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  1. We studied the impact of marker density on the accuracy of association mapping using Genetic Analysis Workshop 15 simulated dense single-nucleotide polymorphism (SNP) data on chromosome 6. A total of 1500 case...

    Authors: Weihua Zhang, Winston Lau, Cheng Hu and Tai-Yue Kuo
    Citation: BMC Proceedings 2007 1(Suppl 1):S166

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

  2. We apply an analysis based upon mixed-models to the Genetic Analysis Workshop 15, Problem 3 simulated data. Such models are commonly used to mitigate the tendency for population structure, or cryptic relatedne...

    Authors: Keyan Zhao, Magnus Nordborg and Paul Marjoram
    Citation: BMC Proceedings 2007 1(Suppl 1):S164

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

  3. While high-throughput genotyping technologies are becoming readily available, the merit of using these technologies to perform genome-wide association studies has not been established. One major concern is tha...

    Authors: Hua Tang, Jie Peng, Pei Wang, Marc Coram and Li Hsu
    Citation: BMC Proceedings 2007 1(Suppl 1):S162

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

  4. It has recently become possible to screen thousands of markers to detect genetic causes of common diseases. Along with this potential comes analytical challenges, and it is important to develop new statistical...

    Authors: Po-Hsiu Kuo, József Bukszár and Edwin JCG van den Oord
    Citation: BMC Proceedings 2007 1(Suppl 1):S143

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

  5. With the availability of very dense genome-wide maps of markers, multiple testing has become a major difficulty for genetic studies. In this context, the false-discovery rate (FDR) and related criteria are wid...

    Authors: Cyril Dalmasso, Joseph Pickrell, Marianne Tuefferd, Emmanuelle Génin, Catherine Bourgain and Philippe Broët
    Citation: BMC Proceedings 2007 1(Suppl 1):S141

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

  6. Genetic association studies offer an opportunity to find genetic variants underlying complex human diseases. Various tests have been developed to improve their power. However, none of these tests is uniformly ...

    Authors: Tao Wang, Qing Lu, Monica Torres-Caban and Robert C Elston
    Citation: BMC Proceedings 2007 1(Suppl 1):S139

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

  7. Finding a genetic marker associated with a trait is a classic problem in human genetics. Recently, two-stage approaches have gained popularity in marker-trait association studies, in part because researchers h...

    Authors: Rori V Rohlfs, Chelsea Taylor, Lucia Mirea, Shelley B Bull, Mary Corey and Amy D Anderson
    Citation: BMC Proceedings 2007 1(Suppl 1):S137

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

  8. Large genetic association studies based on hundreds of thousands of single-nucleotide polymorphisms (SNPs) are a popular option for the study of complex diseases. The evaluation of gene × gene interactions in ...

    Authors: Amina Barhdadi and Marie-Pierre Dubé
    Citation: BMC Proceedings 2007 1(Suppl 1):S135

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

  9. Among the various linkage-disequilibrium (LD) fine-mapping methods, two broad classes have received considerable development recently: those based on coalescent theory and those based on haplotype clustering. ...

    Authors: Sungho Won, Ritwik Sinha and Yuqun Luo
    Citation: BMC Proceedings 2007 1(Suppl 1):S133

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

  10. This paper presents a novel method of identifying phenotypically important regions of the genome. It involves a form of association mapping that works by summarizing properties of the ancestral recombination g...

    Authors: Alexander Platt
    Citation: BMC Proceedings 2007 1(Suppl 1):S131

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

  11. We propose two new haplotype-sharing methods for identifying disease loci: the haplotype sharing statistic (HSS), which compares length of shared haplotypes between cases and controls, and the CROSS test, whic...

    Authors: Ilja M Nolte, André R de Vries, Geert T Spijker, Ritsert C Jansen, Dumitru Brinza, Alexander Zelikovsky and Gerard J te Meerman
    Citation: BMC Proceedings 2007 1(Suppl 1):S129

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

  12. The goal of this study was to identify single-locus and epistasis effects of SNP markers on anti-cyclic citrullinated peptide (anti-CCP) that is associated with rheumatoid arthritis, using the North American R...

    Authors: Li Ma, Daniel Dvorkin, John R Garbe and Yang Da
    Citation: BMC Proceedings 2007 1(Suppl 1):S127

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

  13. Given the increasing size of modern genetic data sets and, in particular, the move towards genome-wide studies, there is merit in considering analyses that gain computational efficiency by being more heuristic...

    Authors: Hsuan Jung, Keyan Zhao and Paul Marjoram
    Citation: BMC Proceedings 2007 1(Suppl 1):S125

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

  14. Rheumatoid arthritis is a complex disease caused by a combination of genetic, environmental, and hormonal factors, and their additive and/or non-additive effects. We performed a linkage analysis to provide evi...

    Authors: Cheongeun Oh
    Citation: BMC Proceedings 2007 1(Suppl 1):S110

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

  15. We proposed a confidence interval method for disease gene localization by testing every position on each chromosome of interest for its possibility of being a disease locus and including those not rejected int...

    Authors: Shuyan Wan and Shili Lin
    Citation: BMC Proceedings 2007 1(Suppl 1):S106

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

  16. We have used the genome-wide marker genotypes from Genetic Analysis Workshop 15 Problem 2 to explore joint evidence for genetic linkage to rheumatoid arthritis across several samples. The data consisted of fou...

    Authors: Ricardo Segurado, Marian L Hamshere, Beate Glaser, Ivan Nikolov, Valentina Moskvina and Peter A Holmans
    Citation: BMC Proceedings 2007 1(Suppl 1):S104

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

  17. Rheumatoid arthritis is the most common systematic autoimmune disease and its etiology is believed to have both strong genetic and environmental components. We demonstrate the utility of including genetic and ...

    Authors: Marian L Hamshere, Ricardo Segurado, Valentina Moskvina, Ivan Nikolov, Beate Glaser and Peter A Holmans
    Citation: BMC Proceedings 2007 1(Suppl 1):S100

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

  18. Rheumatoid arthritis is a complex disease in which environmental factors interact with genetic factors that influence susceptibility. Incorporating information about related quantitative traits or environmenta...

    Authors: Yen-Feng Chiu, Jeng-Min Chiou, Yi-Shin Chen, Hui-Yi Kao and Fang-Chi Hsu
    Citation: BMC Proceedings 2007 1(Suppl 1):S98

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

  19. Genome scan meta-analysis (GSMA) can prove very useful in detecting genetic effects too small to be detected in an individual linkage study and can also lead to more consistent results. In this paper, we propo...

    Authors: Laurent Briollais, Gilles Durrieu and Ranodya Upathilake
    Citation: BMC Proceedings 2007 1(Suppl 1):S96

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

  20. Transcription activity 'hot spots', defined as chromosome regions that contain more expression quantitative trait loci than would have been expected by chance, have been frequently detected both in humans and ...

    Authors: Shuang Wang, Tian Zheng and Yuanjia Wang
    Citation: BMC Proceedings 2007 1(Suppl 1):S94

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

  21. Many traits differ by age and sex in humans, but genetic analysis of gene expression has typically not included them in the analysis.

    Authors: Jagadish Rangrej, Joseph Beyene, Pingzhao Hu and Andrew D Paterson
    Citation: BMC Proceedings 2007 1(Suppl 1):S92

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

  22. Recently, a number of different approaches have been used to examine variation in gene expression and to identify genes whose level of transcript differed greatly among unrelated individuals. Previous studies ...

    Authors: Eunjee Lee, Jung Hoon Woo, Ji Wan Park and Taesung Park
    Citation: BMC Proceedings 2007 1(Suppl 1):S90

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

  23. The regulation of gene expression is an emerging area of investigation. Increased knowledge can deepen our understanding of the genetic contributions to variations in complex traits. The purpose of this study ...

    Authors: Berit Kerner, Julia N Bailey and Rita M Cantor
    Citation: BMC Proceedings 2007 1(Suppl 1):S88

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

  24. Gene expression, as a heritable complex trait, has recently been used in many genome-wide linkage studies. The estimated overall heritability of each trait may be considered as evidence of a genetic contributi...

    Authors: Song Huang, David Ballard and Hongyu Zhao
    Citation: BMC Proceedings 2007 1(Suppl 1):S86

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

  25. Accounting for interactions with environmental factors in association studies may improve the power to detect genetic effects and may help identifying important environmental effect modifiers. The power of unp...

    Authors: Astrid Dempfle, Rebecca Hein, Lars Beckmann, André Scherag, Thuy Trang Nguyen, Helmut Schäfer and Jenny Chang-Claude
    Citation: BMC Proceedings 2007 1(Suppl 1):S73

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

  26. Rheumatoid arthritis (RA) is a complex disease that involves both environmental and genetic factors. Elucidation of the basic etiologic factors involved in RA is essential for preventing and treating this dise...

    Authors: Yi-Shin Chen, Yen-Feng Chiu, Hui-Yi Kao and Fang-Chi Hsu
    Citation: BMC Proceedings 2007 1(Suppl 1):S71

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

  27. It is believed that epistatic interactions among loci contribute to variations in quantitative traits. Several methods are available to detect epistasis using population-based data. However, methods to charact...

    Authors: Hua Li, Guimin Gao, Jian Li, Grier P Page and Kui Zhang
    Citation: BMC Proceedings 2007 1(Suppl 1):S67

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

  28. We performed a genome-wide search for pairs of susceptibility loci that jointly contribute to rheumatoid arthritis in families recruited by the North American Rheumatoid Arthritis Consortium. A complete two-di...

    Authors: Jordana Tzenova Bell
    Citation: BMC Proceedings 2007 1(Suppl 1):S63

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

  29. Significant alterations of T-cell function, along with activation of the inflammatory response system, appear to be linked not only to treatment-resistant schizophrenia, but also to functional psychoses and mo...

    Authors: Hans H Stassen, Armin Szegedi and Christian Scharfetter
    Citation: BMC Proceedings 2007 1(Suppl 1):S61

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

  30. Genomic imprinting is a mechanism in which the expression of a gene copy depends upon the sex of the parent from which it was inherited. This mechanism is now well recognized in humans, and the deregulation of...

    Authors: Xiaojun Zhou, Wei Chen, Michael D Swartz, Yue Lu, Robert Yu, Christopher I Amos, Chih-Chieh Wu and Sanjay Shete
    Citation: BMC Proceedings 2007 1(Suppl 1):S53

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

  31. Several genetic determinants responsible for individual variation in gene expression have been located using linkage and association analyses. These analyses have revealed regulatory relationships between gene...

    Authors: Robert Yu, Kevin DeHoff, Christopher I Amos and Sanjay Shete
    Citation: BMC Proceedings 2007 1(Suppl 1):S51

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

  32. 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

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

  33. 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

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

  34. The simulated data set of the Genetic Analysis Workshop 15 provided affection status, four quantitative traits, and a covariate. After studying the relationship between these variables, linkage analysis was un...

    Authors: Nathan Pankratz
    Citation: BMC Proceedings 2007 1(Suppl 1):S30

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

  35. 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

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

  36. The transmission/disequilibrium test was introduced to test for linkage and association between a marker and a putative disease locus using case-parent triads. Several extensions have been proposed to accommod...

    Authors: Chao-Yu Guo
    Citation: BMC Proceedings 2007 1(Suppl 1):S26

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

  37. The presence of missing data in association studies is an important problem, particularly with high-density single-nucleotide polymorphism (SNP) maps, because the probability that at least one genotype is miss...

    Authors: Pascal Croiseau, Claire Bardel and Emmanuelle Génin
    Citation: BMC Proceedings 2007 1(Suppl 1):S24

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

  38. We recently described a new method to identify disease susceptibility loci, based on the analysis of the evolutionary relationships between haplotypes of cases and controls. However, haplotypes are often unkno...

    Authors: Claire Bardel, Pascal Croiseau and Emmanuelle Génin
    Citation: BMC Proceedings 2007 1(Suppl 1):S22

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

  39. 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

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

  40. 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

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

  41. 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

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

  42. 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

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

  43. 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

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

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