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  1. Genome-wide association studies, which analyzes hundreds of thousands of single-nucleotide polymorphisms to identify disease susceptibility genes, are challenging because the work involves intensive computatio...

    Authors: Hsin-Chou Yang, Yu-Jen Liang, Chia-Min Chung, Jia-Wei Chen and Wen-Harn Pan
    Citation: BMC Proceedings 2009 3(Suppl 7):S135
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  2. In this paper we test for association between copy number variation and diabetes in a subset of individuals from the Framingham Heart Study. We used the 500 k SNP data and called copy number variation using tw...

    Authors: Corina Shtir, Roger Pique-Regi, Kim Siegmund, John Morrison, Fredrick Schumacher and Paul Marjoram
    Citation: BMC Proceedings 2009 3(Suppl 7):S133
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  3. Established loci for rheumatoid arthritis (RA), including HLA-DRB1 and PTPN22, do not fully account for the genetic component of susceptibility to the disease. One possible source of as yet undiscovered susceptib...

    Authors: Andrew P Morris, Eleftheria Zeggini and Cecilia M Lindgren
    Citation: BMC Proceedings 2009 3(Suppl 7):S131
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  4. Multivariate techniques are an important area of investigation for studying contributions of multiple genetic variants to disease onset and pathology. We analyzed the Genetic Analysis Workshop 16 North America...

    Authors: Mary Helen Black and Richard M Watanabe
    Citation: BMC Proceedings 2009 3(Suppl 7):S129
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  5. Due to the high-dimensionality of single-nucleotide polymorphism (SNP) data, region-based methods are an attractive approach to the identification of genetic variation associated with a certain phenotype. A co...

    Authors: Jennifer L Asimit, Yun Joo Yoo, Daryl Waggott, Lei Sun and Shelley B Bull
    Citation: BMC Proceedings 2009 3(Suppl 7):S127
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  6. Both imprinting and maternal effects could lead to parent-of-origin patterns in complex traits of human disorders. Statistical methods that differentiate these two effects and identify them simultaneously by u...

    Authors: Jingyuan Yang and Shili Lin
    Citation: BMC Proceedings 2009 3(Suppl 7):S125
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  7. We investigated efficient case-control association analysis using family data. The outcome of interest was coronary heart disease. We employed existing and new methods that take into account the correlations a...

    Authors: Hae-Won Uh, Henk Jan van der Wijk and Jeanine J Houwing-Duistermaat
    Citation: BMC Proceedings 2009 3(Suppl 7):S123
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  8. The Framingham Heart Study is a well known longitudinal cohort study. In recent years, the community-based Framingham Heart Study has embarked on genome-wide association studies. In this paper, we present a Fr...

    Authors: Wensheng Zhu, Kelly Cho, Xiang Chen, Meizhuo Zhang, Minghui Wang and Heping Zhang
    Citation: BMC Proceedings 2009 3(Suppl 7):S119
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  9. We examined the properties of growth mixture modeling in finding longitudinal quantitative trait loci in a genome-wide association study. Two software packages are commonly used in these analyses: Mplus and th...

    Authors: Su-Wei Chang, Seung Hoan Choi, Ke Li, Rose Saint Fleur, Chengrui Huang, Tong Shen, Kwangmi Ahn, Derek Gordon, Wonkuk Kim, Rongling Wu, Nancy R Mendell and Stephen J Finch
    Citation: BMC Proceedings 2009 3(Suppl 7):S112
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  10. It is well known that conventional association tests can lead to excessive false positives when there is population stratification. We propose a new test for detecting genetic association with a case-control s...

    Authors: Yufang Zhang, Xiangjun Xiao and Kai Wang
    Citation: BMC Proceedings 2009 3(Suppl 7):S111
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  11. Population structure occurs when a sample is composed of individuals with different ancestries and can result in excess type I error in genome-wide association studies. Genome-wide principal-component analysis...

    Authors: Gina M Peloso, Nadia Timofeev and Kathryn L Lunetta
    Citation: BMC Proceedings 2009 3(Suppl 7):S108
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  12. To overcome the "spurious" association caused by population stratification in population-based association studies, we propose a principal-component based method that can use both family and unrelated samples ...

    Authors: Qingfu Feng, Joseph Abraham, Tao Feng, Yeunjoo Song, Robert C Elston and Xiaofeng Zhu
    Citation: BMC Proceedings 2009 3(Suppl 7):S104
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  13. We explored the utility of population- and pedigree-based analyses using the Framingham Heart Study genome-wide 50 k single-nucleotide polymorphism marker data provided for Genetic Analysis Workshop 16. Our ai...

    Authors: Elizabeth E Marchani, Yanming Di, Yoonha Choi, Charles Cheung, Ming Su, Frederick Boehm, Elizabeth A Thompson and Ellen M Wijsman
    Citation: BMC Proceedings 2009 3(Suppl 7):S102
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  14. Over the past decade, genetic analysis has shifted from linkage studies, which identify broad regions containing putative trait loci, to genome-wide association studies, which detect the association of a marke...

    Authors: Audrey E Hendricks, Yanyan Zhu and Josée Dupuis
    Citation: BMC Proceedings 2009 3(Suppl 7):S100
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  15. Recently, gene set analysis (GSA) has been extended from use on gene expression data to use on single-nucleotide polymorphism (SNP) data in genome-wide association studies. When GSA has been demonstrated on SN...

    Authors: Nathan L Tintle, Bryce Borchers, Marshall Brown and Airat Bekmetjev
    Citation: BMC Proceedings 2009 3(Suppl 7):S96
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  16. We describe an empirical Bayesian linear model for integration of functional gene annotation data with genome-wide association data. Using case-control study data from the North American Rheumatoid Arthritis C...

    Authors: Jérémie JP Lebrec, Tom WJ Huizinga, René EM Toes, Jeanine J Houwing-Duistermaat and Hans C van Houwelingen
    Citation: BMC Proceedings 2009 3(Suppl 7):S94
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  17. Gene identification using linkage, association, or genome-wide expression is often underpowered. We propose that formal combination of information from multiple gene-identification approaches may lead to the i...

    Authors: Jac C Charlesworth, Juan M Peralta, Eugene Drigalenko, Harald HH Göring, Laura Almasy, Thomas D Dyer and John Blangero
    Citation: BMC Proceedings 2009 3(Suppl 7):S92
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  18. Rheumatoid arthritis (RA) is three times more common in females than in males, suggesting that sex may play a role in modifying genetic associations with disease. We have addressed this hypothesis by performin...

    Authors: Joanna J Zhuang and Andrew P Morris
    Citation: BMC Proceedings 2009 3(Suppl 7):S90
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  19. Genome-wide association studies are often limited in their ability to attain their full potential due to the sheer volume of information created. We sought to use the random forest algorithm to identify single...

    Authors: Matthew J Maenner, Loren C Denlinger, Asher Langton, Kristin J Meyers, Corinne D Engelman and Halcyon G Skinner
    Citation: BMC Proceedings 2009 3(Suppl 7):S88
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  20. After more than 200 genome-wide association studies, there have been some successful identifications of a single novel locus. Thus, the identification of single-nucleotide polymorphisms (SNP) with interaction ...

    Authors: Jia Li, Rui Tang, Joanna M Biernacka and Mariza de Andrade
    Citation: BMC Proceedings 2009 3(Suppl 7):S78
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  21. Knowledge of simulated genetic effects facilitates interpretation of methodological studies. Genetic interactions for common disorders are likely numerous and weak. Using the 200 replicates of the Genetic Anal...

    Authors: Ilija P Kovac and Marie-Pierre Dubé
    Citation: BMC Proceedings 2009 3(Suppl 7):S77
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  22. Rheumatoid arthritis (RA, MIM 180300) is a chronic and complex autoimmune disease. Using the North American Rheumatoid Arthritis Consortium (NARAC) data set provided in Genetic Analysis Workshop 16 (GAW16), we...

    Authors: Chien-Hsun Huang, Lei Cong, Jun Xie, Bo Qiao, Shaw-Hwa Lo and Tian Zheng
    Citation: BMC Proceedings 2009 3(Suppl 7):S75
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  23. Fifteen known type 2 diabetes (T2D) gene variants were assessed for their associations with T2D status in 228 T2D families from the Framingham Heart Study (FHS) Original, Offspring, and Children Cohorts. Bayes...

    Authors: Ping An, Mary Feitosa, Shamika Ketkar, Avril Adelman, Shiow Lin, Ingrid Borecki and Michael Province
    Citation: BMC Proceedings 2009 3(Suppl 7):S71
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  24. Random forest is an efficient approach for investigating not only the effects of individual markers on a trait but also the effect of the interactions among the markers in genetic association studies. This app...

    Authors: Minghui Wang, Xiang Chen, Meizhuo Zhang, Wensheng Zhu, Kelly Cho and Heping Zhang
    Citation: BMC Proceedings 2009 3(Suppl 7):S69
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  25. Using the North American Rheumatoid Arthritis Consortium genome-wide association dataset, we applied ridged, multiple least-squares regression to identify genetic variants with apparent unique contributions to...

    Authors: Yan V Sun, Kerby A Shedden, Ji Zhu, Nam-Hee Choi and Sharon LR Kardia
    Citation: BMC Proceedings 2009 3(Suppl 7):S67
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  26. Genome-wide association studies (GWAS) have helped to reveal genetic mechanisms of complex diseases. Although commonly used genotyping technology enables us to determine up to a million single-nucleotide polym...

    Authors: Daniel F Schwarz, Silke Szymczak, Andreas Ziegler and Inke R König
    Citation: BMC Proceedings 2009 3(Suppl 7):S65
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  27. The objective of this study was to detect interactions between relevant single-nucleotide polymorphisms (SNPs) associated with rheumatoid arthritis (RA). Data from Problem 1 of the Genetic Analysis Workshop 16...

    Authors: Oscar González-Recio, Evangelina López de Maturana, Andrés T Vega, Corinne D Engelman and Karl W Broman
    Citation: BMC Proceedings 2009 3(Suppl 7):S63
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  28. We applied a penalized regression approach to single-nucleotide polymorphisms in regions on chromosomes 1, 6, and 9 of the North American Rheumatoid Arthritis Consortium data. Results were compared with a stan...

    Authors: Pascal Croiseau and Heather J Cordell
    Citation: BMC Proceedings 2009 3(Suppl 7):S61
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  29. In genome-wide association studies, high-level statistical analyses rely on the validity of the called genotypes, and different genotype calling algorithms (GCAs) have been proposed. We compared the GCAs Bayes...

    Authors: Maren Vens, Arne Schillert, Inke R König and Andreas Ziegler
    Citation: BMC Proceedings 2009 3(Suppl 7):S59
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  30. We explored five sex-specific quality control filters in North American Rheumatoid Arthritis Consortium's Illumina 550 k datasets. Three X chromosome and three autosomal single-nucleotide polymorphisms flagged...

    Authors: Hua Ling, Kurt Hetrick, Joan E Bailey-Wilson and Elizabeth W Pugh
    Citation: BMC Proceedings 2009 3(Suppl 7):S57
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  31. Results from whole-genome association studies of many common diseases are now available. Increasingly, these are being incorporated into meta-analyses to increase the power to detect weak associations with mea...

    Authors: David Hadley and David P Strachan
    Citation: BMC Proceedings 2009 3(Suppl 7):S55
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  32. We used data reduction and clustering methods to identify five phenotypically homogeneous groups of study participants with similar profiles for cardiovascular disease risk factors. We constructed both qualita...

    Authors: Marsha Wilcox, Qingqin Li, Yu Sun, Paul Stang, Jesse Berlin and Dai Wang
    Citation: BMC Proceedings 2009 3(Suppl 7):S53
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  33. While recently performed genome-wide association studies have advanced the identification of genetic variants predisposing to type 2 diabetes (T2D), the potential application of these novel findings for diseas...

    Authors: Qing Lu, Yeunjoo Song, Xuefeng Wang, Sungho Won, Yuehua Cui and Robert C Elston
    Citation: BMC Proceedings 2009 3(Suppl 7):S49
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  34. Metabolic syndrome, by definition, is the manifestation of multiple, correlated metabolic impairments. It is known to have both strong environmental and genetic contributions. However, isolating genetic varian...

    Authors: Allison R Baker, Robert J Goodloe, Emma K Larkin, Dan J Baechle, Yeunjoo E Song, Lynette S Phillips and Courtney L Gray-McGuire
    Citation: BMC Proceedings 2009 3(Suppl 7):S42
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  35. Determining the most promising single-nucleotide polymorphisms (SNPs) presents a challenge in genome-wide association studies, when hundreds of thousands of association tests are conducted. The power to detect...

    Authors: Meredith E Tabangin, Jessica G Woo and Lisa J Martin
    Citation: BMC Proceedings 2009 3(Suppl 7):S41
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  36. After performing a genome-wide association study, it is often difficult to know which regions to follow up, especially when no one marker reaches genome-wide significance. Researchers frequently focus on their...

    Authors: Nathan D Pankratz
    Citation: BMC Proceedings 2009 3(Suppl 7):S39
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  37. Genome-wide association studies often involve testing hundreds of thousands of single-nucleotide polymorphisms (SNPs). These tests may be highly correlated because of linkage disequilibrium among SNPs. Multipl...

    Authors: Guolian Kang, Douglas K Childers, Nianjun Liu, Kui Zhang and Guimin Gao
    Citation: BMC Proceedings 2009 3(Suppl 7):S38
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  38. The importance of considering confounding due to population stratification in genome-wide association analysis using case-control designs has been a source of debate. Armitage's trend test, together with some ...

    Authors: Yixin Fang, Yuanjia Wang and Nanshi Sha
    Citation: BMC Proceedings 2009 3(Suppl 7):S37
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  39. We performed a whole-genome association study of rheumatoid arthritis susceptibility using Illumina 550k single-nucleotide polymorphism (SNP) genotypes of 868 cases and 1194 controls from the North American Rh...

    Authors: Kimberly E Taylor and Lindsey A Criswell
    Citation: BMC Proceedings 2009 3(Suppl 7):S36
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  40. Recent genome-wide association studies on several complex diseases have focused on individual single-nucleotide polymorphism (SNP) analysis; however, not many studies have reported interactions among genes per...

    Authors: Jungsun Park, Junghyun Namkung, Mina Jhun and Taesung Park
    Citation: BMC Proceedings 2009 3(Suppl 7):S34
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  41. In genome-wide association studies, new schemes are needed to incorporate multiple-locus information. In this article, we proposed a two-stage sliding-window approach to detect associations between a disease a...

    Authors: Xuexia Wang, Huaizhen Qin and Qiuying Sha
    Citation: BMC Proceedings 2009 3(Suppl 7):S28
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  42. Most genetic association studies only genotype a small proportion of cataloged single-nucleotide polymorphisms (SNPs) in regions of interest. With the catalogs of high-density SNP data available (e.g., HapMap)...

    Authors: Douglas K Childers, Guolian Kang, Nianjun Liu, Guimin Gao and Kui Zhang
    Citation: BMC Proceedings 2009 3(Suppl 7):S24
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  43. Population stratification is one of the major causes of spurious associations in association studies. A unified association approach based on principal-component analysis can overcome the effect of population ...

    Authors: Xiangqing Sun, Tao Feng, Yeunjoo Song, Robert C Elston and Xiaofeng Zhu
    Citation: BMC Proceedings 2009 3(Suppl 7):S22
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  44. Genetic association of population-based quantitative trait data has traditionally been analyzed using analysis of variance (ANOVA). However, violations of certain statistical assumptions may lead to false-posi...

    Authors: Saurabh Ghosh, Krishna Rao Sanapala, Abhik Ghosh and Sujatro Chakladar
    Citation: BMC Proceedings 2009 3(Suppl 7):S18
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  45. Single-locus analysis is often used to analyze genome-wide association (GWA) data, but such analysis is subject to severe multiple comparisons adjustment. Multivariate logistic regression is proposed to fit a ...

    Authors: Yuanjia Wang, Nanshi Sha and Yixin Fang
    Citation: BMC Proceedings 2009 3(Suppl 7):S16
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  46. With the recent rapid improvements in high-throughout genotyping techniques, researchers are facing a very challenging task of large-scale genetic association analysis, especially at the whole-genome level, wi...

    Authors: Qiuying Sha, Rui Tang and Shuanglin Zhang
    Citation: BMC Proceedings 2009 3(Suppl 7):S14
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  47. We have conducted a genome-wide association study on the Genetic Analysis Workshop (GAW) 16 rheumatoid arthritis data using a multilocus score test based on wavelet transform proposed recently by the authors. ...

    Authors: Renfang Jiang, Jianping Dong and Yilin Dai
    Citation: BMC Proceedings 2009 3(Suppl 7):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  48. We performed a genome-wide association scan on the North American Rheumatoid Arthritis Consortium (NARAC) data using Hotelling's T2 tests, i.e., T H based on allele coding and T ...

    Authors: Lianfu Chen, Ming Zhong, Wei Vivien Chen, Christopher I Amos and Ruzong Fan
    Citation: BMC Proceedings 2009 3(Suppl 7):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  49. The Genetic Analysis Workshop (GAW) 16 Problem 3 comprises simulated phenotypes emulating the lipid domain and its contribution to cardiovascular disease risk. For each replication there were 6,476 subjects in...

    Authors: Aldi T Kraja, Robert Culverhouse, E Warwick Daw, Jun Wu, Andrew Van Brunt, Michael A Province and Ingrid B Borecki
    Citation: BMC Proceedings 2009 3(Suppl 7):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

  50. For Genetic Analysis Workshop 16 Problem 1, we provided data for genome-wide association analysis of rheumatoid arthritis. Single-nucleotide polymorphism (SNP) genotype data were provided for 868 cases and 119...

    Authors: Christopher I Amos, Wei Vivien Chen, Michael F Seldin, Elaine F Remmers, Kimberly E Taylor, Lindsey A Criswell, Annette T Lee, Robert M Plenge, Daniel L Kastner and Peter K Gregersen
    Citation: BMC Proceedings 2009 3(Suppl 7):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 3 Supplement 7

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