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Genetic Epidemiology

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https://www.readbyqxmd.com/read/28211093/gsskat-rapid-gene-set-analysis-and-multiple-testing-correction-for-rare-variant-association-studies-using-weighted-linear-kernels
#1
Nicholas B Larson, Shannon McDonnell, Lisa Cannon Albright, Craig Teerlink, Janet Stanford, Elaine A Ostrander, William B Isaacs, Jianfeng Xu, Kathleen A Cooney, Ethan Lange, Johanna Schleutker, John D Carpten, Isaac Powell, Joan E Bailey-Wilson, Olivier Cussenot, Geraldine Cancel-Tassin, Graham G Giles, Robert J MacInnis, Christiane Maier, Alice S Whittemore, Chih-Lin Hsieh, Fredrik Wiklund, William J Catolona, William Foulkes, Diptasri Mandal, Rosalind Eeles, Zsofia Kote-Jarai, Michael J Ackerman, Timothy M Olson, Christopher J Klein, Stephen N Thibodeau, Daniel J Schaid
Next-generation sequencing technologies have afforded unprecedented characterization of low-frequency and rare genetic variation. Due to low power for single-variant testing, aggregative methods are commonly used to combine observed rare variation within a single gene. Causal variation may also aggregate across multiple genes within relevant biomolecular pathways. Kernel-machine regression and adaptive testing methods for aggregative rare-variant association testing have been demonstrated to be powerful approaches for pathway-level analysis, although these methods tend to be computationally intensive at high-variant dimensionality and require access to complete data...
February 16, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28198095/genetic-risk-models-influence-of-model-size-on-risk-estimates-and-precision
#2
Ying Shan, Gerard Tromp, Helena Kuivaniemi, Diane T Smelser, Shefali S Verma, Marylyn D Ritchie, James R Elmore, David J Carey, Yvette P Conley, Michael B Gorin, Daniel E Weeks
Disease risk estimation plays an important role in disease prevention. Many studies have found that the ability to predict risk improves as the number of risk single-nucleotide polymorphisms (SNPs) in the risk model increases. However, the width of the confidence interval of the risk estimate is often not considered in the evaluation of the risk model. Here, we explore how the risk and the confidence interval width change as more SNPs are added to the model in the order of decreasing effect size, using both simulated data and real data from studies of abdominal aortic aneurysms and age-related macular degeneration...
February 15, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28191685/gene-based-segregation-method-for-identifying-rare-variants-in-family-based-sequencing-studies
#3
Dandi Qiao, Christoph Lange, Nan M Laird, Sungho Won, Craig P Hersh, Jarrett Morrow, Brian D Hobbs, Sharon M Lutz, Ingo Ruczinski, Terri H Beaty, Edwin K Silverman, Michael H Cho
Whole-exome sequencing using family data has identified rare coding variants in Mendelian diseases or complex diseases with Mendelian subtypes, using filters based on variant novelty, functionality, and segregation with the phenotype within families. However, formal statistical approaches are limited. We propose a gene-based segregation test (GESE) that quantifies the uncertainty of the filtering approach. It is constructed using the probability of segregation events under the null hypothesis of Mendelian transmission...
February 13, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28191669/adaptive-testing-for-multiple-traits-in-a-proportional-odds-model-with-applications-to-detect-snp-brain-network-associations
#4
Junghi Kim, Wei Pan
There has been increasing interest in developing more powerful and flexible statistical tests to detect genetic associations with multiple traits, as arising from neuroimaging genetic studies. Most of existing methods treat a single trait or multiple traits as response while treating an SNP as a predictor coded under an additive inheritance mode. In this paper, we follow an earlier approach in treating an SNP as an ordinal response while treating traits as predictors in a proportional odds model (POM). In this way, it is not only easier to handle mixed types of traits, e...
February 13, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28176359/detecting-association-of-rare-and-common-variants-based-on-cross-validation-prediction-error
#5
Xinlan Yang, Shuaichen Wang, Shuanglin Zhang, Qiuying Sha
Despite the extensive discovery of disease-associated common variants, much of the genetic contribution to complex traits remains unexplained. Rare variants may explain additional disease risk or trait variability. Although sequencing technology provides a supreme opportunity to investigate the roles of rare variants in complex diseases, detection of these variants in sequencing-based association studies presents substantial challenges. In this article, we propose novel statistical tests to test the association between rare and common variants in a genomic region and a complex trait of interest based on cross-validation prediction error (PE)...
February 8, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28111783/bayesian-latent-variable-models-for-hierarchical-clustered-count-outcomes-with-repeated-measures-in-microbiome-studies
#6
Lizhen Xu, Andrew D Paterson, Wei Xu
Motivated by the multivariate nature of microbiome data with hierarchical taxonomic clusters, counts that are often skewed and zero inflated, and repeated measures, we propose a Bayesian latent variable methodology to jointly model multiple operational taxonomic units within a single taxonomic cluster. This novel method can incorporate both negative binomial and zero-inflated negative binomial responses, and can account for serial and familial correlations. We develop a Markov chain Monte Carlo algorithm that is built on a data augmentation scheme using Pólya-Gamma random variables...
January 22, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28090672/a-powerful-statistical-framework-for-generalization-testing-in-gwas-with-application-to-the-hchs-sol
#7
Tamar Sofer, Ruth Heller, Marina Bogomolov, Christy L Avery, Mariaelisa Graff, Kari E North, Alex P Reiner, Timothy A Thornton, Kenneth Rice, Yoav Benjamini, Cathy C Laurie, Kathleen F Kerr
In genome-wide association studies (GWAS), "generalization" is the replication of genotype-phenotype association in a population with different ancestry than the population in which it was first identified. Current practices for declaring generalizations rely on testing associations while controlling the family-wise error rate (FWER) in the discovery study, then separately controlling error measures in the follow-up study. This approach does not guarantee control over the FWER or false discovery rate (FDR) of the generalization null hypotheses...
January 15, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28039885/rare-variant-association-test-with-multiple-phenotypes
#8
Selyeong Lee, Sungho Won, Young Jin Kim, Yongkang Kim, Bong-Jo Kim, Taesung Park
Although genome-wide association studies (GWAS) have now discovered thousands of genetic variants associated with common traits, such variants cannot explain the large degree of "missing heritability," likely due to rare variants. The advent of next generation sequencing technology has allowed rare variant detection and association with common traits, often by investigating specific genomic regions for rare variant effects on a trait. Although multiple correlated phenotypes are often concurrently observed in GWAS, most studies analyze only single phenotypes, which may lessen statistical power...
December 31, 2016: Genetic Epidemiology
https://www.readbyqxmd.com/read/28019042/evidence-for-snp-snp-interaction-identified-through-targeted-sequencing-of-cleft-case-parent-trios
#9
Yanzi Xiao, Margaret A Taub, Ingo Ruczinski, Ferdouse Begum, Jacqueline B Hetmanski, Holger Schwender, Elizabeth J Leslie, Daniel C Koboldt, Jeffrey C Murray, Mary L Marazita, Terri H Beaty
Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is the most common craniofacial birth defect in humans, affecting 1 in 700 live births. This malformation has a complex etiology where multiple genes and several environmental factors influence risk. At least a dozen different genes have been confirmed to be associated with risk of NSCL/P in previous studies. However, all the known genetic risk factors cannot fully explain the observed heritability of NSCL/P, and several authors have suggested gene-gene (G × G) interaction may be important in the etiology of this complex and heterogeneous malformation...
December 26, 2016: Genetic Epidemiology
https://www.readbyqxmd.com/read/28019040/a-small-sample-multivariate-kernel-machine-test-for-microbiome-association-studies
#10
Xiang Zhan, Xingwei Tong, Ni Zhao, Arnab Maity, Michael C Wu, Jun Chen
High-throughput sequencing technologies have enabled large-scale studies of the role of the human microbiome in health conditions and diseases. Microbial community level association test, as a critical step to establish the connection between overall microbiome composition and an outcome of interest, has now been routinely performed in many studies. However, current microbiome association tests all focus on a single outcome. It has become increasingly common for a microbiome study to collect multiple, possibly related, outcomes to maximize the power of discovery...
December 26, 2016: Genetic Epidemiology
https://www.readbyqxmd.com/read/28019039/integration-of-gene-expression-and-methylation-to-unravel-biological-networks-in-glioblastoma-patients
#11
Francesco Gadaleta, Kyrylo Bessonov, Kristel Van Steen
The vast amount of heterogeneous omics data, encompassing a broad range of biomolecular information, requires novel methods of analysis, including those that integrate the available levels of information. In this work, we describe Regression2Net, a computational approach that is able to integrate gene expression and genomic or methylation data in two steps. First, penalized regressions are used to build Expression-Expression (EEnet) and Expression-Genomic or Expression-Methylation (EMnet) networks. Second, network theory is used to highlight important communities of genes...
December 26, 2016: Genetic Epidemiology
https://www.readbyqxmd.com/read/27990689/resetting-the-bar-statistical-significance-in-whole-genome-sequencing-based-association-studies-of-global-populations
#12
Sara L Pulit, Sera A J de With, Paul I W de Bakker
Genome-wide association studies (GWAS) of common disease have been hugely successful in implicating loci that modify disease risk. The bulk of these associations have proven robust and reproducible, in part due to community adoption of statistical criteria for claiming significant genotype-phenotype associations. As the cost of sequencing continues to drop, assembling large samples in global populations is becoming increasingly feasible. Sequencing studies interrogate not only common variants, as was true for genotyping-based GWAS, but variation across the full allele frequency spectrum, yielding many more (independent) statistical tests...
December 18, 2016: Genetic Epidemiology
https://www.readbyqxmd.com/read/27943406/fast-genome-wide-qtl-association-mapping-on-pedigree-and-population-data
#13
Hua Zhou, John Blangero, Thomas D Dyer, Kei-Hang K Chan, Kenneth Lange, Eric M Sobel
Since most analysis software for genome-wide association studies (GWAS) currently exploit only unrelated individuals, there is a need for efficient applications that can handle general pedigree data or mixtures of both population and pedigree data. Even datasets thought to consist of only unrelated individuals may include cryptic relationships that can lead to false positives if not discovered and controlled for. In addition, family designs possess compelling advantages. They are better equipped to detect rare variants, control for population stratification, and facilitate the study of parent-of-origin effects...
December 12, 2016: Genetic Epidemiology
https://www.readbyqxmd.com/read/27917519/leveraging-population-information-in-family-based-rare-variant-association-analyses-of-quantitative-traits
#14
Yu Jiang, Yunqi Ji, Alexander B Sibley, Yi-Ju Li, Andrew S Allen
Confounding due to population substructure is always a concern in genetic association studies. Although methods have been proposed to adjust for population stratification in the context of common variation, it is unclear how well these approaches will work when interrogating rare variation. Family-based association tests can be constructed that are robust to population stratification. For example, when considering a quantitative trait, a linear model can be used that decomposes genetic effects into between- and within-family components and a test of the within-family component is robust to population stratification...
December 5, 2016: Genetic Epidemiology
https://www.readbyqxmd.com/read/28019059/impact-of-genotyping-errors-on-statistical-power-of-association-tests-in-genomic-analyses-a-case-study
#15
Lin Hou, Ning Sun, Shrikant Mane, Fred Sayward, Nallakkandi Rajeevan, Kei-Hoi Cheung, Kelly Cho, Saiju Pyarajan, Mihaela Aslan, Perry Miller, Philip D Harvey, J Michael Gaziano, John Concato, Hongyu Zhao
A key step in genomic studies is to assess high throughput measurements across millions of markers for each participant's DNA, either using microarrays or sequencing techniques. Accurate genotype calling is essential for downstream statistical analysis of genotype-phenotype associations, and next generation sequencing (NGS) has recently become a more common approach in genomic studies. How the accuracy of variant calling in NGS-based studies affects downstream association analysis has not, however, been studied using empirical data in which both microarrays and NGS were available...
February 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/27917522/genome-wide-survey-in-african-americans-demonstrates-potential-epistasis-of-fitness-in-the-human-genome
#16
Heming Wang, Yoonha Choi, Bamidele Tayo, Xuefeng Wang, Nathan Morris, Xiang Zhang, Uli Broeckel, Craig Hanis, Sharon Kardia, Susan Redline, Richard S Cooper, Hua Tang, Xiaofeng Zhu
The role played by epistasis between alleles at unlinked loci in shaping population fitness has been debated for many years and the existing evidence has been mainly accumulated from model organisms. In model organisms, fitness epistasis can be systematically inferred by detecting nonindependence of genotypic values between loci in a population and confirmed through examining the number of offspring produced in two-locus genotype groups. No systematic study has been conducted to detect epistasis of fitness in humans owing to experimental constraints...
February 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/27900789/a-general-approach-to-testing-for-pleiotropy-with-rare-and-common-variants
#17
Sharon M Lutz, Tasha E Fingerlin, John E Hokanson, Christoph Lange
Through genome-wide association studies, numerous genes have been shown to be associated with multiple phenotypes. To determine the overlap of genetic susceptibility of correlated phenotypes, one can apply multivariate regression or dimension reduction techniques, such as principal components analysis, and test for the association with the principal components of the phenotypes rather than the individual phenotypes. However, as these approaches test whether there is a genetic effect for at least one of the phenotypes, a significant test result does not necessarily imply pleiotropy...
February 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/27885705/multiple-linear-combination-mlc-regression-tests-for-common-variants-adapted-to-linkage-disequilibrium-structure
#18
Yun Joo Yoo, Lei Sun, Julia G Poirier, Andrew D Paterson, Shelley B Bull
By jointly analyzing multiple variants within a gene, instead of one at a time, gene-based multiple regression can improve power, robustness, and interpretation in genetic association analysis. We investigate multiple linear combination (MLC) test statistics for analysis of common variants under realistic trait models with linkage disequilibrium (LD) based on HapMap Asian haplotypes. MLC is a directional test that exploits LD structure in a gene to construct clusters of closely correlated variants recoded such that the majority of pairwise correlations are positive...
February 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/27917525/a-comparison-study-of-multivariate-fixed-models-and-gene-association-with-multiple-traits-gamut-for-next-generation-sequencing
#19
Chi-Yang Chiu, Jeesun Jung, Yifan Wang, Daniel E Weeks, Alexander F Wilson, Joan E Bailey-Wilson, Christopher I Amos, James L Mills, Michael Boehnke, Momiao Xiong, Ruzong Fan
In this paper, extensive simulations are performed to compare two statistical methods to analyze multiple correlated quantitative phenotypes: (1) approximate F-distributed tests of multivariate functional linear models (MFLM) and additive models of multivariate analysis of variance (MANOVA), and (2) Gene Association with Multiple Traits (GAMuT) for association testing of high-dimensional genotype data. It is shown that approximate F-distributed tests of MFLM and MANOVA have higher power and are more appropriate for major gene association analysis (i...
January 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/27910131/whole-exome-association-of-rare-deletions-in-multiplex-oral-cleft-families
#20
Jack Fu, Terri H Beaty, Alan F Scott, Jacqueline Hetmanski, Margaret M Parker, Joan E Bailey Wilson, Mary L Marazita, Elisabeth Mangold, Hasan Albacha-Hejazi, Jeffrey C Murray, Alexandre Bureau, Jacob Carey, Stephen Cristiano, Ingo Ruczinski, Robert B Scharpf
By sequencing the exomes of distantly related individuals in multiplex families, rare mutational and structural changes to coding DNA can be characterized and their relationship to disease risk can be assessed. Recently, several rare single nucleotide variants (SNVs) were associated with an increased risk of nonsyndromic oral cleft, highlighting the importance of rare sequence variants in oral clefts and illustrating the strength of family-based study designs. However, the extent to which rare deletions in coding regions of the genome occur and contribute to risk of nonsyndromic clefts is not well understood...
January 2017: Genetic Epidemiology
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