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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…
(more)
▼ 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 08, 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. 08 Mar 2021.
Vancouver:
Davis MF. Parkinson Disease Loci in the Mid-Western Amish. [Internet] [Thesis]. Vanderbilt University; 2013. [cited 2021 Mar 08].
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.
Moore, Carrie Colleen Buchanan.
A biologically informed method for detecting associations with rare variants.
Degree: PhD, Human Genetics, 2013, Vanderbilt University
URL: http://hdl.handle.net/1803/14835
► Many recent studies have identified rare variants that contribute to common, complex disease. It is believed that rare variants likely have a larger effect size…
(more)
▼ Many recent studies have identified rare variants that contribute to common, complex disease. It is believed that rare variants likely have a larger effect size (compared to GWAS findings) and can act alone, in concert with other rare variants, or together with common variants. Multiple rare variants can potentially account for a portion of missing heritability in a given trait; therefore, binning or burden testing, may better account for genetic heterogeneity. BioBin, an innovative collapsing method developed in the
Ritchie lab, utilizes a flexible repository of data assembled from multiple public databases.
The novelty of BioBin lies in access to comprehensive knowledge-guided multi-level binning. BioBin can apply multiple levels of burden testing, including: functional regions, evolutionary conserved regions, genes, and/or pathways. BioBin does not include a specific statistical association test, since the application of statistical testing is dependent on data type and analysis in question. Therefore, the user has the flexibility to apply tests appropriately without constraint.
BioBin has been tested in the context of extensive simulation studies, compared with multiple published statistical methods, and applied to the NHLBI GO Exome Sequencing Project for Cystic Fibrosis. BioBin is a very useful and flexible tool to analyze sequence data and can uncover novel associations with complex disease.
Advisors/Committee Members: Tricia Thornton-Wells (committee member), Dan Roden (committee member), William Bush (committee member), Marylyn Ritchie (committee member), Bingshan Li (Committee Chair).
Subjects/Keywords: collapsing methods; 1000 Genomes Project data; next-generation sequencing; genomics; rare variants
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APA (6th Edition):
Moore, C. C. B. (2013). A biologically informed method for detecting associations with rare variants. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/14835
Chicago Manual of Style (16th Edition):
Moore, Carrie Colleen Buchanan. “A biologically informed method for detecting associations with rare variants.” 2013. Doctoral Dissertation, Vanderbilt University. Accessed March 08, 2021.
http://hdl.handle.net/1803/14835.
MLA Handbook (7th Edition):
Moore, Carrie Colleen Buchanan. “A biologically informed method for detecting associations with rare variants.” 2013. Web. 08 Mar 2021.
Vancouver:
Moore CCB. A biologically informed method for detecting associations with rare variants. [Internet] [Doctoral dissertation]. Vanderbilt University; 2013. [cited 2021 Mar 08].
Available from: http://hdl.handle.net/1803/14835.
Council of Science Editors:
Moore CCB. A biologically informed method for detecting associations with rare variants. [Doctoral Dissertation]. Vanderbilt University; 2013. Available from: http://hdl.handle.net/1803/14835
Vanderbilt University
3.
Dumitrescu, Logan Caneel.
Identificatiion and Characterization of Genetic Variants Associated with Lipid and Lipoprotein Levels.
Degree: PhD, Human Genetics, 2011, Vanderbilt University
URL: http://hdl.handle.net/1803/11282
► Low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), and triglyceride (TG) levels are well known independent risk factors for cardiovascular disease. Other lipoproteins, such as…
(more)
▼ Low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), and triglyceride (TG) levels are well known independent risk factors for cardiovascular disease. Other lipoproteins, such as Lp(a), are also emerging, independent risk factors as increasing epidemiologic evidence suggests. Lipid-associated single-nucleotide polymorphisms (SNPs) are being discovered in genome-wide association studies (GWAS) in samples of European descent, but little data exist in other populations. Therefore, there is a strong need to characterize the effect sizes and allele frequencies of these GWAS-identified variants in a diverse, population-based cohort. Also, despite the ever-growing number of loci detected by GWAS, the proportion of trait variation explained is collectively small. To investigate this missing heritability, it is important to continue to identify novel variants that are associated with lipid levels and to explore gene-environment interactions, which may also contribute to trait variation.
The primary objective of this work was to identify and characterize common genetic variants that explain a proportion of the inter-individual variability in lipids levels, including LDL-C, HDL-C, TG, and Lp(a) levels. To achieve this goal, I selected a set of SNPs associated with lipid levels from the literature and demonstrated that the majority of associations replicate and generalize in a diverse, independent cohort. An additional GWAS of children was used to discover a novel variants associated with LDL-C, HDL-C, and TG. I also performed a candidate gene study and determined that common variants in LPA were associated with Lp(a) levels. Lastly, I identified several environmental modifiers of replicated variants associated with LDL-C, HDL-C, and TG.
Advisors/Committee Members: Dana Crawford (committee member), Jonathan Haines (committee member), Mary Relling (committee member), Jay Fowke (committee member), Marylyn Ritchie (Committee Chair).
Subjects/Keywords: genetics; epidemiology; gwas; candidate gene study; lipids; lipoproteins; cardiovascular disease
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APA (6th Edition):
Dumitrescu, L. C. (2011). Identificatiion and Characterization of Genetic Variants Associated with Lipid and Lipoprotein Levels. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/11282
Chicago Manual of Style (16th Edition):
Dumitrescu, Logan Caneel. “Identificatiion and Characterization of Genetic Variants Associated with Lipid and Lipoprotein Levels.” 2011. Doctoral Dissertation, Vanderbilt University. Accessed March 08, 2021.
http://hdl.handle.net/1803/11282.
MLA Handbook (7th Edition):
Dumitrescu, Logan Caneel. “Identificatiion and Characterization of Genetic Variants Associated with Lipid and Lipoprotein Levels.” 2011. Web. 08 Mar 2021.
Vancouver:
Dumitrescu LC. Identificatiion and Characterization of Genetic Variants Associated with Lipid and Lipoprotein Levels. [Internet] [Doctoral dissertation]. Vanderbilt University; 2011. [cited 2021 Mar 08].
Available from: http://hdl.handle.net/1803/11282.
Council of Science Editors:
Dumitrescu LC. Identificatiion and Characterization of Genetic Variants Associated with Lipid and Lipoprotein Levels. [Doctoral Dissertation]. Vanderbilt University; 2011. Available from: http://hdl.handle.net/1803/11282
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 08, 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. 08 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 08].
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.
Zuvich, Rebecca Lynn.
Identification of Additional Independent Loci in the Major Histocompatibility Complex in Multiple Sclerosis Susceptibility.
Degree: MS, Interdisciplinary Studies: Applied Statistics, 2010, Vanderbilt University
URL: http://hdl.handle.net/1803/13435
► Multiple sclerosis (MS) is characterized as an autoimmune neurodegenerative disease. The disease manifests as demyelination or degradation of the myelin sheath in the central nervous…
(more)
▼ Multiple sclerosis (MS) is characterized as an autoimmune neurodegenerative disease. The disease manifests as demyelination or degradation of the myelin sheath in the central nervous system. The Major Histocompatibility Complex (MHC) was associated with MS in the mid-1970’s; the association was later refined to the HLA-DRB1*1501-DQB*0602 haplotype. The MHC region is riddled with complicating factors including high gene content, extreme levels of polymorphism, and a dense pattern of linkage disequilibrium (LD). These characteristics make this region difficult for differentiating whether a single allele or an entire haplotype contributes to disease association. Despite these challenges it is clear that the MHC region harbors MS susceptibility loci in addition to the HLA-DRB1*1501 region. Using the strong LD in this region we can test a model that predicts residual odds ratios (ORs) for a marker in LD with a disease allele such as HLA-DRB1*1501. Comparing the correlation between the observed OR and the calculated OR for multiple SNPs in the MHC region, we hypothesize those SNPs that appear as outliers are suggestive of additional effects independent from the HLA-DRB1*1501 region. We examined ~2,300 SNPs in 1,479 cases and 1,482 controls in the 28 Mb to 36 Mb region on chromosome 6 containing the MHC. The ORs for the SNPs were grouped based on the amount of LD with the HLA-DRB1 surrogate SNP (rs3135388). We identified nine outlying SNPs, which had observed ORs much larger than the calculated OR. These nine SNPs are in six different genes that suggest susceptibility to MS independent of HLA-DRB1*1501.
Advisors/Committee Members: Marylyn Ritchie (committee member), Chun Li (committee member), Jonathan Haines (committee member).
Subjects/Keywords: multiple sclerosis; statistics
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APA (6th Edition):
Zuvich, R. L. (2010). Identification of Additional Independent Loci in the Major Histocompatibility Complex in Multiple Sclerosis Susceptibility. (Thesis). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/13435
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):
Zuvich, Rebecca Lynn. “Identification of Additional Independent Loci in the Major Histocompatibility Complex in Multiple Sclerosis Susceptibility.” 2010. Thesis, Vanderbilt University. Accessed March 08, 2021.
http://hdl.handle.net/1803/13435.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Zuvich, Rebecca Lynn. “Identification of Additional Independent Loci in the Major Histocompatibility Complex in Multiple Sclerosis Susceptibility.” 2010. Web. 08 Mar 2021.
Vancouver:
Zuvich RL. Identification of Additional Independent Loci in the Major Histocompatibility Complex in Multiple Sclerosis Susceptibility. [Internet] [Thesis]. Vanderbilt University; 2010. [cited 2021 Mar 08].
Available from: http://hdl.handle.net/1803/13435.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Zuvich RL. Identification of Additional Independent Loci in the Major Histocompatibility Complex in Multiple Sclerosis Susceptibility. [Thesis]. Vanderbilt University; 2010. Available from: http://hdl.handle.net/1803/13435
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Vanderbilt University
6.
Zuvich, Rebecca Lynn.
Pathway Approach to Decoding Multiple Sclerosis.
Degree: PhD, Human Genetics, 2009, Vanderbilt University
URL: http://hdl.handle.net/1803/15066
► Multiple sclerosis (MS) is characterized as a neurodegenerative autoimmune disease. This clinically complex disease has provided great challenges for geneticists over the years. With the…
(more)
▼ Multiple sclerosis (MS) is characterized as a neurodegenerative autoimmune disease. This clinically complex disease has provided great challenges for geneticists over the years. With the advent of genome-wide association studies (GWAS), the strong genetic component associated with MS is finally beginning to be characterized. One of the first discoveries to emerge in this new era was the association with rs6897932 in the interleukin-7 receptor alpha chain (IL7RA) gene. The goal of the work presented in this dissertation was to identify additional genes that increase one’s susceptibility to MS. Our studies involved examining genes in the extended biological pathway related to IL7RA to identify novel associations. Through this approach, we identified two additional novel gene regions that are likely associated with MS. These results help to further delineate the genetic architecture of MS and validate our pathway approach as an effective method to identify novel associations associated in a complex disease.
We began our investigation with a discovery screen containing SNPs from 73 genes with putative functional relationships to IL7RA and subsequently genotyped 7,865 single nucleotide polymorphism (SNPs) in and around these genes. Two of the gene regions examined, IL7 and SOCS1, had significantly associated SNPs that further replicated in an independent case-control dataset with joint p-values reaching 8.29x10-5 and 3.48x10-7, respectively, exceeding the threshold for experiment-wide significance. Our results also implicated two additional novel gene regions that are likely to be associated with MS: PRKCE with p-values reaching 3.47x10-4 and BCL2 with p-values reaching 4.32x10-4. The TYK2 gene, which emerged in our analysis, also has recently been associated with MS in other studies.
The work presented in this dissertation confirmed two novel regions and implicated several others that need further examination as MS disease loci. Thus, using the pathway approach in conjunction with large datasets and dense genotyping, the etiology of MS is finally starting to be dissected. By building on the knowledge of these gene effects, these studies will hopefully result in further understanding of the pathogenesis of MS.
Advisors/Committee Members: Subramanian Sriram (committee member), Dana Crawford (committee member), Michael Rock (committee member), Jonathan Haines (committee member), Marylyn Ritchie (Committee Chair).
Subjects/Keywords: autoimmune; susceptibility
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APA ·
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APA (6th Edition):
Zuvich, R. L. (2009). Pathway Approach to Decoding Multiple Sclerosis. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/15066
Chicago Manual of Style (16th Edition):
Zuvich, Rebecca Lynn. “Pathway Approach to Decoding Multiple Sclerosis.” 2009. Doctoral Dissertation, Vanderbilt University. Accessed March 08, 2021.
http://hdl.handle.net/1803/15066.
MLA Handbook (7th Edition):
Zuvich, Rebecca Lynn. “Pathway Approach to Decoding Multiple Sclerosis.” 2009. Web. 08 Mar 2021.
Vancouver:
Zuvich RL. Pathway Approach to Decoding Multiple Sclerosis. [Internet] [Doctoral dissertation]. Vanderbilt University; 2009. [cited 2021 Mar 08].
Available from: http://hdl.handle.net/1803/15066.
Council of Science Editors:
Zuvich RL. Pathway Approach to Decoding Multiple Sclerosis. [Doctoral Dissertation]. Vanderbilt University; 2009. Available from: http://hdl.handle.net/1803/15066
Vanderbilt University
7.
Edwards, Todd L.
An Extension to and Application of the Multifactor Dimensionality Reduction Pedigree Disequilibrium Test.
Degree: PhD, Human Genetics, 2008, Vanderbilt University
URL: http://hdl.handle.net/1803/10658
► As the field of genetics explores beyond mapping single-site disease susceptibility loci, epistasis between genes is being considered in disease models. These hypotheses present new…
(more)
▼ As the field of genetics explores beyond mapping single-site disease susceptibility loci, epistasis between genes is being considered in disease models. These hypotheses present new problems for investigators as they search through ever more complex data structures. The dimensionality and size of a search space, the types and strengths of disease associations in data, and the quality of inference allowed given a result are all challenges when testing for putative epistatic disease models.
Method development to analyze family data for epistatic interactions is in a preliminary stage. The multifactor dimensionality reduction pedigree disequilibrium test (MDR-PDT) is one technique for assessing epistatic models in family data. The objective of this proposal is to refine, test, and apply this method to real data.
MDR-PDT is a method that implements the genoPDT statistic within the framework of the MDR algorithm. We hypothesize that at the conclusion of my aims, the MDR-PDT algorithm’s utility and power will be improved. In the following dissertation we developed a cross validation algorithm for pedigree data, and an omnibus model selection method. We also implemented an extension to MDR-PDT that includes a likelihood ratio test for the statistical significance of an interaction found by the MDR-PDT search using logistic regression. Finally, MDR-PDT was applied to Alzheimer’s candidate gene datasets and revealed a multilocus model involving several genes that are functional candidates.
Advisors/Committee Members: Dana Crawford (committee member), Eden Martin (committee member), Charles Matthews (committee member), Marylyn Ritchie (committee member), Jonathan Haines (Committee Chair).
Subjects/Keywords: Association; Epistasis; Interaction; Genetics; Epidemiology
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APA ·
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MLA ·
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APA (6th Edition):
Edwards, T. L. (2008). An Extension to and Application of the Multifactor Dimensionality Reduction Pedigree Disequilibrium Test. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/10658
Chicago Manual of Style (16th Edition):
Edwards, Todd L. “An Extension to and Application of the Multifactor Dimensionality Reduction Pedigree Disequilibrium Test.” 2008. Doctoral Dissertation, Vanderbilt University. Accessed March 08, 2021.
http://hdl.handle.net/1803/10658.
MLA Handbook (7th Edition):
Edwards, Todd L. “An Extension to and Application of the Multifactor Dimensionality Reduction Pedigree Disequilibrium Test.” 2008. Web. 08 Mar 2021.
Vancouver:
Edwards TL. An Extension to and Application of the Multifactor Dimensionality Reduction Pedigree Disequilibrium Test. [Internet] [Doctoral dissertation]. Vanderbilt University; 2008. [cited 2021 Mar 08].
Available from: http://hdl.handle.net/1803/10658.
Council of Science Editors:
Edwards TL. An Extension to and Application of the Multifactor Dimensionality Reduction Pedigree Disequilibrium Test. [Doctoral Dissertation]. Vanderbilt University; 2008. Available from: http://hdl.handle.net/1803/10658
. 
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