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  1. 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

    Content type: Proceedings

    Published on:

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

  2. 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

    Content type: Proceedings

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

  3. We performed a multipoint linkage analysis for rheumatoid arthritis (RA) using high-density single-nucleotide polymorphism (SNP) data for chromosome 6 and chromosome 21 using Genetic Analysis Workshop 15 (GAW1...

    Authors: Kristina Allen-Brady, Benjamin D Horne, Alka Malhotra, Craig Teerlink, Nicola J Camp and Alun Thomas

    Citation: BMC Proceedings 2007 1(Suppl 1):S160

    Content type: Proceedings

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

  4. We compared results from linkage analyses of different phenotype measurements from the same gene expression traits and found that the strongest signals were detected by all expression measures that we consider...

    Authors: Juan Manuel Peralta and Laura Almasy

    Citation: BMC Proceedings 2007 1(Suppl 1):S158

    Content type: Proceedings

    Published on:

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

  5. Variance-components and regression-based methods are frequently used to map quantitative trait loci. The normality of the trait values is usually assumed and violation of this assumption can have a detrimental...

    Authors: Bo Peng, Robert K Yu, Kevin L DeHoff and Christopher I Amos

    Citation: BMC Proceedings 2007 1(Suppl 1):S156

    Content type: Proceedings

    Published on:

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

  6. Several studies have been conducted to assess the influence of genetic variation on genome-wide gene expression profiles measured by the microarray technologies. Due to substantial noise in microarray-based ex...

    Authors: Jun Ma and Zhaohui S Qin

    Citation: BMC Proceedings 2007 1(Suppl 1):S154

    Content type: Proceedings

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

  7. "Genetical genomics", the study of natural genetic variation combining data from genetic marker-based studies with gene expression analyses, has exploded with the recent development of advanced microarray tech...

    Authors: Yoonhee Kim, Betty Q Doan, Priya Duggal and Joan E Bailey-Wilson

    Citation: BMC Proceedings 2007 1(Suppl 1):S152

    Content type: Proceedings

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

  8. Using the Problem 1 data set made available for Genetic Analysis Workshop 15, we assessed sensitivity of linkage results to a correlation-based feature extraction method as well as to different normalization p...

    Authors: Joseph Beyene, Pingzhao Hu, Elena Parkhomenko and David Tritchler

    Citation: BMC Proceedings 2007 1(Suppl 1):S150

    Content type: Proceedings

    Published on:

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

  9. Construction of precise confidence sets of disease gene locations after initial identification of linked regions can improve the efficiency of the ensuing fine mapping effort. We took the confidence set infere...

    Authors: Ritwik Sinha and Yuqun Luo

    Citation: BMC Proceedings 2007 1(Suppl 1):S146

    Content type: Proceedings

    Published on:

    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

    Content type: Proceedings

    Published on:

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

  11. 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

    Content type: Proceedings

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

  12. 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

    Content type: Proceedings

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

  13. We present a class of haplotype-sharing statistics useful for association mapping in case-parent trio data. The framework presented allows derivation of novel tests as well as new simplified variance estimator...

    Authors: Andrew S Allen and Glen A Satten

    Citation: BMC Proceedings 2007 1(Suppl 1):S123

    Content type: Proceedings

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

  14. When the number of phenotypes in a genetic study is on the scale of thousands, such as in studies concerning thousands of gene expression levels, the single-trait analysis is computationally intensive, and hea...

    Authors: Yuanjia Wang, Yixin Fang and Shuang Wang

    Citation: BMC Proceedings 2007 1(Suppl 1):S121

    Content type: Proceedings

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

  15. There is a growing interest in studying natural variation in human gene expression. Studies mapping genetic determinants of expression profiles are often carried out considering the expression of one gene at a...

    Authors: Elena Parkhomenko, David Tritchler and Joseph Beyene

    Citation: BMC Proceedings 2007 1(Suppl 1):S119

    Content type: Proceedings

    Published on:

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

  16. We explored approaches to using multiple related traits (gene expression levels) in linkage analysis. We first grouped mRNA transcripts according to their functions annotated in biological process of gene onto...

    Authors: Na Li, Baolin Wu, Peng Wei, Benhuai Xie, Yang Xie, Guanghua Xiao and Wei Pan

    Citation: BMC Proceedings 2007 1(Suppl 1):S117

    Content type: Proceedings

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

  17. Standard genetic mapping techniques scan chromosomal segments for location of genetic linkage and association signals. The majority of these methods consider only correlations at single markers and/or phenotyp...

    Authors: Kevin C Cartier, Lara Miscimarra, Jean-Eudes Dazard, Yeunjoo Song, Sudha K Iyengar and J Sunil Rao

    Citation: BMC Proceedings 2007 1(Suppl 1):S115

    Content type: Proceedings

    Published on:

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

  18. Bayesian methods continue to permeate genetic epidemiology investigations of genetic markers associated with or linked to causal genes for complex diseases. The attraction of these methods is an ability to cap...

    Authors: Michael D Swartz and Sanjay Shete

    Citation: BMC Proceedings 2007 1(Suppl 1):S113

    Content type: Proceedings

    Published on:

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

  19. We describe a hierarchical Bayes model for the influence of constitutional genotypes from a linkage scan on the expression of a large number of genes. The model comprises linear regression models for the means...

    Authors: Roger Pique-Regi, John Morrison and Duncan C Thomas

    Citation: BMC Proceedings 2007 1(Suppl 1):S111

    Content type: Proceedings

    Published on:

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

  20. Genome-wide association studies usually involve several hundred thousand of single-nucleotide polymorphisms (SNPs). Conventional approaches face challenges when there are enormous number of SNPs but a relative...

    Authors: Soonil Kwon, Dai Wang and Xiuqing Guo

    Citation: BMC Proceedings 2007 1(Suppl 1):S109

    Content type: Proceedings

    Published on:

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

  21. Rheumatoid arthritis is a clinically and genetically heterogeneous disease. Anti-cyclic citrullinated (anti-CCP) antibodies have a high specificity for rheumatoid arthritis and levels correlate with disease se...

    Authors: Xiaohong R Yang, Kimberly F Kerstann, Andrew W Bergen, Alisa M Goldstein and Lynn R Goldin

    Citation: BMC Proceedings 2007 1(Suppl 1):S107

    Content type: Proceedings

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

  22. 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

    Content type: Proceedings

    Published on:

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

  23. 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

    Content type: Proceedings

    Published on:

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

  24. 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

    Content type: Proceedings

    Published on:

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

  25. 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

    Content type: Proceedings

    Published on:

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

  26. The genetic factors underlying many complex traits are not well understood. The Genetic Analysis Workshop 15 Problem 1 data present the opportunity to explore whether gene expression data from microarrays can ...

    Authors: G Bryce Christensen, Lisa A Cannon-Albright, Alun Thomas and Nicola J Camp

    Citation: BMC Proceedings 2007 1(Suppl 1):S82

    Content type: Proceedings

    Published on:

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

  27. Heterogeneity poses a challenge to linkage mapping. Here, we apply a latent class extension of Haseman-Elston regression to expression phenotypes with significant evidence of linkage to trans regulators in 14 lar...

    Authors: Laurel A Bastone, Mary E Putt, Thomas R Ten Have, Vivian G Cheung and Richard S Spielman

    Citation: BMC Proceedings 2007 1(Suppl 1):S80

    Content type: Proceedings

    Published on:

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

  28. Focusing on chromosome 1, a recursive partitioning linkage algorithm (RP) was applied to perform linkage analysis on the rheumatoid arthritis NARAC data, incorporating covariates such as HLA-DRB1 genotype, age...

    Authors: Wei Xu, Hui Lan, Pingzhao Hu, Shelley B Bull and Celia MT Greenwood

    Citation: BMC Proceedings 2007 1(Suppl 1):S78

    Content type: Proceedings

    Published on:

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

  29. Understanding the genetic basis of human variation is an important goal of biomedical research. In this study, we used structural equation models (SEMs) to construct genetic networks to model how specific sing...

    Authors: Seungmook Lee, Mina Jhun, Eun-Kyung Lee and Taesung Park

    Citation: BMC Proceedings 2007 1(Suppl 1):S76

    Content type: Proceedings

    Published on:

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

  30. Identifying gene-environment (G × E) interactions has become a crucial issue in the past decades. Different methods have been proposed to test for G × E interactions in the framework of linkage or association ...

    Authors: Rémi Kazma, Marie-Hélène Dizier, Michel Guilloud-Bataille, Catherine Bonaïti-Pellié and Emmanuelle Génin

    Citation: BMC Proceedings 2007 1(Suppl 1):S74

    Content type: Proceedings

    Published on:

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

  31. The restricted partition method (RPM) provides a way to detect qualitative factors (e.g. genotypes, environmental exposures) associated with variation in quantitative or binary phenotypes, even if the contribu...

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

    Citation: BMC Proceedings 2007 1(Suppl 1):S72

    Content type: Proceedings

    Published on:

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

  32. Rheumatoid arthritis (RA) is a multifactorial disease with complex genetic etiology, about which little is known. Here, we apply a two-stage procedure in which a quick first-stage analysis was used to narrow d...

    Authors: Nandita Mukhopadhyay, Indrani Halder, Samsiddhi Bhattacharjee and Daniel E Weeks

    Citation: BMC Proceedings 2007 1(Suppl 1):S68

    Content type: Proceedings

    Published on:

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

  33. 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

    Content type: Proceedings

    Published on:

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

  34. 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

    Content type: Proceedings

    Published on:

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

  35. 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

    Content type: Proceedings

    Published on:

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

  36. 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

    Content type: Proceedings

    Published on:

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

  37. 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

    Content type: Proceedings

    Published on:

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

  38. 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

    Content type: Proceedings

    Published on:

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

  39. 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

    Content type: Proceedings

    Published on:

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

  40. 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

    Content type: Proceedings

    Published on:

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

  41. 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

    Content type: Proceedings

    Published on:

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

  42. We propose a nonparametric association analysis combining both family and unrelated case-control genotype data. Under the assumption of Hardy-Weinberg equilibrium, we formed an affected group to compare with a...

    Authors: Jun Zhang, Xiaofeng Zhu and Richard S Cooper

    Citation: BMC Proceedings 2007 1(Suppl 1):S35

    Content type: Proceedings

    Published on:

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

  43. 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

  44. 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

    Content type: Proceedings

    Published on:

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

  45. 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

    Content type: Proceedings

    Published on:

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

  46. PedGenie beta version 2.1 is a unique, flexible, and easily implemented analysis software tool that is enhanced significantly by incorporation of meta-statistics to allow valid combined analysis of multiple st...

    Authors: Karen Curtin, Jathine Wong, Kristina Allen-Brady and Nicola J Camp

    Citation: BMC Proceedings 2007 1(Suppl 1):S12

    Content type: Proceedings

    Published on:

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

  47. 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

    Content type: Proceedings

    Published on:

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

  48. 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

    Content type: Proceedings

    Published on:

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

  49. 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

    Content type: Proceedings

    Published on:

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

  50. While genome-wide linkage studies have been successful in mapping variants underlying rare monogenic disorders, genome-wide association studies may be more appropriate for detecting common variants of modest e...

    Authors: Gary K Chen, Eric Jorgenson and John S Witte

    Citation: BMC Proceedings 2007 1(Suppl 1):S5

    Content type: Proceedings

    Published on:

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

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