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Volume 12 Supplement 9

Genetic Analysis Workshop 20: envisioning the future of statistical genetics by exploring methods for epigenetic and pharmacogenomic data

Proceedings

Publication of the proceedings of Genetic Analysis Workshop 20 was supported by National Institutes of Health grant R01 GM031575. The articles have undergone the journal's standard peer review process for supplements. The Supplement Editors declare that they were not involved in the peer review process for any article on which they are an author. They declare no other competing interests.

San Diego, CA, USA4 - 8 March 2017

Edited by Laura Almasy, Mariza de Andrade, Stella W. Aslibekyan, Justo L. Bermejo, Rita Cantor, Saurabh Ghosh, Phillip Melton, Nathan L. Tintle, and Xuexia Wang

Conference website

Articles from this supplement have also been published as a supplement in BMC Genetics.

  1. GAW20 provided a platform for developing and evaluating statistical methods to analyze human lipid-related phenotypes, DNA methylation, and single-nucleotide markers in a study involving a pharmaceutical inter...

    Authors: Nathan L. Tintle, David W. Fardo, Mariza de Andrade, Stella Aslibekyan, Julia N. Bailey, Justo Lorenzo Bermejo, Rita M. Cantor, Saurabh Ghosh, Philip Melton, Xuexia Wang, Jean W. MacCluer and Laura Almasy
    Citation: BMC Proceedings 2018 12(Suppl 9):26
  2. GAW20 provided participants with an opportunity to comprehensively examine genetic and epigenetic variation among related individuals in the context of drug treatment response. GAW20 used data from 188 families (

    Authors: Stella Aslibekyan, Laura Almasy, Michael A. Province, Devin M. Absher and Donna K. Arnett
    Citation: BMC Proceedings 2018 12(Suppl 9):35
  3. The GAW20 simulation data set is based upon the companion Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) study fenofibrate clinical trial data set that forms the real data example for GAW20. The sim...

    Authors: Aldi T. Kraja, Ping An, Petra Lenzini, Shiou J. Lin, Christine Williams, James E. Hicks, E. Warwick Daw and Michael A. Province
    Citation: BMC Proceedings 2018 12(Suppl 9):25
  4. Using data on 680 patients from the GAW20 real data set, we conducted Mendelian randomization (MR) studies to explore the causal relationships between methylation levels at selected probes (cytosine-phosphate-...

    Authors: Lai Jiang, Kaiqiong Zhao, Kathleen Klein, Angelo J. Canty, Karim Oualkacha and Celia M. T. Greenwood
    Citation: BMC Proceedings 2018 12(Suppl 9):20
  5. Even though there has been great success in identifying lipid-associated single-nucleotide polymorphisms (SNPs), the mechanisms through which the SNPs act on each trait are poorly understood. The emergence of ...

    Authors: Anne E. Justice, Annie Green Howard, Lindsay Fernández-Rhodes, Misa Graff, Ran Tao and Kari E. North
    Citation: BMC Proceedings 2018 12(Suppl 9):22
  6. DNA methylation is an epigenetic mechanism that has been proposed as a possible link between genetic and environmental determinants of disease. Prior studies reported robust associations between the methylatio...

    Authors: Sergi Sayols-Baixeras, Hemant K. Tiwari and Stella W. Aslibekyan
    Citation: BMC Proceedings 2018 12(Suppl 9):23
  7. Epigenetic modification has an effect on gene expression under the environmental alteration, but it does not change corresponding genome sequence. DNA methylation (DNAm) is one of the important epigenetic mech...

    Authors: Md. Mohaiminul Islam, Ye Tian, Yan Cheng, Yang Wang and Pingzhao Hu
    Citation: BMC Proceedings 2018 12(Suppl 9):21
  8. The Genetic Analysis Workshop (GAW) presents an opportunity to collaboratively evaluate methodology relevant to current issues in genetic epidemiology. The GAW20 data combine real clinical trial data with fict...

    Authors: Elizabeth R. Piette and Jason H. Moore
    Citation: BMC Proceedings 2018 12(Suppl 9):59
  9. The main goal of this paper is to estimate the effect of triglyceride levels on methylation of cytosine-phosphate-guanine (CpG) sites in multiple-case families. These families are selected because they have 2 ...

    Authors: Angga M. Fuady, Renaud L. M. Tissier and Jeanine J. Houwing-Duistermaat
    Citation: BMC Proceedings 2018 12(Suppl 9):33
  10. Although methylation data continues to rise in popularity, much is still unknown about how to best analyze methylation data in genome-wide analysis contexts. Given continuing interest in gene-based tests for n...

    Authors: Jason Vander Woude, Jordan Huisman, Lucas Vander Berg, Jenna Veenstra, Abbey Bos, Anya Kalsbeek, Karissa Koster, Nathan Ryder and Nathan L. Tintle
    Citation: BMC Proceedings 2018 12(Suppl 9):50
  11. Epigenome-wide association studies (EWAS) have traditionally focused on the association test of single epigenetic markers with complex traits. However, it is possible that multiple cytosine-phosphate-guanine (...

    Authors: Biqi Wang, Anita L. DeStefano and Honghuang Lin
    Citation: BMC Proceedings 2018 12(Suppl 9):28
  12. DNA methylation plays an important role in normal human development and disease. In epigenome-wide association studies (EWAS), a univariate test for association between a phenotype and each cytosine-phosphate-...

    Authors: Chong Wu, Jun Young Park, Weihua Guan and Wei Pan
    Citation: BMC Proceedings 2018 12(Suppl 9):60
  13. Epigenome association studies that test a large number of methylation sites suffer from stringent multiple-testing corrections. This study’s goals were to investigate region-based associations between DNA meth...

    Authors: Kaiqiong Zhao, Lai Jiang, Kathleen Klein, Celia M. T. Greenwood and Karim Oualkacha
    Citation: BMC Proceedings 2018 12(Suppl 9):30
  14. High-throughput platforms allow the characterization of thousands of previously known methylation sites. These platforms have great potential for investigating the epigenetic effects that are partially respons...

    Authors: Marcio Almeida, Juan Peralta, Jose Garcia, Vincent Diego, Harald Goring, Sarah Williams-Blangero and John Blangero
    Citation: BMC Proceedings 2018 12(Suppl 9):29
  15. DNA methylation, an epigenetic modification, can be affected by environmental factors and thus regulate gene expression levels that can lead to alterations of certain phenotypes. Network analysis has been used...

    Authors: Elise Lim, Hanfei Xu, Peitao Wu, Daniel Posner, Jiayi Wu, Gina M. Peloso, Achilleas N. Pitsillides, Anita L. DeStefano, L. Adrienne Cupples and Ching-Ti Liu
    Citation: BMC Proceedings 2018 12(Suppl 9):27
  16. A Bayesian mixed model approach using integrated nested Laplace approximations (INLA) allows us to construct flexible models that can account for pedigree structure. Using these models, we estimate genome-wide...

    Authors: Haakon E. Nustad, Christian M. Page, Andrew H. Reiner, Manuela Zucknick and Marissa LeBlanc
    Citation: BMC Proceedings 2018 12(Suppl 9):31
  17. The heritability of a phenotype is an estimation of the percent of variance in that phenotype that is attributable to additive genetic factors. Heritability is optimally estimated in family-based sample popula...

    Authors: Nicholas B. Blackburn, Arthur Porto, Juan M. Peralta and John Blangero
    Citation: BMC Proceedings 2018 12(Suppl 9):34
  18. Genome-wide association studies often collect multiple phenotypes for complex diseases. Multivariate joint analyses have higher power to detect genetic variants compared with the marginal analysis of each phen...

    Authors: Xuan Deng, Biqi Wang, Virginia Fisher, Gina Peloso, Adrienne Cupples and Ching-Ti Liu
    Citation: BMC Proceedings 2018 12(Suppl 9):55
  19. Triglycerides are an important measure of heart health. Although more than 90 genes have been found to be associated to lipids, they only explain 12 to 15% of the variance in lipid levels. Evidence suggests th...

    Authors: Tony Huayang Gao, Jianjun Zhang, Diaz Medina Miguelangel and Xuexia Wang
    Citation: BMC Proceedings 2018 12(Suppl 9):49
  20. We conducted a genome-wide linkage scan to detect loci that influence the levels of fasting triglycerides in plasma. Fasting triglyceride levels were available at 4 time points (visits), 2 pre- and 2 post-feno...

    Authors: Juan M. Peralta, Nicholas B. Blackburn, Arthur Porto, John Blangero and Jac Charlesworth
    Citation: BMC Proceedings 2018 12(Suppl 9):52
  21. Genome-wide association studies have helped us identify a wealth of genetic variants associated with complex human phenotypes. Because most variants explain a small portion of the total phenotypic variation, h...

    Authors: Arthur Porto, Juan M. Peralta, Nicholas B. Blackburn and John Blangero
    Citation: BMC Proceedings 2018 12(Suppl 9):51
  22. Because of the limited information from the GAW20 samples when only case-control or trio data are considered, we propose eLBL, an extension of the Logistic Bayesian LASSO (least absolute shrinkage and selectio...

    Authors: Xiaofei Zhou, Meng Wang, Han Zhang, William C. L. Stewart and Shili Lin
    Citation: BMC Proceedings 2018 12(Suppl 9):54
  23. To examine whether single-nucleotide polymorphism (SNP) by methylation interactions can be detected, we analyzed GAW20 simulated triglycerides at visits 3 and 4 against baseline (visits 1 and 2) under 4 genera...

    Authors: E. Warwick Daw, James Hicks, Petra Lenzini, Shiow J. Lin, Judy Wang, Christine Williams, Ping An, Michael A. Province and Aldi T. Kraja
    Citation: BMC Proceedings 2018 12(Suppl 9):37
  24. There has been significant interest in investigating genome-wide and epigenome-wide associations with lipids. Testing at the gene or region level may improve power in such studies.

    Authors: Razvan G. Romanescu, Osvaldo Espin-Garcia, Jin Ma and Shelley B. Bull
    Citation: BMC Proceedings 2018 12(Suppl 9):57
  25. An increasing number of studies are focused on the epigenetic regulation of DNA to affect gene expression without modifications to the DNA sequence. Methylation plays an important role in shaping disease trait...

    Authors: Rui Sun, Haoyi Weng, Ruoting Men, Xiaoxuan Xia, Ka Chun Chong, William K. K. Wu, Benny Chung-Ying Zee and Maggie Haitian Wang
    Citation: BMC Proceedings 2018 12(Suppl 9):53
  26. In the search for an understanding of how genetic variation contributes to the heritability of common human disease, the potential role of epigenetic factors, such as methylation, is being explored with increa...

    Authors: Jenna Veenstra, Anya Kalsbeek, Karissa Koster, Nathan Ryder, Abbey Bos, Jordan Huisman, Lucas VanderBerg, Jason VanderWoude and Nathan L. Tintle
    Citation: BMC Proceedings 2018 12(Suppl 9):58
  27. In this paper we analyzed whole-genome genetic information provided by GAW20 from the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) study for family data. Lipid levels such as triglycerides (TGs) a...

    Authors: Sarmistha Das, Pronoy Kanti Mondal, Saurabh Ghosh and Indranil Mukhopadhyay
    Citation: BMC Proceedings 2018 12(Suppl 9):41
  28. Complex genetic traits are often characterized by multiple quantitative phenotypes. Because values of such phenotypes vary over time, it is thought that analyses of longitudinal data on the phenotypes may lead...

    Authors: Hemant Kulkarni, Indranil Mukhopadhyay and Saurabh Ghosh
    Citation: BMC Proceedings 2018 12(Suppl 9):39
  29. As part of GAW20, we analyzed the familiality and variability of methylation to identify cytosine-phosphate-guanine (CpG) sites responsive to treatment with fenofibrate. Methylation was measured at approximate...

    Authors: Rita Cantor, Linda Navarro and Calvin Pan
    Citation: BMC Proceedings 2018 12(Suppl 9):43
  30. In a typical genome-enabled prediction problem there are many more predictor variables than response variables. This prohibits the application of multiple linear regression, because the unique ordinary least s...

    Authors: Svetlana Cherlin, Richard A. J. Howey and Heather J. Cordell
    Citation: BMC Proceedings 2018 12(Suppl 9):38
  31. The study of DNA methylation quantitative trait loci (meQTLs) helps dissect regulatory mechanisms underlying genetic associations of human diseases. In this study, we conducted the first genome-wide examinatio...

    Authors: Jiayi Wu Cox, Devanshi Patel, Jaeyoon Chung, Congcong Zhu, Samantha Lent, Virginia Fisher, Achilleas Pitsillides, Lindsay Farrer and Xiaoling Zhang
    Citation: BMC Proceedings 2018 12(Suppl 9):44
  32. Obesity is a risk factor for heart disease, stroke, diabetes, high blood pressure, and other chronic diseases. Some drugs, including fenofibrate, are used to treat obesity or excessive weight by lowering the l...

    Authors: Zheng Xu, Qing Duan, Juan Cui, Yumou Qiu, Qidong Jia, Cong Wu and Jennifer Clarke
    Citation: BMC Proceedings 2018 12(Suppl 9):46
  33. In GAW20, we investigated the association of specific genetic regions of interest (ROIs) with log-transformed triglyceride (TG) levels following lipid-lowering medication using epigenetic and genetic markers. ...

    Authors: Summaira Yasmeen, Patricia Burger, Stefanie Friedrichs, Sergi Papiol and Heike Bickeböller
    Citation: BMC Proceedings 2018 12(Suppl 9):47

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