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Volume 1 Supplement 1

Genetic Analysis Workshop 15: Gene Expression Analysis and Approaches to Detecting Multiple Functional Loci

Proceedings

Genetic Analysis Workshop 15: Gene Expression Analysis and Approaches to Detecting Multiple Functional Loci. Go to conference site.

St. Pete Beach, Florida, USA11-15 November 2006

Page 1 of 4

  1. Content type: Proceedings

    Authors: Heather J Cordell, Mariza de Andrade, Marie-Claude Babron, Christopher W Bartlett, Joseph Beyene, Heike Bickeböller, Robert Culverhouse, L Adrienne Cupples, E Warwick Daw, Josée Dupuis, Catherine T Falk, Saurabh Ghosh, Katrina A Goddard, Ellen L Goode, Elizabeth R Hauser, Lisa J Martin…

    Citation: BMC Proceedings 2007 1(Suppl 1):S1

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  2. Content type: Proceedings

    For Genetic Analysis Workshop 15 Problem 2, we organized data from several ongoing studies designed to identify genetic and environmental risk factors for rheumatoid arthritis. Data were derived from the North...

    Authors: Christopher I Amos, Wei Vivien Chen, Elaine Remmers, Katherine A Siminovitch, Michael F Seldin, Lindsey A Criswell, Annette T Lee, Sally John, Neil D Shephard, Jane Worthington, Francois Cornelis, Robert M Plenge, Ann B Begovich, Thomas D Dyer, Daniel L Kastner and Peter K Gregersen

    Citation: BMC Proceedings 2007 1(Suppl 1):S3

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  3. Content type: Proceedings

    Data for Problem 3 of the Genetic Analysis Workshop 15 were generated by computer simulation in an attempt to mimic some of the genetic and epidemiological features of rheumatoid arthritis (RA) such as its pop...

    Authors: Michael B Miller, Gregg R Lind, Na Li and Soon-Young Jang

    Citation: BMC Proceedings 2007 1(Suppl 1):S4

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  4. Content type: Proceedings

    Several methods to identify tagging single-nucleotide polymorphisms (SNPs) are in common use for genetic epidemiologic studies; however, there may be loss of information when using only a subset of SNPs. We so...

    Authors: Ellen L Goode, Brooke L Fridley, Zhifu Sun, Elizabeth J Atkinson, Alex S Nord, Shannon K McDonnell, Gail P Jarvik, Mariza de Andrade and Susan L Slager

    Citation: BMC Proceedings 2007 1(Suppl 1):S6

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  5. Content type: Proceedings

    Assuming multiple loci play a role in regulating the expression level of a single phenotype, we propose a new approach to identify cis- and trans-acting loci that regulate gene expression. Using the Problem 1 dat...

    Authors: Pingzhao Hu, Hui Lan, Wei Xu, Joseph Beyene and Celia MT Greenwood

    Citation: BMC Proceedings 2007 1(Suppl 1):S7

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  6. Content type: Proceedings

    Genotype-expression association analysis using linear regression may produce different test results depending on whether founders only or all pedigreed members are used. This difference is not due to the corre...

    Authors: Young Ju Suh, Hye-Soon Lee, Franak Batliwalla and Wentian Li

    Citation: BMC Proceedings 2007 1(Suppl 1):S8

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  7. Content type: Proceedings

    Mutual information (MI) is a robust nonparametric statistical approach for identifying associations between genotypes and gene expression levels. Using the data of Problem 1 provided for the Genetic Analysis W...

    Authors: Silke Szymczak, Angelo Nuzzo, Christian Fuchsberger, Daniel F Schwarz, Andreas Ziegler, Riccardo Bellazzi and Bernd-Wolfgang Igl

    Citation: BMC Proceedings 2007 1(Suppl 1):S9

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  8. Content type: Proceedings

    The mRNA expression levels of genes have been shown to have discriminating power for the classification of breast cancer. Studying the heritability of gene expression levels on breast cancer related transcript...

    Authors: Tian Zheng, Shuang Wang, Lei Cong, Yuejing Ding, Iuliana Ionita-Laza and Shaw-Hwa Lo

    Citation: BMC Proceedings 2007 1(Suppl 1):S10

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  9. Content type: Proceedings

    Rheumatoid arthritis (RA, MIM 180300) is a common and complex inflammatory disorder. The North American Rheumatoid Arthritis Consortium (NARAC) data, as part of the Genetic Analysis Workshop 15 data, consists ...

    Authors: Yuejing Ding, Lei Cong, Iuliana Ionita-Laza, Shaw-Hwa Lo and Tian Zheng

    Citation: BMC Proceedings 2007 1(Suppl 1):S13

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  10. Content type: Proceedings

    In the present paper, we used the North American Rheumatoid Arthritis Consortium data provided for Genetic Analysis Workshop 15 Problem 2 to: 1) estimate the penetrances of PTPN22 and HLA-DRB1 and, 2) test the...

    Authors: France Gagnon, David Hajage, Sabine Plancoulaine and Sophie Tezenas du Montcel

    Citation: BMC Proceedings 2007 1(Suppl 1):S14

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  11. Content type: Proceedings

    We analyzed a case-control data set for chromosome 18q from the Genetic Analysis Workshop 15 to detect susceptibility loci for rheumatoid arthritis (RA). A total number of 460 cases and 460 unaffected controls...

    Authors: Tai-Yue Kuo, Winston Lau, Cheng Hu and Weihua Zhang

    Citation: BMC Proceedings 2007 1(Suppl 1):S15

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  12. Content type: Proceedings

    As genome-wide association studies grow in popularity for the identification of genetic factors for common and rare diseases, analytical methods to comb through large numbers of genetic variants efficiently to...

    Authors: Zhong Li, Tian Zheng, Andrea Califano and Aris Floratos

    Citation: BMC Proceedings 2007 1(Suppl 1):S16

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  13. Content type: Proceedings

    We examined the potential gene × gene interactions and gene × smoking interactions in rheumatoid arthritis (RA) using the candidate gene data sets provided by Genetic Analysis Workshop 15 Problem 2. The multif...

    Authors: Ling Mei, Xiaohui Li, Kai Yang, Jinrui Cui, Belle Fang, Xiuqing Guo and Jerome I Rotter

    Citation: BMC Proceedings 2007 1(Suppl 1):S17

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  14. Content type: Proceedings

    Although single chi-square analysis of the North American Rheumatoid Arthritis Consortium (NARAC) data identifies many single-nucleotide polymorphisms (SNPs) with p-values less than 0.05, none remain significant ...

    Authors: William Tapper, Andrew Collins and Newton E Morton

    Citation: BMC Proceedings 2007 1(Suppl 1):S18

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  15. Content type: Proceedings

    Rheumatoid arthritis (RA) is a disorder with important public health implications. It is possible that there are clinically distinctive subtypes of the disorder with different genetic etiologies. We used the d...

    Authors: Marsha A Wilcox and Andrew T McAfee

    Citation: BMC Proceedings 2007 1(Suppl 1):S20

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  16. Content type: Proceedings

    We performed linkage and family-based association analysis across chromosomes 1–22 in Replicates 1–5 of the Genetic Analysis Workshop 15 simulated data. Linkage analysis was performed using the Kong and Cox al...

    Authors: Pimphen Charoen, Joanna M Biernacka and Heather J Cordell

    Citation: BMC Proceedings 2007 1(Suppl 1):S23

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  17. Content type: Proceedings

    Several recent papers have suggested that two-locus tests of association that incorporate gene × gene interaction can be more powerful than marginal, single-locus tests across a broad range of multilocus inter...

    Authors: Fangyi Gu, Genevieve Monsees and Peter Kraft

    Citation: BMC Proceedings 2007 1(Suppl 1):S25

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  18. Content type: Proceedings

    Clustering of related haplotypes in haplotype-based association mapping has the potential to improve power by reducing the degrees of freedom without sacrificing important information about the underlying gene...

    Authors: Robert P Igo Jr, Douglas Londono, Katherine Miller, Antonio R Parrado, Shannon RE Quade, Moumita Sinha, Sulgi Kim, Sungho Won, Jing Li and Katrina AB Goddard

    Citation: BMC Proceedings 2007 1(Suppl 1):S27

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  19. Content type: Proceedings

    We present a new method for testing association when data from both case-parents trios and unrelated controls are available. Our method combines test statistics for case-parents trio and unrelated case-control...

    Authors: Jungnam Joo, Xin Tian, Gang Zheng, Mario Stylianou, Jing-Ping Lin and Nancy L Geller

    Citation: BMC Proceedings 2007 1(Suppl 1):S28

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  20. Content type: Proceedings

    Related cases may be included in case-control association studies if correlations between related individuals due to identity-by-descent (IBD) sharing are taken into account. We derived a framework to test for...

    Authors: Karola Köhler, Melanie Sohns and Heike Bickeböller

    Citation: BMC Proceedings 2007 1(Suppl 1):S29

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  21. Content type: Proceedings

    Family-based association approaches such as the transmission-disequilibrium test (TDT) are used extensively in the study of genetic traits because they are generally robust to the presence of population struct...

    Authors: Hongyan Xu and Varghese George

    Citation: BMC Proceedings 2007 1(Suppl 1):S32

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  22. Content type: Proceedings

    We compared and evaluated several variable and model selection methods using Bayesian and non-Bayesian approaches for three replicates of the Genetic Analysis Workshop 15 (GAW15) simulated data. In doing so, t...

    Authors: Zhan Ye, Elizabeth J Atkinson, Brooke L Fridley and Mariza de Andrade

    Citation: BMC Proceedings 2007 1(Suppl 1):S34

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  23. Content type: Proceedings

    In a small chromosomal region, a number of polymorphisms may be both linked to and associated with a disease. Potentially directly associated causal loci may be distinguished from indirectly associated loci by...

    Authors: Joanna M Biernacka, Pimphen Charoen and Heather J Cordell

    Citation: BMC Proceedings 2007 1(Suppl 1):S36

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  24. Content type: Proceedings

    In order to model the effect of PTPN22 on rheumatoid arthritis (RA), we determined the combination of single-nucleotide-polymorphisms (SNPs) showing the strongest association with RA. Three SNPs (rs2476601-rs1273...

    Authors: Mathieu Bourgey, Hervé Perdry and Françoise Clerget-Darpoux

    Citation: BMC Proceedings 2007 1(Suppl 1):S37

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  25. Content type: Proceedings

    There has been a growing interest in developing strategies for identifying single-nucleotide polymorphisms (SNPs) that explain a linkage signal by joint modeling of linkage and association. We compare several ...

    Authors: Ming-Huei Chen, Jing Cui, Chao-Yu Guo, L Adrienne Cupples, Paul Van Eerdewegh, Josée Dupuis and Qiong Yang

    Citation: BMC Proceedings 2007 1(Suppl 1):S38

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  26. Content type: Proceedings

    To detect association of the DR1 allele with rheumatoid arthritis (RA) given linkage in the affected sibling pairs of the replicates of Problem 3 of Genetic Analysis Workshop 15 (GAW15), we propose a new score...

    Authors: Jeanine J Houwing-Duistermaat, Hae Won Uh and Hans C van Houwelingen

    Citation: BMC Proceedings 2007 1(Suppl 1):S39

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  27. Content type: Proceedings

    This study evaluated the utility of unrelated controls and flanking markers when performing joint modeling of linkage and association by the LAMP software (version 0.0.6) [Am J Hum Genet 2005, 76:934–949; Am J Hu...

    Authors: Wan-Yu Lin and Daniel J Schaid

    Citation: BMC Proceedings 2007 1(Suppl 1):S40

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  28. Content type: Proceedings

    After genetic linkage has been identified for a complex disease, the next step is often fine-mapping by association analysis, using single-nucleotide polymorphisms (SNPs) within a linkage region. If a SNP show...

    Authors: Xuemei Lou, Silke Schmidt and Elizabeth R Hauser

    Citation: BMC Proceedings 2007 1(Suppl 1):S41

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  29. Content type: Proceedings

    The influence of certain alleles of the HLA-DRB1 locus on risk for rheumatoid arthritis has been well established through linkage and association studies. In addition, other loci in the HLA region on 6p21 may ...

    Authors: Richard Sherva, Lingwei Sun, Joanna Biernacka and Rosalind Neuman

    Citation: BMC Proceedings 2007 1(Suppl 1):S42

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  30. Content type: Proceedings

    We carried out an analysis of the Genetic Analysis Workshop 15 simulated Problem 3 data. We restricted ourselves to the present/absent phenotype. Linkage analysis revealed a very strong signal on chromosome 6....

    Authors: Brian K Suarez, Robert Culverhouse, Carol H Jin and Anthony Hinrichs

    Citation: BMC Proceedings 2007 1(Suppl 1):S43

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  31. Content type: Proceedings

    A family-based association study design is not only able to localize causative genes more precisely than linkage analysis, but it also helps explain the genetic mechanism underlying the trait under study. Ther...

    Authors: Guan Xing, Chao Xing, Qing Lu and Robert C Elston

    Citation: BMC Proceedings 2007 1(Suppl 1):S44

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  32. Content type: Proceedings

    Gene expression profiles and single-nucleotide polymorphism (SNP) profiles are modern data for genetic analysis. It is possible to use the two types of information to analyze the relationships among genes by s...

    Authors: Bin-Sheng Gong, Qing-Pu Zhang, Guang-Mei Zhang, Shao-Jun Zhang, Wei Zhang, Hong-Chao Lv, Fan Zhang, Sa-Li Lv, Chuan-Xing Li, Shao-Qi Rao and Xia Li

    Citation: BMC Proceedings 2007 1(Suppl 1):S45

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  33. Content type: Proceedings

    Using single-nucleotide polymorphism (SNP) genotypes and selected gene expression phenotypes from 14 CEPH (Centre d'Etude du Polymorphisme Humain) pedigrees provided for Genetic Analysis Workshop 15 (GAW15), w...

    Authors: Ying Liu, Weimin Duan, Justin Paschall and Nancy L Saccone

    Citation: BMC Proceedings 2007 1(Suppl 1):S47

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  34. Content type: Proceedings

    Extensive studies have been performed to analyze variation in gene expression data by using multistage approaches, including a combination of microarray and linkage analysis. Such a method was recently used in...

    Authors: Alka Malhotra, Helen C Looker and Robert L Hanson

    Citation: BMC Proceedings 2007 1(Suppl 1):S48

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  35. Content type: Proceedings

    Traditional studies of familial aggregation are aimed at defining the genetic (and non-genetic) causes of a disease from physiological or clinical traits. However, there has been little attempt to use genome-w...

    Authors: Shao-Qi Rao, Liang-De Xu, Guang-Mei Zhang, Xia Li, Lin Li, Gong-Qing Shen, Yang Jiang, Yue-Ying Yang, Bin-Sheng Gong, Wei Jiang, Fan Zhang, Yun Xiao and Qing K Wang

    Citation: BMC Proceedings 2007 1(Suppl 1):S49

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  36. Content type: Proceedings

    About 28% of genes appear to have an expression pattern that follows a mixture distribution. We use first- and second-order partial correlation coefficients to identify trios and quartets of non-sex-linked gen...

    Authors: Yang Yang, Adam P Tashman, Jung Yeon Lee, Seungtai Yoon, Wenyang Mao, Kwangmi Ahn, Wonkuk Kim, Nancy R Mendell, Derek Gordon and Stephen J Finch

    Citation: BMC Proceedings 2007 1(Suppl 1):S50

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