risk and greater mortality compared to other U.S. racial/ethnic groups. This dissertation sought to expand our present understanding of the role of genetics in lung cancer survival and risk in African Americans. In a population of African Americans and whites from the Southern Community Cohort Study (SCCS), we examined the association between global African ancestry and overall survival and found no significant association. Stage and treatment, however, were strong predictors of overall survival. Since both stage and treatment are highly dependent on external social factors such as access to healthcare and willingness to seek treatment, we conclude that the observed racial disparity in lung cancer survival is strongly driven social determinants. We next examined genetic variants associated with lung cancer survival in the SCCS African Americans. We identified rs1878022 to be significantly associated with lung cancer survival, though in opposing direction to a previous study in whites. We also identified a region on chromosome 6p21.33 as suggestive of association with lung cancer survival. Finally, we sought to identify cross-cancer pleiotropic associations of lung cancer risk in African Americans by examining variant regions previously associated with cancer risk. We confirmed previous associations between chromosomes 15q25 and 5p15 and lung cancer risk. We also identified a peak on chromosome 16q22.2 significantly associated with increased lung cancer risk. Cumulatively these findings deepen our understanding of the role of genetics in both lung cancer risk and survival, particularly in African Americans. Future studies in African Americans are necessary to confirm these genetic associations.
Advisors/Committee Members: Jeffrey Blume (committee member), Eric Grogan (committee member), Scott Williams (committee member), Melinda Aldrich (committee member), Digna Velez Edwards (Committee Chair).
Subjects/Keywords: survival; African Americans; risk; lung cancer; genetics
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APA (6th Edition):
Jones, C. C. (2017). Examining the role of genetics in lung cancer survival and risk in African Americans. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/13799
Chicago Manual of Style (16th Edition):
Jones, Carissa Christine. “Examining the role of genetics in lung cancer survival and risk in African Americans.” 2017. Doctoral Dissertation, Vanderbilt University. Accessed March 07, 2021.
http://hdl.handle.net/1803/13799.
MLA Handbook (7th Edition):
Jones, Carissa Christine. “Examining the role of genetics in lung cancer survival and risk in African Americans.” 2017. Web. 07 Mar 2021.
Vancouver:
Jones CC. Examining the role of genetics in lung cancer survival and risk in African Americans. [Internet] [Doctoral dissertation]. Vanderbilt University; 2017. [cited 2021 Mar 07].
Available from: http://hdl.handle.net/1803/13799.
Council of Science Editors:
Jones CC. Examining the role of genetics in lung cancer survival and risk in African Americans. [Doctoral Dissertation]. Vanderbilt University; 2017. Available from: http://hdl.handle.net/1803/13799
Vanderbilt University
4.
Jeff, Janina Maria.
The Genetics of Quantitative Traits Associated with Cardiovascular Disease in African Americans.
Degree: PhD, Human Genetics, 2012, Vanderbilt University
URL: http://hdl.handle.net/1803/10690
► Cardiovascular disease (CVD) is the leading cause of death in most developed countries. In addition to environmental risk factors, such as diet and physical activity,…
(more)
▼ Cardiovascular disease (CVD) is the leading cause of death in most developed countries. In addition to environmental risk factors, such as diet and physical activity, genetic risk factors contribute to the CVD risk. Risk of CVD is not uniformly distributed across populations, as African Americans and Hispanics have more risk factors for CVD compared with European Americans. The use of quantitative traits to identify genetic risk factors is a potentially more powerful, informative and uniform approach compared with the use of binary or qualitative traits (such as CVD case status).
My primary objective is to identify genetic risk factors associated with the regulation fibrinogen/hematological and electrocardiogram (ECG) traits in African Americans. Both fibrinogen/hematological and ECG traits are common clinical characteristics of CVD and have a strong genetic component. The primary objective of this work is to identify genetic risk factors associated with the regulation fibrinogen/hematological and electrocardiogram (ECG) traits in African Americans. Both fibrinogen/hematological and ECG traits are common clinical characteristics of CVD and have a strong genetic component. Using three approaches: candidate gene, genome-wide association studies (GWAS), and testing for genetic interactions (gene-gene and gene-environment); we identify novel and previously identified genetic associations with ECG traits and fibrinogen/hematological traits in African Americans and other global populations.
Advisors/Committee Members: Dan Roden (committee member), Alyssa Hasty (committee member), Dana Crawford (committee member), Marylyn Ritchie (Committee Chair), Scott Williams (Committee Chair).
Subjects/Keywords: electrocardiographic traits; fibrinogen; African Americans; quantitative traits
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APA (6th Edition):
Jeff, J. M. (2012). The Genetics of Quantitative Traits Associated with Cardiovascular Disease in African Americans. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/10690
Chicago Manual of Style (16th Edition):
Jeff, Janina Maria. “The Genetics of Quantitative Traits Associated with Cardiovascular Disease in African Americans.” 2012. Doctoral Dissertation, Vanderbilt University. Accessed March 07, 2021.
http://hdl.handle.net/1803/10690.
MLA Handbook (7th Edition):
Jeff, Janina Maria. “The Genetics of Quantitative Traits Associated with Cardiovascular Disease in African Americans.” 2012. Web. 07 Mar 2021.
Vancouver:
Jeff JM. The Genetics of Quantitative Traits Associated with Cardiovascular Disease in African Americans. [Internet] [Doctoral dissertation]. Vanderbilt University; 2012. [cited 2021 Mar 07].
Available from: http://hdl.handle.net/1803/10690.
Council of Science Editors:
Jeff JM. The Genetics of Quantitative Traits Associated with Cardiovascular Disease in African Americans. [Doctoral Dissertation]. Vanderbilt University; 2012. Available from: http://hdl.handle.net/1803/10690
Vanderbilt University
5.
Reif, David Michael.
Integrated Analysis of Genetic and Proteomic Data.
Degree: PhD, Human Genetics, 2006, Vanderbilt University
URL: http://hdl.handle.net/1803/14337
► Biological organisms are complex systems that dynamically integrate inputs from a multitude of physiological and environmental factors. Complex clinical outcomes arise from the concerted interactions…
(more)
▼ Biological organisms are complex systems that dynamically integrate inputs from a multitude of physiological and environmental factors. Complex clinical outcomes arise from the concerted interactions among the myriad components of a biological system. Therefore, in addressing questions concerning the etiology of phenotypes as complex as common human disease or adverse reaction to vaccination, it is essential that the systemic nature of biology be taken into account. Analysis methods must integrate the information provided by each data type in a manner analogous to the operation of the body itself. It is hypothesized that such integrated approaches will provide a more comprehensive portrayal of the mechanisms underlying complex phenotypes and lend confidence to the biological interpretation of analytical conclusions.This dissertation concerns the development of a comprehensive analysis paradigm wherein experimental data of multiple types were analyzed jointly in the study of complex phenotypes. Flexible machine learning methods were used to integrate information that is insensitive to spatial and temporal flux (genetic polymorphisms) with information subject to dynamic changes (protein concentrations measured at multiple time points). This strategy was applied to genetic and proteomic data in both simulated and real analysis situations. Results of studies using simulated data indicated that utilizing multiple data types is beneficial when the disease model is complex and the phenotypic outcome-associated data type is unknown. The successful application to combined genetic and proteomic data from smallpox vaccine studies supported the hypothesis that such integrated approaches are analytically beneficial.
Considering the rapid progress in experimental technologies able to reliably generate vast quantities of data, as well as continual improvements in cost efficiency, it is expected that datasets including multiple types of experimental information will become commonplace in the near future. It is hoped that the positive conclusions from this dissertation will help spur the adoption of an analytical approach that rightfully takes the broader physiological context of complex biological systems into account.
Advisors/Committee Members: James Crowe, Jr. (committee member), Douglas Fisher (committee member), Jonathan Haines (committee member), Jason Moore (committee member), Scott Williams (Committee Chair).
Subjects/Keywords: machine learning; statistics; Systems biology; immunology; Genetic polymorphisms; Smallpox – Vaccination – Complications; Proteomics
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APA (6th Edition):
Reif, D. M. (2006). Integrated Analysis of Genetic and Proteomic Data. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/14337
Chicago Manual of Style (16th Edition):
Reif, David Michael. “Integrated Analysis of Genetic and Proteomic Data.” 2006. Doctoral Dissertation, Vanderbilt University. Accessed March 07, 2021.
http://hdl.handle.net/1803/14337.
MLA Handbook (7th Edition):
Reif, David Michael. “Integrated Analysis of Genetic and Proteomic Data.” 2006. Web. 07 Mar 2021.
Vancouver:
Reif DM. Integrated Analysis of Genetic and Proteomic Data. [Internet] [Doctoral dissertation]. Vanderbilt University; 2006. [cited 2021 Mar 07].
Available from: http://hdl.handle.net/1803/14337.
Council of Science Editors:
Reif DM. Integrated Analysis of Genetic and Proteomic Data. [Doctoral Dissertation]. Vanderbilt University; 2006. Available from: http://hdl.handle.net/1803/14337
Vanderbilt University
6.
Delahanty, Ryan James.
Towards an understanding of the role of chromosome 15q11-q13 in idiopathic autism.
Degree: PhD, Human Genetics, 2010, Vanderbilt University
URL: http://hdl.handle.net/1803/10492
► TOWARD AN UNDERSTANDING OF THE ROLE OF CHROMOSOME 15Q11-Q13 IN IDIOPATHIC AUTISM RYAN JAMES DELAHANTY Dissertation under the direction of Dr. James S. Sutcliffe The…
(more)
▼ TOWARD AN UNDERSTANDING OF THE ROLE OF CHROMOSOME
15Q11-Q13 IN IDIOPATHIC AUTISM
RYAN JAMES DELAHANTY
Dissertation under the direction of Dr. James S. Sutcliffe
The 15q11-q13 region is a genomic interval involved in a growing number of genomic disorders. The genes in the interval are subject to imprinting and parent-of-origin expression effects. Maternal duplication of the 15q11-q13 region is the most frequent chromosomal abnormality associated with autism. Extensive work has indicated that two genes in this interval, UBE3A and GABRB3, show very strong evidence for association with autism.
To examine the extent to which these genes may contribute to autism, family-based association studies of UBE3A and GABRB3 were undertaken. Here we have investigated the role of common variants of UBE3A and GABRB3 in autism as well as the an intense investigation of the association of a rare variant, P11S in GABRB3 and its role in autism. In addition, we have investigated MECP2, a gene which when defective causes Rett syndrome, and potentially regulates gene expression of UBE3A and GABRB3. e have used genetic and biochemical methods to investigate two genes in the UBE3A network, ECT2 and GCH1. Finally, we used genotype data and multiplex ligation probe amplification (MLPA) to determine if copy number variation in the form of deletions and duplications in UBE3A and GABRB3 may play a role in the etiology of autism.
Our findings indicated that a common allele of MECP2 is associated with autism, which was replicated by another group. We show association with UBE3A and its associated genes ECT2 and GCH1 as well as a relationship between UBE3A and GCH1 gene and protein expression, observed in a model system, and validated in our samples, which may provide guidance and support for a role of UBE3A and its action at the synapse and potential contribution to autism. We show modest association of GABRB3 with autism and epilepsy, but find a single coding variant, P11S, maternally overtransmitted and in such cases dramatically increasing autism risk. Finally, we found little evidence for microdeletions or microduplications in UBE3A and GABRB3 to contribute to autism pathology.
The work presented in this thesis expands on earlier findings with regard to the role of GABRB3 and UBE3A in autism and represents an investigation of variants in these and their related genes spanning the spectrum from common variants of modest effect to rare variants of more profound effect. The availability of new technologies to evaluate copy number variation and next generation sequencing will likely uncover a wider role for 15q11-q13 and related loci in autism. The role of more highly penetrant private mutations of this nature is suggested as an avenue for further investigation.
Advisors/Committee Members: Lawrence T. Reiter (committee member), John A. Phillips III (committee member), Chun Li (committee member), James Sutcliffe (committee member), Scott Williams (Committee Chair).
Subjects/Keywords: 15q11-q13; association; autism; GABRB3; UBE3A; ECT2; GCH1; CNV; MECP2
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APA (6th Edition):
Delahanty, R. J. (2010). Towards an understanding of the role of chromosome 15q11-q13 in idiopathic autism. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/10492
Chicago Manual of Style (16th Edition):
Delahanty, Ryan James. “Towards an understanding of the role of chromosome 15q11-q13 in idiopathic autism.” 2010. Doctoral Dissertation, Vanderbilt University. Accessed March 07, 2021.
http://hdl.handle.net/1803/10492.
MLA Handbook (7th Edition):
Delahanty, Ryan James. “Towards an understanding of the role of chromosome 15q11-q13 in idiopathic autism.” 2010. Web. 07 Mar 2021.
Vancouver:
Delahanty RJ. Towards an understanding of the role of chromosome 15q11-q13 in idiopathic autism. [Internet] [Doctoral dissertation]. Vanderbilt University; 2010. [cited 2021 Mar 07].
Available from: http://hdl.handle.net/1803/10492.
Council of Science Editors:
Delahanty RJ. Towards an understanding of the role of chromosome 15q11-q13 in idiopathic autism. [Doctoral Dissertation]. Vanderbilt University; 2010. Available from: http://hdl.handle.net/1803/10492
. 
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