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Volume 1 Supplement 1

Genetic Analysis Workshop 15: Gene Expression Analysis and Approaches to Detecting Multiple Functional Loci

Proceedings

Genetic Analysis Workshop 15: Gene Expression Analysis and Approaches to Detecting Multiple Functional Loci. Go to conference site.

St. Pete Beach, Florida, USA11-15 November 2006

Page 3 of 4

  1. 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 Published on:

  2. Three LOD score statistics are often used for genome-wide linkage analysis: the maximum LOD score, the LOD score statistic proposed by Kong and Cox, both based on the allele-sharing between affected sib pairs,...

    Authors: Patricia Margaritte-Jeannin, Marie-Claude Babron and FranƧoise Clerget-Darpoux
    Citation: BMC Proceedings 2007 1(Suppl 1):S102
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  4. 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
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  5. We applied nonparametric quantitative trait linkage analysis to two rheumatoid arthritis quantitative phenotypes, IgM rheumatoid factor (RF) and anti-cyclic citrullinated peptide autoantibody titer measurement...

    Authors: Kimberly E Taylor, Wei Chen, Christopher I Amos and Lindsey A Criswell
    Citation: BMC Proceedings 2007 1(Suppl 1):S105
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  7. 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
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  9. 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
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  12. 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
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  14. 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
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  15. 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
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  16. 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
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  17. 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
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  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
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  20. 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
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  22. 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
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  23. 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
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  24. 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
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  26. The nuclear factor-kappaB (NF-ĪŗB) 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
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  27. 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
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  28. 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
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  29. 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, AndrƩ 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
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  30. Haplotypes are composed of specific combinations of alleles at the several loci on the same chromosome. Because haplotypes incorporate linkage disequilibrium (LD) information from multiple loci, haplotype-base...

    Authors: Sohee Oh and Taesung Park
    Citation: BMC Proceedings 2007 1(Suppl 1):S130
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  33. 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
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  37. 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
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  38. 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 Published on:

  40. 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 ā€“ nuclear families (paren...

    Authors: Xuexia Wang, Zhaogong Zhang, Shuanglin Zhang and Qiuying Sha
    Citation: BMC Proceedings 2007 1(Suppl 1):S140
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  41. 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 GƩnin, Catherine Bourgain and Philippe Broƫt
    Citation: BMC Proceedings 2007 1(Suppl 1):S141
    Content type: Proceedings Published on:

  42. 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
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  43. 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, JĆ³zsef BukszĆ”r and Edwin JCG van den Oord
    Citation: BMC Proceedings 2007 1(Suppl 1):S143
    Content type: Proceedings Published on:

  44. 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 Published on:

  45. Morley et al. (Nature 2004, 430:743ā€“747) detected significant linkages to the expression levels of 142 genes (of 3554) at a reported threshold of genome-wide p = 0.001 (LOD ā‰ˆ 5.3), using 14 three-generation Centr...

    Authors: Jianxin Shi, David O Siegmund and Douglas F Levinson
    Citation: BMC Proceedings 2007 1(Suppl 1):S145
    Content type: Proceedings Published on:

  47. 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
    Content type: Proceedings Published on:

  48. With technological advances in high-throughput genotyping, it is not unusual to perform hundreds of thousands of tests for each phenotype. Thus, correction to control type I error is essential. The false-disco...

    Authors: Meredith E Tabangin, Jessica G Woo, Chunyan Liu, Todd G Nick and Lisa J Martin
    Citation: BMC Proceedings 2007 1(Suppl 1):S148
    Content type: Proceedings Published on:

  49. 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
    Content type: Proceedings Published on:

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