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  1. 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

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

  2. 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

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

  3. 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

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

  4. "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

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

  5. 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

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

  6. 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

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

  7. 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

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

  8. 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

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

  9. 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

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

  10. 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

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

  11. 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

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

  12. 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

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

  13. 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

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

  14. 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

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

  15. 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

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

  16. 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

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

  17. 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

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

  18. 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

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

  19. 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

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

  20. 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

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

  21. 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

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

  22. 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

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

  23. 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

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

  24. 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

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

  25. 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

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

  26. 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

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

  27. 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

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

  28. 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

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

  29. 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

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

  30. 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

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

  31. 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

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

  32. 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

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

  33. 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

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

  34. 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

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

  35. 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

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

  36. 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

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

  37. 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

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

  38. 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

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

  39. 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

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

  40. 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

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

  41. 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

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

  42. 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

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

  43. 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

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

  44. 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

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

  45. 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

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

  46. 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

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

  47. 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

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

  48. 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

    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

    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

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

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