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  1. 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 ...

    Authors: Heike Bickeböller, Julia N Bailey, Joseph Beyene, Rita M Cantor, Heather J Cordell, Robert C Culverhouse, Corinne D Engelman, David W Fardo, Saurabh Ghosh, Inke R König, Justo Lorenzo Bermejo, Phillip E Melton, Stephanie A Santorico, Glen A Satten, Lei Sun, Nathan L Tintle…
    Citation: BMC Proceedings 2014 8(Suppl 1):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  2. Admixture mapping is a disease-mapping strategy to identify disease susceptibility variants in an admixed population that is a result of mating between 2 historically separated populations differing in allele ...

    Authors: Mengjie Chen, Can Yang, Cong Li, Lin Hou, Xiaowei Chen and Hongyu Zhao
    Citation: BMC Proceedings 2014 8(Suppl 1):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  3. It is well known that genetic association studies are not robust to population stratification. Two widely used approaches for the detection and correction of population structure are principal component analys...

    Authors: Timothy Thornton, Matthew P Conomos, Serge Sverdlov, Elizabeth M Blue, Charles YK Cheung, Christopher G Glazner, Steven M Lewis and Ellen M Wijsman
    Citation: BMC Proceedings 2014 8(Suppl 1):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  4. In this study, we analyze the Genetic Analysis Workshop 18 (GAW18) data to identify regions of single-nucleotide polymorphisms (SNPs), which significantly influence hypertension status among individuals. We ha...

    Authors: Michael Agne, Chien-Hsun Huang, Inchi Hu, Haitian Wang, Tian Zheng and Shaw-Hwa Lo
    Citation: BMC Proceedings 2014 8(Suppl 1):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  5. Sequencing technologies have enabled the investigation of whole genomes of many individuals in parallel. Studies have shown that the joint consideration of multiple rare variants may explain a relevant proport...

    Authors: Carmen Dering, Arne Schillert, Inke R König and Andreas Ziegler
    Citation: BMC Proceedings 2014 8(Suppl 1):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  6. Grouping variants based on gene mapping can augment the power of rare variant association tests. Weighting or sorting variants based on their expected functional impact can provide additional benefit. We defin...

    Authors: Thomas Nalpathamkalam, Andriy Derkach, Andrew D Paterson and Daniele Merico
    Citation: BMC Proceedings 2014 8(Suppl 1):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  7. We are now well into the sequencing era of genetic analysis, and methods to investigate rare variants associated with disease remain in high demand. Currently, the more common rare variant analysis methods are...

    Authors: Michael D Swartz, Taebeom Kim, Jiangong Niu, Robert K Yu, Sanjay Shete and Iuliana Ionita-Laza
    Citation: BMC Proceedings 2014 8(Suppl 1):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  8. We derive the analytical mean and variance of the score test statistic in gene-dropping simulations and approximate the null distribution of the test statistic by a normal distribution. We provide insights int...

    Authors: Yuan Jiang, Sarah Emerson, Lu Wang, Lujing Li and Yanming Di
    Citation: BMC Proceedings 2014 8(Suppl 1):S18
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  9. Genotype errors are well known to increase type I errors and/or decrease power in related tests of genotype-phenotype association, depending on whether the genotype error mechanism is associated with the pheno...

    Authors: Ally Rogers, Andrew Beck and Nathan L Tintle
    Citation: BMC Proceedings 2014 8(Suppl 1):S22
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  10. De novo mutations enrich the sequence diversity and carry the clue of evolutional selection. Recent studies suggest the de novo mutations could be one of the risk factors for complex diseases. We conducted a surv...

    Authors: Heming Wang and Xiaofeng Zhu
    Citation: BMC Proceedings 2014 8(Suppl 1):S24
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  11. Family based association studies are employed less often than case-control designs in the search for disease-predisposing genes. The optimal statistical genetic approach for complex pedigrees is unclear when e...

    Authors: David W Fardo, Xue Zhang, Lili Ding, Hua He, Brad Kurowski, Eileen S Alexander, Tesfaye B Mersha, Valentina Pilipenko, Leah Kottyan, Kannabiran Nandakumar and Lisa Martin
    Citation: BMC Proceedings 2014 8(Suppl 1):S26
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  12. Rare variants may, in part, explain some of the hereditability missing in current genome-wide association studies. Many gene-based rare-variant analysis approaches proposed in recent years are aimed at populat...

    Authors: Dalin Li, Jerome I Rotter, and Xiuqing Guo
    Citation: BMC Proceedings 2014 8(Suppl 1):S28
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  13. Identifying genetic variants associated with complex diseases is an important task in genetic research. Although association studies based on unrelated individuals (ie, case-control genome-wide association stu...

    Authors: Jian Wang, Robert Yu and Sanjay Shete
    Citation: BMC Proceedings 2014 8(Suppl 1):S30
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  15. In this analysis, we investigate the contributions that linkage-based methods, such as identical-by-descent mapping, can make to association mapping to identify rare variants in next-generation sequencing data...

    Authors: Brunilda Balliu, Hae-Won Uh, Roula Tsonaka, Stefan Boehringer, Quinta Helmer and Jeanine J Houwing-Duistermaat
    Citation: BMC Proceedings 2014 8(Suppl 1):S34
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  16. Until very recently, few methods existed to analyze rare-variant association with binary phenotypes in complex pedigrees. We consider a set of recently proposed methods applied to the simulated and real hypert...

    Authors: Allison Hainline, Carolina Alvarez, Alexander Luedtke, Brian Greco, Andrew Beck and Nathan L Tintle
    Citation: BMC Proceedings 2014 8(Suppl 1):S36
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  17. As the cost of DNA sequencing decreases, association studies based on whole genome sequencing are now becoming feasible. It is still unclear, however, how much more we could gain from whole genome sequencing c...

    Authors: Sean Lacey, Jae Yoon Chung and Honghuang Lin
    Citation: BMC Proceedings 2014 8(Suppl 1):S38
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  18. High-throughput sequencing technology allows researchers to test associations between phenotypes and all the variants identified throughout the genome, and is especially useful for analyzing rare variants. How...

    Authors: Cong Li, Can Yang, Mengjie Chen, Xiaowei Chen, Lin Hou and Hongyu Zhao
    Citation: BMC Proceedings 2014 8(Suppl 1):S39
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  19. Family data and rare variants are two key features of whole genome sequencing analysis for hunting the missing heritability of common human diseases. Recently, Zhu and Xiong proposed the generalized T2 tests that...

    Authors: Yiwei Liu, Jing Xuan and Zheyang Wu
    Citation: BMC Proceedings 2014 8(Suppl 1):S40
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  20. To avoid inflated type I error and reduced power in genetic association studies, it is necessary to adjust properly for population stratification and known/unknown subject relatedness. It would be interesting ...

    Authors: Yiwei Zhang and Wei Pan
    Citation: BMC Proceedings 2014 8(Suppl 1):S42
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  21. Next-generation sequencing technologies have been designed to discover rare and de novo variants and are an important tool for identifying rare disease variants. Many statistical methods have been developed to te...

    Authors: Tao Feng and Xiaofeng Zhu
    Citation: BMC Proceedings 2014 8(Suppl 1):S44
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  22. Systolic blood pressure and diastolic blood pressure are known risk factors for cardiovascular diseases and understanding their genetic basis will have important public health implications. For rare variants, ...

    Authors: Xiaofeng Liu and Joseph Beyene
    Citation: BMC Proceedings 2014 8(Suppl 1):S46
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  23. Advances in next-generation sequencing technology have made it possible to comprehensively interrogate the entire spectrum of genomic variations including rare variants. They may help capture the remaining gen...

    Authors: Wei Wang and Zhi Wei
    Citation: BMC Proceedings 2014 8(Suppl 1):S50
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  24. Imprinting effects can lead to parent-of-origin patterns in many complex human diseases. For hypertension, previous studies revealed the possible involvement of imprinted genes. Genetic Analysis Workshop 18 re...

    Authors: Fangyuan Zhang and Shili Lin
    Citation: BMC Proceedings 2014 8(Suppl 1):S52
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  25. Inferring population genetic structure from large-scale genotyping of single-nucleotide polymorphisms or variants is an important technique for studying the history and distribution of extant human populations...

    Authors: Omar De la Cruz and Paola Raska
    Citation: BMC Proceedings 2014 8(Suppl 1):S55
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  26. We applied a gene-based haplotype approach for the genome-wide association analysis on hypertension using Genetic Analysis Workshop 18 data for unrelated individuals. Association of single-nucleotide polymorph...

    Authors: Xiaowei Shen, Osvaldo Espin-Garcia, Xin Qiu, Yonathan Brhane, Geoffrey Liu and Wei Xu
    Citation: BMC Proceedings 2014 8(Suppl 1):S57
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  27. Testing rare variants directly is possible with next-generation sequencing technology. In this article, we propose a sliding-window-based optimal-weighted approach to test for the effects of both rare and comm...

    Authors: Xingwang Zhao, Qiuying Sha, Shuanglin Zhang and Xuexia Wang
    Citation: BMC Proceedings 2014 8(Suppl 1):S59
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  28. The genetic basis of blood pressure often involves multiple genetic factors and their interactions with environmental factors. Gene-environment interaction is assumed to play an important role in determining i...

    Authors: Honglang Wang, Tao He, Cen Wu, Ping-Shou Zhong and Yuehua Cui
    Citation: BMC Proceedings 2014 8(Suppl 1):S61
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  29. Genome-wide association studies have proven successful but they remain underpowered for detecting variants of weaker effect. Alternative methods propose to test for association by using an aggregate score that...

    Authors: Nora Bohossian, Mohamad Saad, Andrés Legarra and Maria Martinez
    Citation: BMC Proceedings 2014 8(Suppl 1):S63
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  30. Logistic regression is usually applied to investigate the association between inherited genetic variants and a binary disease phenotype. A limitation of standard methods used to estimate the parameters of logi...

    Authors: Miriam Kesselmeier, Carine Legrand, Barbara Peil, Maria Kabisch, Christine Fischer, Ute Hamann and Justo Lorenzo Bermejo
    Citation: BMC Proceedings 2014 8(Suppl 1):S65
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  31. Genetic Analysis Workshop 18 provided a platform for evaluating genomic prediction power based on single-nucleotide polymorphisms from single-nucleotide polymorphism array data and sequencing data. Also, Genet...

    Authors: Can Yang, Cong Li, Mengjie Chen, Xiaowei Chen, Lin Hou and Hongyu Zhao
    Citation: BMC Proceedings 2014 8(Suppl 1):S67
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  32. Genetic studies often collect data on multiple traits. Most genetic association analyses, however, consider traits separately and ignore potential correlation among traits, partially because of difficulties in...

    Authors: Lili Ding, Brad G Kurowski, Hua He, Eileen S Alexander, Tesfaye B Mersha, David W Fardo, Xue Zhang, Valentina V Pilipenko, Leah Kottyan and Lisa J Martin
    Citation: BMC Proceedings 2014 8(Suppl 1):S69
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  33. Unlike case-control studies, family-based tests for association are protected against population stratification. Complex genetic traits are often governed by quantitative precursors and it has been argued that...

    Authors: Tanushree Haldar, Indranil Mukhopadhyay and Saurabh Ghosh
    Citation: BMC Proceedings 2014 8(Suppl 1):S71
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  34. We consider analysis of Genetic Analysis Workshop 18 data, which involves multiple longitudinal traits and dense genome-wide single-nucleotide polymorphism (SNP) markers. We use a multivariate linear mixed mod...

    Authors: Jin Liu, Jian Huang and Shuangge Ma
    Citation: BMC Proceedings 2014 8(Suppl 1):S73
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  35. Genetic variants that predispose adults and the elderly to high blood pressure are largely unknown. We used a bivariate linear mixed model approach to jointly test the associations of common single-nucleotide ...

    Authors: Binod Neupane and Joseph Beyene
    Citation: BMC Proceedings 2014 8(Suppl 1):S75
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  36. Pleiotropy, which occurs when a single genetic factor influences multiple phenotypes, is present in many genetic studies of complex human traits. Longitudinal family data, such as the Genetic Analysis Workshop...

    Authors: Lizhen Xu, Radu V Craiu, Andriy Derkach, Andrew D Paterson and Lei Sun
    Citation: BMC Proceedings 2014 8(Suppl 1):S77
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  37. In the last few years, a bewildering variety of methods/software packages that use linear mixed models to account for sample relatedness on the basis of genome-wide genomic information have been proposed. We c...

    Authors: Jakris Eu-ahsunthornwattana, Richard AJ Howey and Heather J Cordell
    Citation: BMC Proceedings 2014 8(Suppl 1):S79
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  38. Most association studies focus on disease risk, with less attention paid to disease progression or severity. These phenotypes require longitudinal data. This paper presents a new method for analyzing longitudi...

    Authors: Anthony Musolf, Alejandro Q Nato Jr, Douglas Londono, Lisheng Zhou, Tara C Matise and Derek Gordon
    Citation: BMC Proceedings 2014 8(Suppl 1):S81
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  39. We present a genome-wide association study of a quantitative trait, "progression of systolic blood pressure in time," in which 142 unrelated individuals of the Genetic Analysis Workshop 18 real genotype data w...

    Authors: Tatsiana Vaitsiakhovich, Dmitriy Drichel, Marina Angisch, Tim Becker, Christine Herold and André Lacour
    Citation: BMC Proceedings 2014 8(Suppl 1):S83
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  40. The behavior of a gene can be dynamic; thus, if longitudinal data are available, it is important that we study the dynamic effects of genes on a trait over time. The effect of a haplotype can be expressed by t...

    Authors: Shuang Xia and Shili Lin
    Citation: BMC Proceedings 2014 8(Suppl 1):S85
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  42. Every known link between a genetic variant and blood pressure improves the understanding and potentially the risk assessment of related diseases such as hypertension. Genetic data have become increasingly comp...

    Authors: Erin Austin, Wei Pan and Xiaotong Shen
    Citation: BMC Proceedings 2014 8(Suppl 1):S94
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  43. In this paper, we compare logistic regression and 2 other classification methods in predicting hypertension given the genotype information. We use logistic regression analysis in the first step to detect signi...

    Authors: Hsin-Hsiung Huang, Tu Xu and Jie Yang
    Citation: BMC Proceedings 2014 8(Suppl 1):S96
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  44. As the availability of cost-effective high-throughput sequencing technology increases, genetic research is beginning to focus on identifying the contributions of rare variants (RVs) to complex traits. Using RV...

    Authors: Ake T Lu and Rita M Cantor
    Citation: BMC Proceedings 2014 8(Suppl 1):S98
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  45. The new generation of sequencing platforms opens new horizons in the genetics field. It is possible to exhaustively assay all genetic variants in an individual and search for phenotypic associations. The whole...

    Authors: Marcio Almeida, Juan M Peralta, Vidya Farook, Sobha Puppala, John W Kent Jr, Ravindranath Duggirala and John Blangero
    Citation: BMC Proceedings 2014 8(Suppl 1):S100
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  46. Following the publication of the ENCODE project results, there has been increasing interest in investigating different areas of the chromosome and evaluating the relative contribution of each area to expressed...

    Authors: Stella Aslibekyan, Howard W Wiener, Guodong Wu, Degui Zhi, Sadeep Shrestha, Gustavo de los Campos and Ana I Vazquez
    Citation: BMC Proceedings 2014 8(Suppl 1):S102
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  47. Genome wide association studies (GWAS) have been used to search for associations between genetic variants and a phenotypic trait of interest. New technologies, such as next-generation sequencing, hold the pote...

    Authors: Jeremy S Edwards, Susan R Atlas, Susan M Wilson, Candice F Cooper, Li Luo and Christine A Stidley
    Citation: BMC Proceedings 2014 8(Suppl 1):S104
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  48. Groups of genes assigned to a pathway, also called a module, have similar functions. Finding such modules, and the topology of the changes of the modules over time, is a fundamental problem in understanding th...

    Authors: Pingzhao Hu and Andrew D Paterson
    Citation: BMC Proceedings 2014 8(Suppl 1):S106
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  49. We apply a multiphase strategy for pedigree-based genetic analysis of systolic blood pressure data collected in a longitudinal study of large Mexican American pedigrees. In the first phase, we conduct variance...

    Authors: Zhijian Chen, Kuan-Rui Tan and Shelley B Bull
    Citation: BMC Proceedings 2014 8(Suppl 1):S108
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

  50. Two-point linkage analyses of whole genome sequence data are a promising approach to identify rare variants that segregate with complex diseases in large pedigrees because, in theory, the causal variants have ...

    Authors: Silke Szymczak, Claire L Simpson, Cheryl D Cropp and Joan E Bailey-Wilson
    Citation: BMC Proceedings 2014 8(Suppl 1):S110
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 1

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