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  1. In whole-genome association studies, at the first stage, all markers are tested for association and their test statistics or p-values are ranked. At the second stage, some most significant markers are further ana...

    Authors: Gang Zheng, Jungnam Joo, Jing-Ping Lin, Mario Stylianou, Myron A Waclawiw and Nancy L Geller

    Citation: BMC Proceedings 2007 1(Suppl 1):S165

    Content type: Proceedings

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

  2. A number of autoimmune and other diseases have well established HLA associations; in many cases there is strong evidence for the direct involvement of the HLA class II peptide-presenting antigens, e.g., HLA DR...

    Authors: Glenys Thomson and Ana Maria Valdes

    Citation: BMC Proceedings 2007 1(Suppl 1):S163

    Content type: Proceedings

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

  3. The presence of linkage disequilibrium violates the underlying assumption of linkage equilibrium in most traditional multipoint linkage approaches. Studies have shown that such violation leads to bias in quali...

    Authors: Kelly Cho, Qiong Yang and Josée Dupuis

    Citation: BMC Proceedings 2007 1(Suppl 1):S161

    Content type: Proceedings

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

  4. Recent studies have shown that linkage disequilibrium (LD) between single-nucleotide polymorphism (SNP) markers is widespread. Assuming linkage equilibrium has been shown to cause false positives in linkage st...

    Authors: Cornelis A Albers and Hilbert J Kappen

    Citation: BMC Proceedings 2007 1(Suppl 1):S159

    Content type: Proceedings

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

  5. In the fast-developing field of expression quantitative traits loci (eQTL) studies, much interest has been concentrated on detecting genomic regions containing transcriptional regulators that influence multipl...

    Authors: Jie Peng, Pei Wang and Hua Tang

    Citation: BMC Proceedings 2007 1(Suppl 1):S157

    Content type: Proceedings

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

  6. We applied a simple and efficient two-step method to analyze a family-based association study of gene expression quantitative trait loci (eQTL) in a mixed model framework. This two-step method produces very si...

    Authors: Alex C Lam, Michael Schouten, Yurii S Aulchenko, Chris S Haley and Dirk-Jan de Koning

    Citation: BMC Proceedings 2007 1(Suppl 1):S144

    Content type: Proceedings

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

  7. In this report, we focused on the multiplicity issue in Problem 1 of Genetic Analysis Workshop 15. We investigated and compared the performance of the stratified false-discovery rate control method with the tr...

    Authors: Baisong Huang, Jagadish Rangrej, Andrew D Paterson and Lei Sun

    Citation: BMC Proceedings 2007 1(Suppl 1):S142

    Content type: Proceedings

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

  8. Multiple testing is a problem in genome-wide or region-wide association studies. In this report, we consider a study design given by the Genetic Analysis Workshop 15 (GAW15) Problem 3 – nuclear families (paren...

    Authors: Xuexia Wang, Zhaogong Zhang, Shuanglin Zhang and Qiuying Sha

    Citation: BMC Proceedings 2007 1(Suppl 1):S140

    Content type: Proceedings

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

  9. The incorporation of disease-associated covariates into studies aiming to identify susceptibility genes for complex human traits is a challenging problem. Accounting for such covariates in genetic linkage and ...

    Authors: Mike Schmidt, Xuejun Qin, Eden R Martin, Elizabeth R Hauser and Silke Schmidt

    Citation: BMC Proceedings 2007 1(Suppl 1):S138

    Content type: Proceedings

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

  10. Large-scale genome-wide association studies are increasingly common, due in large part to recent advances in genotyping technology. Despite a dramatic drop in genotyping costs, it is still too expensive to gen...

    Authors: Jing Li

    Citation: BMC Proceedings 2007 1(Suppl 1):S136

    Content type: Proceedings

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

  11. Genome-wide association studies raise study-design and analytical issues that are still being debated. Among them, stands the issue of reducing the number of markers to be genotyped without loss of efficiency ...

    Authors: Hugues Aschard, Mickaël Guedj and Florence Demenais

    Citation: BMC Proceedings 2007 1(Suppl 1):S134

    Content type: Proceedings

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

  12. We have developed a graphical display tool called SIMLAPLOT for visualizing different ways in which continuous covariates may influence the genotype-specific risk for complex human diseases. The purpose of our...

    Authors: Xuejun Qin, Silke Schmidt, Eden Martin and Elizabeth R Hauser

    Citation: BMC Proceedings 2007 1(Suppl 1):S132

    Content type: Proceedings

    Published on:

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

  13. Measuring the association of haplotype similarities with phenotype similarities has been used to develop statistical tests of genetic association. Previously, we applied the general approach of Mantel statisti...

    Authors: Vivien Marquard, Lars Beckmann, Justo L Bermejo, Christine Fischer and Jenny Chang-Claude

    Citation: BMC Proceedings 2007 1(Suppl 1):S128

    Content type: Proceedings

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

  14. The nuclear factor-kappaB (NF-κB) family of transcription factors regulates the expression of a variety of genes involved in apoptosis and immune response. We examined relationships between genotypes at five N...

    Authors: Wen Liu-Mares, Zhifu Sun, William R Bamlet, Elizabeth J Atkinson, Brooke L Fridley, Susan L Slager, Mariza de Andrade and Ellen L Goode

    Citation: BMC Proceedings 2007 1(Suppl 1):S126

    Content type: Proceedings

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

  15. Non-inherited maternal antigens encoded by specific HLA-DRB1 alleles (NIMA) have been implicated as a rheumatoid arthritis (RA) risk factor. Using genotype data from North American Rheumatoid Arthritis Consortium...

    Authors: Hsin-Ju Hsieh, Christina GS Palmer, Sinead Harney, Hsiu-Wen Chen, Lara Bauman, Matthew A Brown and Janet S Sinsheimer

    Citation: BMC Proceedings 2007 1(Suppl 1):S124

    Content type: Proceedings

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

  16. Inter-individual variation in gene expression levels can arise as an effect of variation in DNA markers. When associating multiple gene expression variables with multiple DNA marker variables, multivariate tec...

    Authors: Sandra Waaijenborg and Aeilko H Zwinderman

    Citation: BMC Proceedings 2007 1(Suppl 1):S122

    Content type: Proceedings

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

  17. Rheumatoid arthritis is a complex disease that appears to involve multiple genetic and environmental factors. Using the Genetic Analysis Workshop 15 simulated rheumatoid arthritis data and the structural equat...

    Authors: Nora L Nock, Emma K Larkin, Nathan J Morris, Yali Li and Catherine M Stein

    Citation: BMC Proceedings 2007 1(Suppl 1):S118

    Content type: Proceedings

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

  18. Rheumatoid arthritis (RA) is a chronic, complex autoimmune inflammatory disorder with poorly known etiology. Approximately 1% of the adult population is afflicted with RA. Linkage analysis of RA can be complic...

    Authors: Desh Deep Mandhyan, Xana Kim-Howard, Matthew Gaines and Swapan K Nath

    Citation: BMC Proceedings 2007 1(Suppl 1):S101

    Content type: Proceedings

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

  19. Parametric linkage methods for quantitative trait locus mapping require explicit specification of the probability model of the quantitative trait and hence can lead to misleading linkage inferences when the mo...

    Authors: Saurabh Ghosh, P Samba Siva Rao, Gourab De and Partha P Majumder

    Citation: BMC Proceedings 2007 1(Suppl 1):S99

    Content type: Proceedings

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

  20. We performed linkage analysis on families with rheumatoid arthritis, stratifying by ethnic origin. We compared results using either Kong and Cox nonparametric LOD scores or MOD score analysis using the softwar...

    Authors: Wei V Chen, Christopher I Amos, Carol J Etzel, Sanjay Shete and Peter K Gregersen

    Citation: BMC Proceedings 2007 1(Suppl 1):S97

    Content type: Proceedings

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

  21. The COMT and DBH genes are physically located at chromosomes 22q11 and 9q34, respectively, and both COMT and DBH are involved in catecholamine metabolism and are strong candidates for certain psychiatric and neur...

    Authors: Chao Xing, Monica Torres-Caban, Tao Wang, Qing Lu, Guan Xing and Robert C Elston

    Citation: BMC Proceedings 2007 1(Suppl 1):S95

    Content type: Proceedings

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

  22. We performed multipoint linkage analyses with multiple programs and models for several gene expression traits in the Centre d'Etude du Polymorphisme Humain families. All analyses provided consistent results fo...

    Authors: Yun Ju Sung, Yanming Di, Audrey Q Fu, Joseph H Rothstein, Weiva Sieh, Liping Tong, Elizabeth A Thompson and Ellen M Wijsman

    Citation: BMC Proceedings 2007 1(Suppl 1):S93

    Content type: Proceedings

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

  23. A new method for constructing confidence intervals for the location of putative genes regulating expression levels (quantitative traits) is proposed. This method is suitable for the "intermediate" fine-mapping...

    Authors: Charalampos Papachristou, Mark Abney and Shili Lin

    Citation: BMC Proceedings 2007 1(Suppl 1):S91

    Content type: Proceedings

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

  24. We used the Genetic Analysis Workshop 15 Problem 1 data set to search for expression phenotype quantitative trait loci in a highly selected group of genes with a supposedly correlated role in the development o...

    Authors: Francesca Lantieri, Halfdan Rydbeck, Paola Griseri, Isabella Ceccherini and Marcella Devoto

    Citation: BMC Proceedings 2007 1(Suppl 1):S89

    Content type: Proceedings

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

  25. Recently, gene expression levels have been shown to demonstrate familial aggregation, suggesting a direct role of heritable DNA variation. We studied the gene expression levels in lymphoblastoid cells of the C...

    Authors: Donghui Kan, Richard Cooper and Xiaofeng Zhu

    Citation: BMC Proceedings 2007 1(Suppl 1):S87

    Content type: Proceedings

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

  26. In order to identify regulatory genes, we determined the heritability of gene transcripts, performed linkage analysis to identify quantitative trait loci (QTLs), and evaluated the evidence for shared genetic e...

    Authors: Nora Franceschini, Mary K Wojczynski, Harald HH Göring, Juan Manuel Peralta, Thomas D Dyer, Xia Li, Hao Li and Kari E North

    Citation: BMC Proceedings 2007 1(Suppl 1):S85

    Content type: Proceedings

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

  27. The identification of susceptibility genes for common, chronic disease presents great challenges. The development of novel statistical and computational methodologies to help identify these genes is an area of...

    Authors: Marylyn D Ritchie, Jacquelaine Bartlett, William S Bush, Todd L Edwards, Alison A Motsinger and Eric S Torstenson

    Citation: BMC Proceedings 2007 1(Suppl 1):S70

    Content type: Proceedings

    Published on:

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

  28. Non-parametric linkage methods have had limited success in detecting gene by gene interactions. Using affected sibling-pair (ASP) data from all replicates of the simulated data from Problem 3, we assessed the ...

    Authors: Emma K Larkin, Nathan J Morris, Yali Li, Nora L Nock and Catherine M Stein

    Citation: BMC Proceedings 2007 1(Suppl 1):S66

    Content type: Proceedings

    Published on:

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

  29. When two genes interact to cause a clinically important phenotype, it would seem reasonable to expect that we could leverage genotypic information at one of the loci in order to improve our ability to detect t...

    Authors: Yungui Huang, Christopher W Bartlett, Alberto M Segre, Jeffrey R O'Connell, LaVonne Mangin and Veronica J Vieland

    Citation: BMC Proceedings 2007 1(Suppl 1):S64

    Content type: Proceedings

    Published on:

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

  30. Using the North American Rheumatoid Arthritis Consortium (NARAC) candidate gene and genome-wide single-nucleotide polymorphism (SNP) data sets, we applied regression methods and tree-based random forests to id...

    Authors: Yan V Sun, Zhaohui Cai, Kaushal Desai, Rachael Lawrance, Richard Leff, Ansar Jawaid, Sharon LR Kardia and Huiying Yang

    Citation: BMC Proceedings 2007 1(Suppl 1):S62

    Content type: Proceedings

    Published on:

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

  31. The Genetic Analysis Workshop 15 Problem 3 simulated rheumatoid arthritis data set provided 100 replicates of simulated single-nucleotide polymorphism (SNP) and covariate data sets for 1500 families with an af...

    Authors: Weiliang Shi, Kristine E Lee and Grace Wahba

    Citation: BMC Proceedings 2007 1(Suppl 1):S60

    Content type: Proceedings

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

  32. Risk of complex disorders is thought to be multifactorial, involving interactions between risk factors. However, many genetic studies assess association between disease status and markers one single-nucleotide...

    Authors: Kristin K Nicodemus, Wenyi Wang and Yin Yao Shugart

    Citation: BMC Proceedings 2007 1(Suppl 1):S58

    Content type: Proceedings

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

  33. We used the simulated data set from Genetic Analysis Workshop 15 Problem 3 to assess a two-stage approach for identifying single-nucleotide polymorphisms (SNPs) associated with rheumatoid arthritis (RA). In th...

    Authors: Yan Meng, Qiong Yang, Karen T Cuenco, L Adrienne Cupples, Anita L DeStefano and Kathryn L Lunetta

    Citation: BMC Proceedings 2007 1(Suppl 1):S56

    Content type: Proceedings

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

  34. Using parametric and nonparametric techniques, our study investigated the presence of single locus and pairwise effects between 20 markers of the Genetic Analysis Workshop 15 (GAW15) North American Rheumatoid ...

    Authors: Beate Glaser, Ivan Nikolov, Daniel Chubb, Marian L Hamshere, Ricardo Segurado, Valentina Moskvina and Peter Holmans

    Citation: BMC Proceedings 2007 1(Suppl 1):S54

    Content type: Proceedings

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

  35. 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

    Content type: Proceedings

    Published on:

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

  36. 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

    Content type: Proceedings

    Published on:

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

  37. Performing linkage and association analyses on a large set of correlated data presents an interesting set of problems. In the current setting, we have 3554 expression levels from lymphoblastoid cell lines in 1...

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

    Citation: BMC Proceedings 2007 1(Suppl 1):S46

    Content type: Proceedings

    Published on:

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

  38. We performed a case-control association analysis of rheumatoid arthritis (RA) for several candidate genes using the North American Rheumatoid Arthritis Consortium (NARAC) data provided in Genetic Analysis Work...

    Authors: Yun Joo Yoo, Guimin Gao and Kui Zhang

    Citation: BMC Proceedings 2007 1(Suppl 1):S33

    Content type: Proceedings

    Published on:

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

  39. The goal of this analysis is to compare different test strategies for genetic association in case-control studies using related individuals. The first test is the trend test that is corrected for related indiv...

    Authors: Xin Tian, Jungnam Joo, Colin O Wu and Jing-Ping Lin

    Citation: BMC Proceedings 2007 1(Suppl 1):S31

    Content type: Proceedings

    Published on:

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

  40. 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

    Content type: Proceedings

    Published on:

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

  41. 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

    Content type: Proceedings

    Published on:

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

  42. 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

    Content type: Proceedings

    Published on:

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

  43. 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

    Content type: Proceedings

    Published on:

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

  45. Rheumatoid arthritis (RA) is an autoimmune disease with a moderately strong genetic component. Previous linkage and candidate gene studies have identified several regions that predispose to RA, including the HLA-...

    Authors: Zhi Wei and Mingyao Li

    Citation: BMC Proceedings 2007 1(Suppl 1):S19

    Content type: Proceedings

    Published on:

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

  46. 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

    Content type: Proceedings

    Published on:

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

  47. 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

    Content type: Proceedings

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

  48. 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

    Content type: Proceedings

    Published on:

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

  49. 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

    Content type: Proceedings

    Published on:

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

  50. 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

    Content type: Proceedings

    Published on:

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

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