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Articles 1 - 12 of 12
Full-Text Articles in Life Sciences
The Detection Of Putative Recessive Lethal Haplotypes In Irish Sheep Populations, Rory Mcauley
The Detection Of Putative Recessive Lethal Haplotypes In Irish Sheep Populations, Rory Mcauley
ORBioM (Open Research BioSciences Meeting)
In livestock populations, recessive lethal alleles are a known contributor to poor reproductive performance due to embryonic death in homozygous individuals. Despite their lethal effect in the recessive form, these alleles may be maintained at high frequencies among carrier animals because of their positive pleiotropic effects on economically important traits. Although several such recessive alleles have been identified in cattle and pig populations, limited studies have been completed in sheep, and none within Irish sheep populations. Genotype data for 69,034 animals from five major Irish sheep breeds genotyped on a variety of panels was available for this study. Only animals …
Thinking Computationally About Forensics: Anthropological Perspectives On Advancements In Technologies, Data, And Algorithms, Bridget F.B. Algee-Hewitt, Jieun Kim, Cris E. Hughes
Thinking Computationally About Forensics: Anthropological Perspectives On Advancements In Technologies, Data, And Algorithms, Bridget F.B. Algee-Hewitt, Jieun Kim, Cris E. Hughes
Human Biology Open Access Pre-Prints
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A Multistep Approach To Single Nucleotide Polymorphism–Set Analysis: An Evaluation Of Power And Type I Error Of Gene-Based Tests Of Association After Pathway-Based Association Tests, Alessandra Valcarcel, Kelsey Griinde, Kaitlyn Cook, Alden Green, Nathan L. Tintle
A Multistep Approach To Single Nucleotide Polymorphism–Set Analysis: An Evaluation Of Power And Type I Error Of Gene-Based Tests Of Association After Pathway-Based Association Tests, Alessandra Valcarcel, Kelsey Griinde, Kaitlyn Cook, Alden Green, Nathan L. Tintle
Faculty Work Comprehensive List
The aggregation of functionally associated variants given a priori biological information can aid in the discovery of rare variants associated with complex diseases. Many methods exist that aggregate rare variants into a set and compute a single p value summarizing association between the set of rare variants and a phenotype of interest. These methods are often called gene-based, rare variant tests of association because the variants in the set are often all contained within the same gene. A reasonable extension of these approaches involves aggregating variants across an even larger set of variants (eg, all variants contained in genes within …
General Approaches For Combining Multiple Rare Variant Associate Tests Provide Improved Power Across A Wider Range Of Genetic Architecture, Nathan L. Tintle, Brian Greco, Allison Hainline, Keli Liu, Jaron Arbet, Alejandra Benitez, Kelsey Grinde
General Approaches For Combining Multiple Rare Variant Associate Tests Provide Improved Power Across A Wider Range Of Genetic Architecture, Nathan L. Tintle, Brian Greco, Allison Hainline, Keli Liu, Jaron Arbet, Alejandra Benitez, Kelsey Grinde
Faculty Work Comprehensive List
In the wake of the widespread availability of genome sequencing data made possible by way of nextgeneration technologies, a flood of gene‐based rare variant tests have been proposed. Most methods claim superior power against particular genetic architectures. However, an important practical issue remains for the applied researcher—namely, which test should be used for a particular association study which may consider multiple genes and/or multiple phenotypes. Recently, tests have been proposed which combine individual tests to minimize power loss while improving the robustness to a wide range of genetic architectures. In our analysis, we propose an expansion of these approaches, by …
Evaluating The Concordance Between Sequencing, Imputation And Microarray Genotype Calls In The Gaw18 Data, Ally Rogers, Andrew Beck, Nathan L. Tintle
Evaluating The Concordance Between Sequencing, Imputation And Microarray Genotype Calls In The Gaw18 Data, Ally Rogers, Andrew Beck, Nathan L. Tintle
Faculty Work Comprehensive List
Genotype errors are well known to increase type I errors and/or decrease power in related tests of genotypephenotype association, depending on whether the genotype error mechanism is associated with the phenotype. These relationships hold for both single and multimarker tests of genotype-phenotype association. To assess the potential for genotype errors in Genetic Analysis Workshop 18 (GAW18) data, where no gold standard genotype calls are available, we explored concordance rates between sequencing, imputation, and microarray genotype calls. Our analysis shows that missing data rates for sequenced individuals are high and that there is a modest amount of called genotype discordance between …
Genetic Analysis Workshop 18: Methods And Strategies For Analyzing Human Sequence And Phenotype Data In Members Of Extended Pedigrees, Heike Bickeboller, Julia N. Bailey, Joseph Beyene, Rita M. Cantor, Heather J. Cordell, Robert C. Culverhouse, Corinne D. Engelman, David W. Fardo, Saurabh Ghosh, Inke R. Konig, Justo Lorenzo Bermejo, Phillip E. Melton, Stephanie A. Santorico, Glen A. Satten, Lei Sun, Nathan L. Tintle, Andreas Ziegler, Jean W. Maccluer, Laura Almasy
Genetic Analysis Workshop 18: Methods And Strategies For Analyzing Human Sequence And Phenotype Data In Members Of Extended Pedigrees, Heike Bickeboller, Julia N. Bailey, Joseph Beyene, Rita M. Cantor, Heather J. Cordell, Robert C. Culverhouse, Corinne D. Engelman, David W. Fardo, Saurabh Ghosh, Inke R. Konig, Justo Lorenzo Bermejo, Phillip E. Melton, Stephanie A. Santorico, Glen A. Satten, Lei Sun, Nathan L. Tintle, Andreas Ziegler, Jean W. Maccluer, Laura Almasy
Faculty Work Comprehensive List
Genetic Analysis Workshop 18 provided a platform for developing and evaluating statistical methods to analyze whole-genome sequence data from a pedigree-based sample. In this article we present an overview of the data sets and the contributions that analyzed these data. The family data, donated by the Type 2 Diabetes Genetic Exploration by Next-Generation Sequencing in Ethnic Samples Consortium, included sequence-level genotypes based on sequencing and imputation, genome-wide association genotypes from prior genotyping arrays, and phenotypes from longitudinal assessments. The contributions from individual research groups were extensively discussed before, during, and after the workshop in theme-based discussion groups before being submitted …
Multiplexing With Three-Primer Pcr For Rapid And Economical Microsatellite Validation, Salla Vartia, Patrick C. Collins, Thomas F. Cross, Richard D. Fitzgerald, David T. Gauthier, Philip Mcginnity, Luca Mirimin, Jens Carlsson
Multiplexing With Three-Primer Pcr For Rapid And Economical Microsatellite Validation, Salla Vartia, Patrick C. Collins, Thomas F. Cross, Richard D. Fitzgerald, David T. Gauthier, Philip Mcginnity, Luca Mirimin, Jens Carlsson
Biological Sciences Faculty Publications
The next generation sequencing revolution has enabled rapid discovery of genetic markers, however, development of fully functioning new markers still requires a long and costly process of marker validation. This study reports a rapid and economical approach for the validation and deployment of polymorphic microsatellite markers obtained from a 454 pyrosequencing library of Atlantic cod, Gadus morhua, Linnaeus 1758. Primers were designed from raw reads to amplify specific amplicon size ranges, allowing effective PCR multiplexing. Multiplexing was combined with a three-primer PCR approach using four universal tails to label amplicons with separate fluorochromes. A total of 192 primer pairs …
Genome-Wide Expression Analysis In Down Syndrome: Insight Into Immunodeficiency, Chong Li, Lei Jin, Yun Bai, Qimin Chen, Lijun Fu, Minjun Yang, Huasheng Xiao, Guoping Zhao, Shengyue Wang
Genome-Wide Expression Analysis In Down Syndrome: Insight Into Immunodeficiency, Chong Li, Lei Jin, Yun Bai, Qimin Chen, Lijun Fu, Minjun Yang, Huasheng Xiao, Guoping Zhao, Shengyue Wang
PCOM Scholarly Papers
Down syndrome (DS) is caused by triplication of Human chromosome 21 (Hsa21) and associated with an array of deleterious phenotypes, including mental retardation, heart defects and immunodeficiency. Genome-wide expression patterns of uncultured peripheral blood cells are useful to understanding of DS-associated immune dysfunction. We used a Human Exon microarray to characterize gene expression in uncultured peripheral blood cells derived from DS individuals and age-matched controls from two age groups: neonate (N) and child (C). A total of 174 transcript clusters (gene-level) with eight located on Hsa21 in N group and 383 transcript clusters including 56 on Hsa21 in C group …
Identifying Rare Variants From Exome Scans: The Gaw17 Experience, Saurabh Ghosh, Heike Bickeboller, Julia Bailey, Joan E. Bailey-Wilson, Rita Cantor, Robert Culverhouse, Warwick Daw, Anita L. Destefano, Corinne D. Engelman, Anthony Hinrichs, Jeanine Houwing-Duistermaat, Inke R. Konig, Jack Kent, Nan Laird, Nathan Pankratz, Andrew Paterson, Elizabeth Pugh, Brian Suarez, Yan Sun, Alun Thomas, Nathan L. Tintle, Xiaofeng Zhu, Andreas Ziegler, Jean W. Maccluer, Laura Almasy
Identifying Rare Variants From Exome Scans: The Gaw17 Experience, Saurabh Ghosh, Heike Bickeboller, Julia Bailey, Joan E. Bailey-Wilson, Rita Cantor, Robert Culverhouse, Warwick Daw, Anita L. Destefano, Corinne D. Engelman, Anthony Hinrichs, Jeanine Houwing-Duistermaat, Inke R. Konig, Jack Kent, Nan Laird, Nathan Pankratz, Andrew Paterson, Elizabeth Pugh, Brian Suarez, Yan Sun, Alun Thomas, Nathan L. Tintle, Xiaofeng Zhu, Andreas Ziegler, Jean W. Maccluer, Laura Almasy
Faculty Work Comprehensive List
Genetic Analysis Workshop 17 (GAW17) provided a platform for evaluating existing statistical genetic methods and for developing novel methods to analyze rare variants that modulate complex traits. In this article, we present an overview of the 1000 Genomes Project exome data and simulated phenotype data that were distributed to GAW17 participants for analyses, the different issues addressed by the participants, and the process of preparation of manuscripts resulting from the discussions during the workshop
Capturing Changes In Gene Expression Dynamics By Gene Set Differential Coordination Analysis, Tianwei Yu, Yun Bai
Capturing Changes In Gene Expression Dynamics By Gene Set Differential Coordination Analysis, Tianwei Yu, Yun Bai
PCOM Scholarly Papers
Analyzing gene expression data at the gene set level greatly improves feature extraction and data interpretation. Currently most efforts in gene set analysis are focused on differential expression analysis - finding gene sets whose genes show first-order relationship with the clinical outcome. However the regulation of the biological system is complex, and much of the change in gene expression dynamics do not manifest in the form of differential expression. At the gene set level, capturing the change in expression dynamics is difficult due to the complexity and heterogeneity of the gene sets. Here we report a systematic approach to detect …
Genomic Foundations Of Carbon Fixation In Bacteria Living In Hot Springs, Rachel K. Skinner, Brian P. Hedlund, Jeremy A. Dodsworth
Genomic Foundations Of Carbon Fixation In Bacteria Living In Hot Springs, Rachel K. Skinner, Brian P. Hedlund, Jeremy A. Dodsworth
Undergraduate Research Opportunities Program (UROP)
Photosynthesis does not occur above 73°C, so organisms living above this temperature must obtain useable carbon by some other mechanism. It is generally assumed that carbon is fixed by thermophiles through the process of chemolithoautotrophy; however, primary production has never been demonstrated to occur in hot springs >73°C. We have shown that two organisms, Thermocrinis and Pyrobaculum, make up more than 90% of the cells in an 80°C Great Basin hot spring, Great Boiling Spring. We hypothesize that these organisms fix carbon in the hot spring via the reverse tricarboxylic acid (rTCA) cycle. To test this hypothesis we will: i) …
Genetic Analysis Of A Novel Pathway For D-Xylose Metabolism In Caulobacter Crescentus, Craig Stephens, Beat Christen, Thomas Fuchs, Vidyodhaya Sundaram, Kelly Watanabe, Urs Jenal
Genetic Analysis Of A Novel Pathway For D-Xylose Metabolism In Caulobacter Crescentus, Craig Stephens, Beat Christen, Thomas Fuchs, Vidyodhaya Sundaram, Kelly Watanabe, Urs Jenal
Biology
Genetic data suggest that the oligotrophic freshwater bacterium Caulobacter crescentus metabolizes D-xylose through a pathway yielding -ketoglutarate, comparable to the recently described L-arabinose degradation pathway of Azospirillum brasilense. Enzymes of the C. crescentus pathway, including an NAD -dependent xylose dehydrogenase, are encoded in the xylose-inducible xylXABCD operon (CC0823-CC0819).