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Volume 8 Supplement 1

Genetic Analysis Workshop 18: Human sequence data in extended pedigrees


Edited by H Bickeböller, JN Bailey, J Beyene, RM Cantor, HJ Cordell, RC Culverhouse, CD Engelman, DW Fardo, S Ghosh, IR König, J Lorenzo Bermejo, PE Melton, SA Santorico, GA Satten, L Sun, NL Tintle, A Ziegler, JW MacCluer and L Almasy

Publication charges for this supplement were funded by the Texas Biomedical Research Institute. Articles have undergone the journal's standard review process for supplements. AZ received intramural funding from the University of Lübeck, Germany. The remaining Supplement Editors declare that they have no competing interests.

Genetic Analysis Workshop 18. Go to conference site.

Stevenson, WA, USA13-17 October 2012

Page 1 of 3

  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
  2. Genetic Analysis Workshop 18 (GAW18) focused on identification of genes and functional variants that influence complex phenotypes in human sequence data. Data for the workshop were donated by the T2D-GENES Con...

    Authors: Laura Almasy, Thomas D Dyer, Juan M Peralta, Goo Jun, Andrew R Wood, Christian Fuchsberger, Marcio A Almeida, Jack W Kent Jr, Sharon Fowler, Tom W Blackwell, Sobha Puppala, Satish Kumar, Joanne E Curran, Donna Lehman, Goncalo Abecasis, Ravindranath Duggirala…
    Citation: BMC Proceedings 2014 8(Suppl 1):S2
  3. 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
  4. Cryptic population structure can increase both type I and type II errors. This is particularly problematic in case-control association studies of unrelated individuals. Some researchers believe that these prob...

    Authors: Robert C Culverhouse, Anthony L Hinrichs and Brian K Suarez
    Citation: BMC Proceedings 2014 8(Suppl 1):S4
  5. 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
  6. Admixture mapping and association testing have been successfully applied to the detection of genes for complex diseases. Methods have also been developed to combine these approaches. As an initial step to dete...

    Authors: Daniel Yorgov, Karen L Edwards and Stephanie A Santorico
    Citation: BMC Proceedings 2014 8(Suppl 1):S6
  7. 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
  8. 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
  9. The focus of our work is to evaluate several recently developed pooled association tests for rare variants and assess the impact of different gene annotation methods and binning strategies on the analyses of r...

    Authors: Andriy Derkach, Jerry F Lawless, Daniele Merico, Andrew D Paterson and Lei Sun
    Citation: BMC Proceedings 2014 8(Suppl 1):S9
  10. Sequence kernel association test (SKAT) has become one of the most commonly used nonburden tests for analyzing rare variants. Performance of burden tests depends on the weighting of rare and common variants wh...

    Authors: Cates Mallaney and Yun Ju Sung
    Citation: BMC Proceedings 2014 8(Suppl 1):S10
  11. 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
  12. Analysis of longitudinal family data is challenging because of 2 sources of correlations: correlations across longitudinal measurements and correlations among related individuals. We investigated whether analy...

    Authors: Yun Ju Sung, Jacob Basson and Dabeeru C Rao
    Citation: BMC Proceedings 2014 8(Suppl 1):S12
  13. 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
  14. Whole genome sequencing (WGS) remains prohibitively expensive, which has encouraged the development of methods to impute WGS data into nonsequenced individuals using a framework of single nucleotide polymorphi...

    Authors: August N Blackburn, Angela K Dean and Donna M Lehman
    Citation: BMC Proceedings 2014 8(Suppl 1):S16
  15. The ideal genetic analysis of family data would include whole genome sequence on all family members. A strategy of combining sequence data from a subset of key individuals with inexpensive, genome-wide associa...

    Authors: Anthony L Hinrichs, Robert C Culverhouse and Brian K Suarez
    Citation: BMC Proceedings 2014 8(Suppl 1):S17
  16. We demonstrate the flexibility of identity-by-descent (IBD) graphs for genotype imputation and testing relationships between genotype and phenotype. We analyzed chromosome 3 and the first replicate of simulate...

    Authors: Elizabeth Marchani Blue, Charles YK Cheung, Christopher G Glazner, Matthew P Conomos, Steven M Lewis, Serge Sverdlov, Timothy Thornton and Ellen M Wijsman
    Citation: BMC Proceedings 2014 8(Suppl 1):S19
  17. We developed a general framework for family-based imputation using single-nucleotide polymorphism data and sequence data distributed by Genetic Analysis Workshop 18. By using PedIBD, we first inferred haplotyp...

    Authors: Sunah Song, Robert Shields, Xin Li and Jing Li
    Citation: BMC Proceedings 2014 8(Suppl 1):S20
  18. Although the technical and analytic complexity of whole genome sequencing is generally appreciated, best practices for data cleaning and quality control have not been defined. Family based data can be used to ...

    Authors: Valentina V Pilipenko, Hua He, Brad G Kurowski, Eileen S Alexander, Xue Zhang, Lili Ding, Tesfaye B Mersha, Leah Kottyan, David W Fardo and Lisa J Martin
    Citation: BMC Proceedings 2014 8(Suppl 1):S21
  19. Large-scale genetic studies are often composed of related participants, and utilizing familial relationships can be cumbersome and computationally challenging. We present an approach to efficiently handle sequ...

    Authors: Xiuhua Ding, Shaoyong Su, Kannabiran Nandakumar, Xiaoling Wang and David W Fardo
    Citation: BMC Proceedings 2014 8(Suppl 1):S25
  20. 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
  21. We apply a family-based extension of the sequence kernel association test (SKAT) to 93 trios extracted from the 20 pedigrees in the Genetic Analysis Workshop 18 simulated data. Each extracted trio includes a u...

    Authors: Jing Huang, Yong Chen, Michael D Swartz and Iuliana Ionita-Laza
    Citation: BMC Proceedings 2014 8(Suppl 1):S27
  22. Because the genotype-phenotype correlation information is investigated differently by linkage and association analyses, various efforts have been made to model linkage and association jointly. However, joint m...

    Authors: Yi Li, Jia Nee Foo, Herty Liany, Hui-Qi Low and Jianjun Liu
    Citation: BMC Proceedings 2014 8(Suppl 1):S29
  23. 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
  24. The application of family-based tests to whole-genome sequenced data provides a new window on the role of rare variant alleles in the etiology of disease. By applying family-based tests to these data, we can n...

    Authors: Mengyuan Xu, Harold Z Wang, Wei Guo, Haide Qin and Yin Y Shugart
    Citation: BMC Proceedings 2014 8(Suppl 1):S31
  25. The cost of next-generation sequencing is now approaching that of the first generation of genome-wide single-nucleotide genotyping panels, but this is still out of reach for large-scale epidemiologic studies w...

    Authors: Zhao Yang and Duncan C Thomas
    Citation: BMC Proceedings 2014 8(Suppl 1):S32
  26. The revolution in next-generation sequencing has made obtaining both common and rare high-quality sequence variants across the entire genome feasible. Because researchers are now faced with the analytical chal...

    Authors: Jin J Zhou, Wai-Ki Yip, Michael H Cho, Dandi Qiao, Merry-Lynn N McDonald and Nan M Laird
    Citation: BMC Proceedings 2014 8(Suppl 1):S33
  27. 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
  28. The genetic variants associated with blood pressure identified so far explain only a small proportion of the total heritability of this trait. With recent advances in sequencing technology and statistical meth...

    Authors: Han Chen, Seung Hoan Choi, Jaeyoung Hong, Chen Lu, Jacqueline N Milton, Catherine Allard, Sean M Lacey, Honghuang Lin and Josée Dupuis
    Citation: BMC Proceedings 2014 8(Suppl 1):S35
  29. 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
  30. 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
  31. The kernel score statistic is a global covariance component test over a set of genetic markers. It provides a flexible modeling framework and does not collapse marker information. We generalize the kernel scor...

    Authors: Dörthe Malzahn, Stefanie Friedrichs, Albert Rosenberger and Heike Bickeböller
    Citation: BMC Proceedings 2014 8(Suppl 1):S41
  32. 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
  33. Current sequencing technology enables generation of whole genome sequencing data sets that contain a high density of rare variants, each of which is carried by, at most, 5% of the sampled subjects. Such varian...

    Authors: Ying Liu, ChienHsun Huang, Inchi Hu, Shaw-Hwa Lo and Tian Zheng
    Citation: BMC Proceedings 2014 8(Suppl 1):S47

    The Erratum to this article has been published in BMC Proceedings 2014 8:S112

  34. We propose a novel variance component approach for the analysis of next-generation sequencing data. Our method is based on the detection of the proportion of the trait phenotypic variance that can be explained...

    Authors: Juan M Peralta, Marcio Almeida, Jack W Kent Jr and John Blangero
    Citation: BMC Proceedings 2014 8(Suppl 1):S49

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