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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

    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

    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

    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

    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

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

  6. To explore the mapping of factors regulating gene expression, we have carried out linkage studies using expression data from individual transcripts (from Affymetrix microarrays; Genetic Analysis Workshop 15 Pr...

    Authors: Jeanette N McClintick, Yunlong Liu and Howard J Edenberg
    Citation: BMC Proceedings 2007 1(Suppl 1):S155

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

  7. We evaluate the impact of three pre-processing methods for Affymetrix microarray data on expression quantitative trait locus (eQTL) mapping, using 14 CEPH Utah families (GAW Problem 1 data). Different sets of ...

    Authors: Aurelie Labbe, Marie-Paule Roth, Pierre-Hugues Carmichael and Maria Martinez
    Citation: BMC Proceedings 2007 1(Suppl 1):S153

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

  8. The goal of this paper is to investigate the effects of normalization procedures for expression data on linkage results. We selected the two most commonly used expression data extraction and normalization meth...

    Authors: Mariza de Andrade, Elizabeth J Atkinson, Brooke L Fridley, Ellen L Goode, Shannon McDonnell, Wen Liu-Mares, Kari G Rabe, Zhifu Sun and Susan L Slager
    Citation: BMC Proceedings 2007 1(Suppl 1):S151

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

  9. By applying an association test to analyze the data sets from Genetic Analysis Workshop 15 Problem 3, we compare power using different haplotype-block information. The results from using both of the two differ...

    Authors: Rui Tang, Fei Wang, Qiuying Sha, Shuanglin Zhang and Huann-Sheng Chen
    Citation: BMC Proceedings 2007 1(Suppl 1):S149

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

  10. A new type of test is presented for genome-wide association studies using a case-control design. It is referred to as the adaptive two-stage (ATS) analysis, being based on both the Hardy-Weinberg disequilibriu...

    Authors: Kijoung Song, Qing Lu, Xiwu Lin, Dawn Waterworth and Robert C Elston
    Citation: BMC Proceedings 2007 1(Suppl 1):S147

    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

    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

    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

    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

    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

    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

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

  17. We sought to i) identify putative genetic determinants of the severity of rheumatoid arthritis in the NARAC (North American Rheumatoid Arthritis Consortium) data, ii) assess whether known candidate genes for d...

    Authors: Rinku Sutradhar, Dushanthi Pinnaduwage and Shelley B Bull
    Citation: BMC Proceedings 2007 1(Suppl 1):S120

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

  18. 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

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

  19. We studied rheumatoid arthritis (RA) in the North American Rheumatoid Arthritis Consortium (NARAC) data (1499 subjects; 757 families). Identical methods were applied for studying RA in the Genetic Analysis Wor...

    Authors: Aldi T Kraja, Jon Corbett, An Ping, Rosa S Lin, Petra A Jacobsen, Michael Crosswhite, Ingrid B Borecki and Michael A Province
    Citation: BMC Proceedings 2007 1(Suppl 1):S116

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

  20. Our aim is to develop methods for identifying a (causal) variant or variants from a dense panel of single-nucleotide polymorphisms (SNPs) that are genotyped on the evidence of previous studies. Because a large...

    Authors: Hae-Won Uh, Bart JA Mertens, Henk Jan van der Wijk, Hein Putter, Hans C van Houwelingen and Jeanine J Houwing-Duistermaat
    Citation: BMC Proceedings 2007 1(Suppl 1):S114

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

  21. Although rheumatoid arthritis, a chronic and inflammatory disease affecting numerous adults, has a complex genetic component involving the human leukocyte antigen region, additional genomic regions most likely...

    Authors: Fredrick R Schumacher and Peter Kraft
    Citation: BMC Proceedings 2007 1(Suppl 1):S112

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

  22. The CEPH samples are an invaluable resource for mapping genes that contribute to traits that can be measured in cell lines. With the many markers that have already been genotyped for the Centre d'Etude du Poly...

    Authors: E Warwick Daw and Robert Yu
    Citation: BMC Proceedings 2007 1(Suppl 1):S108

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

  23. 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

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

  24. 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

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

  25. 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

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

  26. 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

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

  27. 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

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

  28. 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

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

  29. With the availability of high-throughput microarray technologies, investigators can simultaneously measure the expression levels of many thousands of genes in a short period. Although there are rich statistica...

    Authors: Guoqing Diao and DY Lin
    Citation: BMC Proceedings 2007 1(Suppl 1):S83

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

  30. The goal of this paper is to investigate the effect of using principal components as a data reduction method for expression data in linkage analysis. We used 45 probes normalized using the Affymetrix Global Sc...

    Authors: Elizabeth J Atkinson, Brooke L Fridley, Ellen L Goode, Shannon K McDonnell, Wen Liu-Mares, Kari G Rabe, Zhifu Sun, Susan L Slager and Mariza de Andrade
    Citation: BMC Proceedings 2007 1(Suppl 1):S79

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

  31. Clinical heterogeneity of a disease may reflect an underlying genetic heterogeneity, which may hinder the detection of trait loci. Consequently, many statistical methods have been developed that allow for the ...

    Authors: Hervé Perdry, Brion S Maher, Marie-Claude Babron, Toby McHenry, Françoise Clerget-Darpoux and Mary L Marazita
    Citation: BMC Proceedings 2007 1(Suppl 1):S77

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

  32. We incorporate population effects of sex and antibodies directed against cyclic citrullinated peptides (anti-CCP) into the linkage analysis of rheumatoid arthritis (RA) with microsatellites data provided by th...

    Authors: Jérémie JP Lebrec, Quinta Helmer, Iryna Nishchenko and Hans C van Houwelingen
    Citation: BMC Proceedings 2007 1(Suppl 1):S75

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

  33. Many genes with major effects on quantitative traits have been reported to interact with other genes. However, finding a group of interacting genes from thousands of SNPs is challenging. Hence, an efficient an...

    Authors: Junghyun Namkung, Jin-Wu Nam and Taesung Park
    Citation: BMC Proceedings 2007 1(Suppl 1):S69

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

  34. 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

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

  35. 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

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

  36. 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

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

  37. 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

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

  38. 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

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

  39. 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

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

  40. 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

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

  41. 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

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

  42. 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

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

  43. 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

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

  44. 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

    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

    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

    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

    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

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

  49. 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

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

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