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  1. Using the exome sequencing data from 697 unrelated individuals and their simulated disease phenotypes from Genetic Analysis Workshop 17, we develop and apply a gene-based method to identify the relationship be...

    Authors: Yan V Sun, Wei Zhao, Kerby A Shedden and Sharon LR Kardia
    Citation: BMC Proceedings 2011 5(Suppl 9):S120
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  2. Genome-wide association studies have successfully identified many common variants associated with complex human diseases. However, a large portion of the remaining heritability cannot be explained by these com...

    Authors: Wan-Yu Lin, Boshao Zhang, Nengjun Yi, Guimin Gao and Nianjun Liu
    Citation: BMC Proceedings 2011 5(Suppl 9):S118
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  3. Principal components analysis (PCA) has been successfully used to correct for population stratification in genome-wide association studies of common variants. However, rare variants also have a role in common ...

    Authors: Hua He, Xue Zhang, Lili Ding, Tesfaye M Baye, Brad G Kurowski and Lisa J Martin
    Citation: BMC Proceedings 2011 5(Suppl 9):S116
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  4. Genome-wide association studies have been used successfully to detect associations between common genetic variants and complex diseases, but common single-nucleotide polymorphisms (SNPs) detected by these stud...

    Authors: Yilin Dai, Ling Guo, Jianping Dong and Renfang Jiang
    Citation: BMC Proceedings 2011 5(Suppl 9):S114
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  5. We develop statistical methods for detecting rare variants that are associated with quantitative traits. We propose two strategies and their combination for this purpose: the iterative regression strategy and ...

    Authors: Zhaogong Zhang, Qiuying Sha, Xinli Wang and Shuanglin Zhang
    Citation: BMC Proceedings 2011 5(Suppl 9):S112
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  6. Genome-wide association studies have been firmly established in investigations of the associations between common genetic variants and complex traits or diseases. However, a large portion of complex traits and...

    Authors: Yue S Niu, Ning Hao and Lingling An
    Citation: BMC Proceedings 2011 5(Suppl 9):S108
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  7. Both common variants and rare variants are involved in the etiology of most complex diseases in humans. Developments in sequencing technology have led to the identification of a high density of rare variant si...

    Authors: Ying Liu, Chien Hsun Huang, Inchi Hu, Shaw-Hwa Lo and Tian Zheng
    Citation: BMC Proceedings 2011 5(Suppl 9):S106
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  8. Machine learning approaches are an attractive option for analyzing large-scale data to detect genetic variants that contribute to variation of a quantitative trait, without requiring specific distributional as...

    Authors: Yoonhee Kim, Qing Li, Cheryl D Cropp, Heejong Sung, Juanliang Cai, Claire L Simpson, Brian Perry, Abhijit Dasgupta, James D Malley, Alexander F Wilson and Joan E Bailey-Wilson
    Citation: BMC Proceedings 2011 5(Suppl 9):S104
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  9. Existing methods for analyzing rare variant data focus on collapsing a group of rare variants into a single common variant; collapsing is based on an intuitive function of the rare variant genotype information...

    Authors: Yuan Jiang, Jennifer S Brennan, Rose Calixte, Yunxiao He, Epiphanie Nyirabahizi and Heping Zhang
    Citation: BMC Proceedings 2011 5(Suppl 9):S102
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  10. Recent advances in next-generation sequencing technologies have made it possible to generate large amounts of sequence data with rare variants in a cost-effective way. Statistical methods that test variants in...

    Authors: Aimin Yan, Nan M Laird and Cheng Li
    Citation: BMC Proceedings 2011 5(Suppl 9):S99
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  11. The upcoming release of new whole-genome genotyping technologies will shed new light on whether there is an associative effect of previously immeasurable rare variants on incidence of disease. For Genetic Anal...

    Authors: Jenna Sykes, Lu Cheng, Wei Xu, Ming-Sound Tsao, Geoffrey Liu and Melania Pintilie
    Citation: BMC Proceedings 2011 5(Suppl 9):S97
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  12. To enable the assessment of compound heterozygosity, we propose a simple approach for incorporating genotype phase in a rare variant collapsing procedure for the analysis of DNA sequence data. When multiple va...

    Authors: G Bryce Christensen and Christophe G Lambert
    Citation: BMC Proceedings 2011 5(Suppl 9):S95
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  13. Next-generation sequencing technologies are rapidly changing the field of genetic epidemiology and enabling exploration of the full allele frequency spectrum underlying complex diseases. Although sequencing te...

    Authors: Julio S Bueno Filho, Gota Morota, Quoc Tran, Matthew J Maenner, Lina M Vera-Cala, Corinne D Engelman and Kristin J Meyers
    Citation: BMC Proceedings 2011 5(Suppl 9):S93
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  14. Rare variants are believed to play an important role in disease etiology. Recent advances in high-throughput sequencing technology enable investigators to systematically characterize the genetic effects of bot...

    Authors: Ru Wang, Jie Peng and Pei Wang
    Citation: BMC Proceedings 2011 5(Suppl 9):S91
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  15. Genome-wide association studies have helped us identify thousands of common variants associated with several widespread complex diseases. However, for most traits, these variants account for only a small fract...

    Authors: Anbupalam Thalamuthu, Jingyuan Zhao, Garrett Teoh Hor Keong, Venkateswarlu Kondragunta and Indranil Mukhopadhyay
    Citation: BMC Proceedings 2011 5(Suppl 9):S89
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  16. We evaluate an approach to detect single-nucleotide polymorphisms (SNPs) that account for a linkage signal with covariate-based affected relative pair linkage analysis in a conditional-logistic model framework...

    Authors: Yeunjoo E Song, Junghyun Namkung, Robert W Shields, Daniel J Baechle, Sunah Song and Robert C Elston
    Citation: BMC Proceedings 2011 5(Suppl 9):S84
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  17. Genome-wide association studies have been successful in identifying common variants for common complex traits in recent years. However, common variants have generally failed to explain substantial proportions ...

    Authors: Gang Shi, Jeannette Simino and Dabeeru C Rao
    Citation: BMC Proceedings 2011 5(Suppl 9):S82
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  18. Rare variants are becoming the new candidates in the search for genetic variants that predispose individuals to a phenotype of interest. Their low prevalence in a population requires the development of dedicat...

    Authors: Marcio Augusto Alfonso de Almeida, Andrea Roseli Vançan Russo Horimoto, Paulo Sérgio Lopes de Oliveira, José Eduardo Krieger and Alexandre da Costa Pereira
    Citation: BMC Proceedings 2011 5(Suppl 9):S78
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  19. Large-scale, deep resequencing may be the next logical step in the genetic investigation of common complex diseases. Because each individual is likely to carry many thousands of variants, the identification of...

    Authors: Nirmala Akula, Sevilla Detera-Wadleigh, Yin Yao Shugart, Michael Nalls, Jo Steele and Francis J McMahon
    Citation: BMC Proceedings 2011 5(Suppl 9):S76
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  20. Joint analyses of correlated phenotypes in genetic epidemiology studies are common. However, these analyses primarily focus on genetic correlation between traits and do not take into account environmental corr...

    Authors: Phillip E Melton, Jack W Kent Jr, Thomas D Dyer, Laura Almasy and John Blangero
    Citation: BMC Proceedings 2011 5(Suppl 9):S72
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  21. We conducted a genome-wide association study on the Genetic Analysis Workshop 17 simulated unrelated individuals data using a multilocus score test based on wavelet transformation that we proposed recently. Wa...

    Authors: Renfang Jiang and Jianping Dong
    Citation: BMC Proceedings 2011 5(Suppl 9):S70
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  22. Compared to genome-wide association analysis, linkage analysis is less influenced by allelic heterogeneity. The use of linkage information in large families should provide a great opportunity to identify less ...

    Authors: Wei-Min Chen, Ani Manichaikul and Stephen S Rich
    Citation: BMC Proceedings 2011 5(Suppl 9):S68
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  23. Statistical tests on rare variant data may well have type I error rates that differ from their nominal levels. Here, we use the Genetic Analysis Workshop 17 data to estimate type I error rates and powers of th...

    Authors: Jing Jin, Jane E Cerise, Sun Jung Kang, Eun Jung Yoon, Seungtai Yoon, Nancy R Mendell and Stephen J Finch
    Citation: BMC Proceedings 2011 5(Suppl 9):S66
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  24. Genome-wide association studies (GWAS) test for disease-trait associations and estimate effect sizes at tag single-nucleotide polymorphisms (SNPs), which imperfectly capture variation at causal SNPs. Sequencin...

    Authors: Laura L Faye and Shelley B Bull
    Citation: BMC Proceedings 2011 5(Suppl 9):S64
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  25. We generalize recent work on graphical models for linkage disequilibrium to estimate the conditional independence structure between all variables for individuals in the Genetic Analysis Workshop 17 unrelated i...

    Authors: Haley J Abel and Alun Thomas
    Citation: BMC Proceedings 2011 5(Suppl 9):S62
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  26. Significance of genetic association to a marker has been traditionally evaluated through statistics that are standardized such that their null distributions conform to some known ones. Distributional assumptio...

    Authors: Kai Wang and Jian Huang
    Citation: BMC Proceedings 2011 5(Suppl 9):S60
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  27. As genetic maps become more highly dense, the ability to sufficiently localize putative disease loci becomes an achievable goal. This has prompted an increased interest in methods for constructing confidence i...

    Authors: Charalampos Papachristou
    Citation: BMC Proceedings 2011 5(Suppl 9):S58
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  28. Genome-wide association studies are a powerful approach used to identify common variants for complex disease. However, the traditional genome-wide association methods may not be optimal when they are applied t...

    Authors: Xin Huang, Yixin Fang and Junhui Wang
    Citation: BMC Proceedings 2011 5(Suppl 9):S56
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  29. As the cost of sequencing decreases, the demand for association tests that use exhaustive DNA sequence information increases. One such association test is multivariate distance matrix regression (MDMR). We exp...

    Authors: Doyoung Chung, Qunyuan Zhang, Aldi T Kraja, Ingrid B Borecki and Michael A Province
    Citation: BMC Proceedings 2011 5(Suppl 9):S54
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  30. Methods that can evaluate aggregate effects of rare and common variants are limited. Therefore, we applied a two-stage approach to evaluate aggregate gene effects in the 1000 Genomes Project data, which contai...

    Authors: NL Nock and LX Zhang
    Citation: BMC Proceedings 2011 5(Suppl 9):S47
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  31. Pathway-based analysis has been recently used in joint tests of association between disease and a group of common genetic variants. Here we explore this idea for the joint effects analysis of rare genetic vari...

    Authors: Pingzhao Hu, Wei Xu, Lu Cheng, Xiang Xing and Andrew D Paterson
    Citation: BMC Proceedings 2011 5(Suppl 9):S45
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  32. Quantitative trait locus (QTL) mapping using deep DNA sequencing data is a challenging task. In this study we performed region-based and pathway-based QTL mappings using a p-value combination method to analyze th...

    Authors: Hsin-Chou Yang and Chia-Wei Chen
    Citation: BMC Proceedings 2011 5(Suppl 9):S43
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  33. We compare the SNP-based and gene-based association studies using 697 unrelated individuals. The Benjamini-Hochberg procedure was applied to control the false discovery rate for all the multiple comparisons. W...

    Authors: Liping Tong, Bamidele Tayo, Jie Yang and Richard S Cooper
    Citation: BMC Proceedings 2011 5(Suppl 9):S41
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  34. Next-generation sequencing allows for a new focus on rare variant density for conducting analyses of association to disease and for narrowing down the genomic regions that show evidence of functionality. In th...

    Authors: Paola Raska and Xiaofeng Zhu
    Citation: BMC Proceedings 2011 5(Suppl 9):S39
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  35. Complex diseases are often the downstream event of a number of risk factors, including both environmental and genetic variables. To better understand the mechanism of disease onset, it is of great interest to ...

    Authors: Jia Kang, Wei Zheng, Lun Li, Joon Sang Lee, Xiting Yan and Hongyu Zhao
    Citation: BMC Proceedings 2011 5(Suppl 9):S37
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  36. Genome-wide association studies for complex traits are based on the common disease/common variant (CDCV) and common disease/rare variant (CDRV) assumptions. Under the CDCV hypothesis, classical genome-wide ass...

    Authors: Mohamad Saad, Aude Saint Pierre, Nora Bohossian, Matthias Macé and Maria Martinez
    Citation: BMC Proceedings 2011 5(Suppl 9):S33
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  37. The goals of our analysis were to map functional loci, which contribute to the case-control status of a trait of interest, using large pedigrees. We used logistic regression fitted with the generalized estimat...

    Authors: Tian Liu and Anbupalam Thalamuthu
    Citation: BMC Proceedings 2011 5(Suppl 9):S31
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  38. Rare variants may help to explain some of the missing heritability of complex diseases. Technological advances in next-generation sequencing give us the opportunity to test this hypothesis. We propose two new ...

    Authors: Rémi Kazma, Thomas J Hoffmann and John S Witte
    Citation: BMC Proceedings 2011 5(Suppl 9):S29
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  39. Association studies using tag SNPs have been successful in detecting disease-associated common variants. However, common variants, with rare exceptions, explain only at most 5–10% of the heritability resulting...

    Authors: Xiting Yan, Lun Li, Joon Sang Lee, Wei Zheng, John Ferguson and Hongyu Zhao
    Citation: BMC Proceedings 2011 5(Suppl 9):S27
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  40. We propose a novel aggregating U-test for gene-based association analysis. The method considers both rare and common variants. It adaptively searches for potential disease-susceptibility rare variants and collaps...

    Authors: Ming Li, Wenjiang Fu and Qing Lu
    Citation: BMC Proceedings 2011 5(Suppl 9):S23
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  41. Linkage- and association-based methods have been proposed for mapping disease-causing rare variants. Based on the family information provided in the Genetic Analysis Workshop 17 data set, we formulate a two-pr...

    Authors: Wai-Ki Yip, Gourab De, Benjamin A Raby and Nan Laird
    Citation: BMC Proceedings 2011 5(Suppl 9):S21
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  42. Genome-wide association studies are largely based on single-nucleotide polymorphisms and rest on the common disease/common variants (single-nucleotide polymorphisms) hypothesis. However, it has been argued in ...

    Authors: Asuman S Turkmen and Shili Lin
    Citation: BMC Proceedings 2011 5(Suppl 9):S19
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  43. Genome-wide association studies have been successful at identifying common disease variants associated with complex diseases, but the common variants identified have small effect sizes and account for only a s...

    Authors: Ruixue Fan, Chien-Hsun Huang, Shaw-Hwa Lo, Tian Zheng and Iuliana Ionita-Laza
    Citation: BMC Proceedings 2011 5(Suppl 9):S17
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  44. Tiled regression is an approach designed to determine the set of independent genetic variants that contribute to the variation of a quantitative trait in the presence of many highly correlated variants. In thi...

    Authors: Heejong Sung, Yoonhee Kim, Juanliang Cai, Cheryl D Cropp, Claire L Simpson, Qing Li, Brian C Perry, Alexa JM Sorant, Joan E Bailey-Wilson and Alexander F Wilson
    Citation: BMC Proceedings 2011 5(Suppl 9):S15
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  45. The Genetic Analysis Workshop 17 data we used comprise 697 unrelated individuals genotyped at 24,487 single-nucleotide polymorphisms (SNPs) from a mini-exome scan, using real sequence data for 3,205 genes anno...

    Authors: Wei Guo, Robert C Elston and Xiaofeng Zhu
    Citation: BMC Proceedings 2011 5(Suppl 9):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  46. We propose a nonparametric Bayes-based clustering algorithm to detect associations with rare and common single-nucleotide polymorphisms (SNPs) for quantitative traits. Unlike current methods, our approach iden...

    Authors: Lili Ding, Tesfaye M Baye, Hua He, Xue Zhang, Brad G Kurowski and Lisa J Martin
    Citation: BMC Proceedings 2011 5(Suppl 9):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  47. Next-generation sequencing technologies now make it possible to genotype and measure hundreds of thousands of rare genetic variations in individuals across the genome. Characterization of high-density genetic ...

    Authors: Tesfaye M Baye, Hua He, Lili Ding, Brad G Kurowski, Xue Zhang and Lisa J Martin
    Citation: BMC Proceedings 2011 5(Suppl 9):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  48. Currently there is a great deal of interest in developing methods for testing the role that rare variation plays in disease development. Here we propose a weighted association test that accumulates genetic var...

    Authors: Chuanhua Xing, Glen A Satten and Andrew S Allen
    Citation: BMC Proceedings 2011 5(Suppl 9):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  49. We propose a factor-screening method based on a Bayesian model selection framework and apply it to Genetic Analysis Workshop 17 simulated data with unrelated individuals to identify genes and SNP variants asso...

    Authors: Kith Pradhan, Seungtai Chris Yoon, Tao Wang and Kenny Ye
    Citation: BMC Proceedings 2011 5(Suppl 9):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

  50. The data set simulated for Genetic Analysis Workshop 17 was designed to mimic a subset of data that might be produced in a full exome screen for a complex disorder and related risk factors in order to permit w...

    Authors: Laura Almasy, Thomas D Dyer, Juan Manuel Peralta, Jack W Kent Jr, Jac C Charlesworth, Joanne E Curran and John Blangero
    Citation: BMC Proceedings 2011 5(Suppl 9):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 5 Supplement 9

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