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  1. Proceedings

    Incorporation of protein binding effects into likelihood ratio test for exome sequencing data

    Statistical association studies are an important tool in detecting novel disease genes. However, for sequencing data, association studies confront the challenge of low power because of relatively small data sa...

    Dongni Zhang, Hongzhu Cui, Dmitry Korkin and Zheyang Wu

    BMC Proceedings 2016 10(Suppl 7):18

    Published on: 18 October 2016

    This article is part of a Supplement: Volume 10 Supplement 7

  2. Proceedings

    Homozygosity disequilibrium and its gene regulation

    Homozygosity disequilibrium (HD) describes a nonrandom pattern of sizable runs of homozygosity (ROH) that deviated from a random distribution of homozygotes and heterozygotes in the genome. In this study, we d...

    Hsin-Chou Yang and Yu-Ting Lin

    BMC Proceedings 2016 10(Suppl 7):27

    Published on: 18 October 2016

    This article is part of a Supplement: Volume 10 Supplement 7

  3. Proceedings

    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

    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 vari...

    Alessandra Valcarcel, Kelsey Grinde, Kaitlyn Cook, Alden Green and Nathan Tintle

    BMC Proceedings 2016 10(Suppl 7):16

    Published on: 18 October 2016

    This article is part of a Supplement: Volume 10 Supplement 7

  4. Proceedings

    Testing rare variants for hypertension using family-based tests with different weighting schemes

    Next-generation sequencing technology makes directly testing rare variants possible. However, existing statistical methods to detect common variants may not be optimal for testing rare variants because of alle...

    Xuexia Wang, Xingwang Zhao and Jin Zhou

    BMC Proceedings 2016 10(Suppl 7):61

    Published on: 18 October 2016

    This article is part of a Supplement: Volume 10 Supplement 7

  5. Proceedings

    Gene coexpression network analysis for family studies based on a meta-analytic approach

    For a better understanding of the biological mechanisms involved in complex traits or diseases, networks are often useful tools in genetic studies: coexpression networks based on pairwise correlations between ...

    Renaud Tissier, Hae-Won Uh, Erik van den Akker, Brunilda Balliu, Spyridoula Tsonaka and Jeanine Houwing-Duistermaat

    BMC Proceedings 2016 10(Suppl 7):35

    Published on: 18 October 2016

    This article is part of a Supplement: Volume 10 Supplement 7

  6. Proceedings

    Assessing transmission ratio distortion in extended families: a comparison of analysis methods

    A statistical departure from Mendel’s law of segregation is known as transmission ratio distortion. Although well documented in many other organisms, the extent of transmission ratio distortion and its influen...

    Sahir R. Bhatnagar, Celia M. T. Greenwood and Aurélie Labbe

    BMC Proceedings 2016 10(Suppl 7):12

    Published on: 18 October 2016

    This article is part of a Supplement: Volume 10 Supplement 7

  7. Proceedings

    Joint analysis of multiple blood pressure phenotypes in GAW19 data by using a multivariate rare-variant association test

    Large-scale sequencing studies often measure many related phenotypes in addition to the genetic variants. Joint analysis of multiple phenotypes in genetic association studies may increase power to detect disea...

    Jianping Sun, Sahir R. Bhatnagar, Karim Oualkacha, Antonio Ciampi and Celia M. T. Greenwood

    BMC Proceedings 2016 10(Suppl 7):14

    Published on: 18 October 2016

    This article is part of a Supplement: Volume 10 Supplement 7

  8. Proceedings

    Factors associated with heterogeneity in microarray gene expression in peripheral blood mononuclear cells from large pedigrees

    Genome-wide microarray expression is a rich source of functional genomic data. We examined evidence for differences in expression from peripheral blood mononuclear cells between individuals, examined some of f...

    Michael Gallaugher, Angelo J. Canty and Andrew D. Paterson

    BMC Proceedings 2016 10(Suppl 7):58

    Published on: 18 October 2016

    This article is part of a Supplement: Volume 10 Supplement 7

  9. Proceedings

    A novel statistical method for rare-variant association studies in general pedigrees

    Both population-based and family-based designs are commonly used in genetic association studies to identify rare variants that underlie complex diseases. For any type of study design, the statistical power wil...

    Huanhuan Zhu, Zhenchuan Wang, Xuexia Wang and Qiuying Sha

    BMC Proceedings 2016 10(Suppl 7):22

    Published on: 18 October 2016

    This article is part of a Supplement: Volume 10 Supplement 7

  10. Proceedings

    Using gene expression data to identify causal pathways between genotype and phenotype in a complex disease: application to Genetic Analysis Workshop 19

    We explore causal relationships between genotype, gene expression and phenotype in the Genetic Analysis Workshop 19 data. We compare the use of structural equation modeling and a Bayesian unified framework app...

    Holly F. Ainsworth and Heather J. Cordell

    BMC Proceedings 2016 10(Suppl 7):49

    Published on: 18 October 2016

    This article is part of a Supplement: Volume 10 Supplement 7

  11. Proceedings

    Network-guided interaction mining for the blood pressure phenotype of unrelated individuals in genetic analysis workshop 19

    Interactions between genes are an important part of the genetic architecture of complex diseases. In this paper, we use literature-guided individual genes known to be associated with type 2 diabetes (referred ...

    Adeline Lo, Michael Agne, Jonathan Auerbach, Rachel Fan, Shaw-Hwa Lo, Pei Wang and Tian Zheng

    BMC Proceedings 2016 10(Suppl 7):13

    Published on: 18 October 2016

    This article is part of a Supplement: Volume 10 Supplement 7

  12. Proceedings

    Imputing rare variants in families using a two-stage approach

    Recent focus on studying rare variants makes imputation accuracy of rare variants an important issue. Many approaches have been proposed to increase imputation accuracy among rare variants, from reference pane...

    Samantha Lent, Xuan Deng, L. Adrienne Cupples, Kathryn L. Lunetta, CT Liu and Yanhua Zhou

    BMC Proceedings 2016 10(Suppl 7):48

    Published on: 18 October 2016

    This article is part of a Supplement: Volume 10 Supplement 7

  13. Proceedings

    Causal effect estimation in sequencing studies: a Bayesian method to account for confounder adjustment uncertainty

    Estimating the causal effect of a single nucleotide variant (SNV) on clinical phenotypes is of interest in many genetic studies. The effect estimation may be confounded by other SNVs as a result of linkage dis...

    Chi Wang, Jinpeng Liu and David W. Fardo

    BMC Proceedings 2016 10(Suppl 7):38

    Published on: 18 October 2016

    This article is part of a Supplement: Volume 10 Supplement 7

  14. Proceedings

    Genetic association analysis based on a joint model of gene expression and blood pressure

    Recent work on genetic association studies suggests that much of the heritable variation in complex traits is unexplained, which indicates a need for using more biologically meaningful modeling approaches and ...

    Stefan Konigorski, Yildiz E. Yilmaz and Tobias Pischon

    BMC Proceedings 2016 10(Suppl 7):57

    Published on: 18 October 2016

    This article is part of a Supplement: Volume 10 Supplement 7

  15. Proceedings

    The impact of genetic structure on sequencing analysis

    Genome-wide association studies have made substantial progress in identifying common variants associated with human diseases. Despite such success, a large portion of heritability remains unexplained. Evolutio...

    Sneha Jadhav, Olga A. Vsevolozhskaya, Xiaoran Tong and Qing Lu

    BMC Proceedings 2016 10(Suppl 7):60

    Published on: 18 October 2016

    This article is part of a Supplement: Volume 10 Supplement 7

  16. Proceedings

    On combining family- and population-based sequencing data

    Several statistical group-based approaches have been proposed to detect effects of variation within a gene for each of the population- and family-based designs. However, unified tests to combine gene-phenotype...

    Yuriko Katsumata and David W. Fardo

    BMC Proceedings 2016 10(Suppl 7):21

    Published on: 18 October 2016

    This article is part of a Supplement: Volume 10 Supplement 7

  17. Proceedings

    Comparing machine learning and logistic regression methods for predicting hypertension using a combination of gene expression and next-generation sequencing data

    Machine learning methods continue to show promise in the analysis of data from genetic association studies because of the high number of variables relative to the number of observations. However, few best prac...

    Elizabeth Held, Joshua Cape and Nathan Tintle

    BMC Proceedings 2016 10(Suppl 7):34

    Published on: 18 October 2016

    This article is part of a Supplement: Volume 10 Supplement 7

  18. Proceedings

    Independent test assessment using the extreme value distribution theory

    The new generation of whole genome sequencing platforms offers great possibilities and challenges for dissecting the genetic basis of complex traits. With a very high number of sequence variants, a naïve multi...

    Marcio Almeida, Lucy Blondell, Juan M. Peralta, Jack W. Kent Jr, Goo Jun, Tanya M. Teslovich, Christian Fuchsberger, Andrew R. Wood, Alisa K. Manning, Timothy M. Frayling, Pablo E. Cingolani, Robert Sladek, Thomas D. Dyer, Goncalo Abecasis, Ravindranath Duggirala and John Blangero

    BMC Proceedings 2016 10(Suppl 7):63

    Published on: 18 October 2016

    This article is part of a Supplement: Volume 10 Supplement 7

  19. Proceedings

    Identity-by-descent mapping for diastolic blood pressure in unrelated Mexican Americans

    Population-based identity by descent (IBD) mapping is a statistical method for detection of genetic loci that share an ancestral segment among “unrelated” pairs of individuals for a disease. As a complementary...

    Xiao-Qing Liu, Jillian Fazio, Pingzhao Hu and Andrew D. Paterson

    BMC Proceedings 2016 10(Suppl 7):8

    Published on: 18 October 2016

    This article is part of a Supplement: Volume 10 Supplement 7

  20. Proceedings

    Finding potential cis-regulatory loci using allele-specific chromatin accessibility as weights in a kernel-based variance component test

    We present a novel approach to detect potential cis-acting regulatory loci that combines the functional potential, an empirical DNase-seq based estimate of the allele-specificity of DNase-I hypersensitivity sites...

    Juan Manuel Peralta, Marcio Almeida, Lawrence J. Abraham, Eric Moses and John Blangero

    BMC Proceedings 2016 10(Suppl 7):50

    Published on: 18 October 2016

    This article is part of a Supplement: Volume 10 Supplement 7

  21. Proceedings

    Comparing strategies for combined testing of rare and common variants in whole sequence and genome-wide genotype data

    We used our extension of the kernel score test to family data to analyze real and simulated baseline systolic blood pressure in extended pedigrees. We compared the power for different kernels and for different...

    Dörthe Malzahn, Stefanie Friedrichs and Heike Bickeböller

    BMC Proceedings 2016 10(Suppl 7):17

    Published on: 18 October 2016

    This article is part of a Supplement: Volume 10 Supplement 7

  22. Proceedings

    Association of polymorphisms in the aldosterone-regulated sodium reabsorption pathway with blood pressure among Hispanics

    Whereas genome-wide association study (GWAS) has proven to be an important tool for discovery of variants influencing many human diseases and traits, unfortunately its performance has not been much of all-arou...

    Bamidele O. Tayo, Liping Tong and Richard S. Cooper

    BMC Proceedings 2016 10(Suppl 7):15

    Published on: 18 October 2016

    This article is part of a Supplement: Volume 10 Supplement 7

  23. Proceedings

    Prioritization of family member sequencing for the detection of rare variants

    The advent of affordable sequencing has enabled researchers to discover many variants contributing to disease, including rare variants. There are methods for determining the most informative individuals for se...

    Rachel Sippy, Jill M Kolesar, Burcu F Darst and Corinne D Engelman

    BMC Proceedings 2016 10(Suppl 7):11

    Published on: 18 October 2016

    This article is part of a Supplement: Volume 10 Supplement 7

  24. Proceedings

    Analysis of gene expression to predict dynamics of future hypertension incidence in type 2 diabetic patients

    The main focus of the Genetic Analysis Workshop 19 (GAW19) is identification of genes related to the occurrence of hypertension in the cohort of patients with type 2 diabetes mellitus (T2DM). The aim of our st...

    Piotr Radkowski, Gracjan Wątor, Jan Skupien, Anna Bogdali and Paweł Wołkow

    BMC Proceedings 2016 10(Suppl 7):64

    Published on: 18 October 2016

    This article is part of a Supplement: Volume 10 Supplement 7

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