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  1. Genetic Analysis Workshop 17 used real sequence data from the 1000 Genomes Project and simulated phenotypes influenced by a large number of rare variants. Our aim is to evaluate the performance of various coll...

    Authors: Yun Ju Sung, Treva K Rice and Dabeeru C Rao
    Citation: BMC Proceedings 2011 5(Suppl 9):S121
    Content type: Proceedings Published on:

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

  2. A number of rare variant statistical methods have been proposed for analysis of the impending wave of next-generation sequencing data. To date, there are few direct comparisons of these methods on real sequenc...

    Authors: Alexander Luedtke, Scott Powers, Ashley Petersen, Alexandra Sitarik, Airat Bekmetjev and Nathan L Tintle
    Citation: BMC Proceedings 2011 5(Suppl 9):S119
    Content type: Proceedings Published on:

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

  3. Recently there has been great interest in identifying rare variants associated with common diseases. We apply several collapsing-based and kernel-based single-gene association tests to Genetic Analysis Worksho...

    Authors: Lun Li, Wei Zheng, Joon Sang Lee, Xianghua Zhang, John Ferguson, Xiting Yan and Hongyu Zhao
    Citation: BMC Proceedings 2011 5(Suppl 9):S117
    Content type: Proceedings Published on:

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

  4. With recent advances in technology, deep sequencing data will be widely used to further the understanding of genetic influence on traits of interest. Therefore not only common variants but also rare variants n...

    Authors: Han Chen, Audrey E Hendricks, Yansong Cheng, Adrienne L Cupples, Josée Dupuis and Ching-Ti Liu
    Citation: BMC Proceedings 2011 5(Suppl 9):S113
    Content type: Proceedings Published on:

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

  5. Use of trait-dependent sampling designs in whole-genome association studies of sequence data can reduce total sequencing costs with modest losses of statistical efficiency. In a quantitative trait (QT) analysi...

    Authors: Yildiz E Yilmaz and Shelley B Bull
    Citation: BMC Proceedings 2011 5(Suppl 9):S111
    Content type: Proceedings Published on:

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

  6. Using single-nucleotide polymorphism (SNP) genotypes from the 1000 Genomes Project pilot3 data provided for Genetic Analysis Workshop 17 (GAW17), we applied Bayesian network structure learning (BNSL) to identi...

    Authors: Christopher E Schlosberg, Tae-Hwi Schwantes-An, Weimin Duan and Nancy L Saccone
    Citation: BMC Proceedings 2011 5(Suppl 9):S109
    Content type: Proceedings Published on:

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

  7. Human genome resequencing technologies are becoming ever more affordable and provide a valuable source of data about rare genetic variants in the human genome. Such rare variation may play an important role in...

    Authors: Reedik Mägi, Ashish Kumar and Andrew P Morris
    Citation: BMC Proceedings 2011 5(Suppl 9):S107
    Content type: Proceedings Published on:

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

  8. The common disease/rare variant hypothesis predicts that rare variants with large effects will have a strong impact on corresponding phenotypes. Therefore it is assumed that rare functional variants are enrich...

    Authors: Claudia Lamina
    Citation: BMC Proceedings 2011 5(Suppl 9):S105
    Content type: Proceedings Published on:

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

  9. Identifying rare variants that are responsible for complex disease has been promoted by advances in sequencing technologies. However, statistical methods that can handle the vast amount of data generated and t...

    Authors: Jeesun Jung, Jessica Dantzer and Yunlong Liu
    Citation: BMC Proceedings 2011 5(Suppl 9):S103
    Content type: Proceedings Published on:

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

  10. The unrelated individuals sample from Genetic Analysis Workshop 17 consists of a small number of subjects from eight population samples and genetic data composed mostly of rare variants. We compare two simple ...

    Authors: Robert C Culverhouse, Anthony L Hinrichs and Brian K Suarez
    Citation: BMC Proceedings 2011 5(Suppl 9):S101
    Content type: Proceedings Published on:

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

  11. We present a new statistical method to identify genes in which one or more variants influence quantitative traits. We use the Genetic Analysis Workshop 17 (GAW17) data set of unrelated individuals as a test of...

    Authors: Ian J Wilson, Richard AJ Howey, Darren T Houniet and Mauro Santibanez-Koref
    Citation: BMC Proceedings 2011 5(Suppl 9):S98
    Content type: Proceedings Published on:

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

  12. In addition to methods that can identify common variants associated with susceptibility to common diseases, there has been increasing interest in approaches that can identify rare genetic variants. We use the ...

    Authors: Yauheniya Cherkas, Nandini Raghavan, Stephan Francke, Frank DeFalco and Marsha A Wilcox
    Citation: BMC Proceedings 2011 5(Suppl 9):S94
    Content type: Proceedings Published on:

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

  13. Testing for association between multiple markers and a phenotype can not only capture untyped causal variants in weak linkage disequilibrium with nearby typed markers but also identify the effect of a combinat...

    Authors: Kristin L Ayers, Chrysovalanto Mamasoula and Heather J Cordell
    Citation: BMC Proceedings 2011 5(Suppl 9):S92
    Content type: Proceedings Published on:

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

  14. Analyzing sequencing data is difficult because of the low frequency of rare variants, which may result in low power to detect associations. We consider pathway analysis to detect multiple common and rare varia...

    Authors: Hae-Won Uh, Roula Tsonaka and Jeanine J Houwing-Duistermaat
    Citation: BMC Proceedings 2011 5(Suppl 9):S90
    Content type: Proceedings Published on:

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

  15. Genome-wide association studies are based on the linkage disequilibrium pattern between common tagging single-nucleotide polymorphisms (SNPs) (i.e., SNPs having only common alleles) and true causal variants, a...

    Authors: Xiangqing Sun, Junghyun Namkung, Xiaofeng Zhu and Robert C Elston
    Citation: BMC Proceedings 2011 5(Suppl 9):S88
    Content type: Proceedings Published on:

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

  16. We evaluate four association tests for rare variants—the combined multivariate and collapsing (CMC) method, two weighted-sum methods, and a variable threshold method—by applying them to the simulated data sets...

    Authors: Wenan Chen, Xi Gao, Jiexun Wang, Chuanyu Sun, Wen Wan, Degui Zhi, Nianjun Liu, Xiangning Chen and Guimin Gao
    Citation: BMC Proceedings 2011 5(Suppl 9):S86
    Content type: Proceedings Published on:

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

  17. Family-based study designs are again becoming popular as new next-generation sequencing technologies make whole-exome and whole-genome sequencing projects economically and temporally feasible. Here we evaluate...

    Authors: Claire L Simpson, Cristina M Justice, Mera Krishnan, Robert Wojciechowski, Heejong Sung, Jerry Cai, Tiffany Green, Deyana Lewis, Dana Behneman, Alexander F Wilson and Joan E Bailey-Wilson
    Citation: BMC Proceedings 2011 5(Suppl 9):S83
    Content type: Proceedings Published on:

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

  18. We report two approaches for linkage analysis of data consisting of replicate phenotypes. The first approach is specifically designed for the unusual (in human data) replicate structure of the Genetic Analysis...

    Authors: Anthony L Hinrichs, Robert C Culverhouse and Brian K Suarez
    Citation: BMC Proceedings 2011 5(Suppl 9):S81
    Content type: Proceedings Published on:

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

  19. To date, genome-wide association studies have yielded discoveries of common variants that partly explain familial aggregation of diseases and traits. Researchers are now turning their attention to less common ...

    Authors: Seung-Hoan Choi, Chunyu Liu, Josée Dupuis, Mark W Logue and Gyungah Jun
    Citation: BMC Proceedings 2011 5(Suppl 9):S79
    Content type: Proceedings Published on:

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

  20. Linkage analysis has the potential to localize disease genes of interest, but the choice of which subjects to select for follow-up sequencing after identifying a linkage peak might influence the ability to fin...

    Authors: Kristina Allen-Brady, James Farnham and Lisa Cannon-Albright
    Citation: BMC Proceedings 2011 5(Suppl 9):S77
    Content type: Proceedings Published on:

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

  21. The common genetic variants identified through genome-wide association studies explain only a small proportion of the genetic risk for complex diseases. The advancement of next-generation sequencing technologi...

    Authors: Jingyuan Zhao and Anbupalam Thalamuthu
    Citation: BMC Proceedings 2011 5(Suppl 9):S75
    Content type: Proceedings Published on:

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

  22. Genetic Analysis Workshop 17 provided simulated phenotypes and exome sequence data for 697 independent individuals (209 case subjects and 488 control subjects). The disease liability in these data was influenc...

    Authors: Chen Min Lin, Fah J Sathirapongsasuti and Berit Kerner
    Citation: BMC Proceedings 2011 5(Suppl 9):S71
    Content type: Proceedings Published on:

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

  23. We use least absolute shrinkage and selection operator (LASSO) regression to select genetic markers and phenotypic features that are most informative with respect to a trait of interest. We compare several str...

    Authors: Joel B Fontanarosa and Yang Dai
    Citation: BMC Proceedings 2011 5(Suppl 9):S69
    Content type: Proceedings Published on:

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

  24. In genome-wide association studies, gene-based methods measure potential joint genetic effects of loci within genes and are promising for detecting causative genetic variations. Following recent theoretical re...

    Authors: Shiquan He and Zheyang Wu
    Citation: BMC Proceedings 2011 5(Suppl 9):S65
    Content type: Proceedings Published on:

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

  25. We show that the statistical power of a single single-nucleotide polymorphism (SNP) score test for genetic association reflects the cumulative effect of all causal SNPs that are correlated with the test SNP. S...

    Authors: Yanming Di, Gu Mi, Luna Sun, Rongrong Dong, Hong Zhu and Lili Peng
    Citation: BMC Proceedings 2011 5(Suppl 9):S63
    Content type: Proceedings Published on:

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

  26. A number of studies have been conducted to investigate the predictive value of common genetic variants for complex diseases. To date, these studies have generally shown that common variants have no appreciable...

    Authors: Chengqing Wu, Kyle M Walsh, Andrew T DeWan, Josephine Hoh and Zuoheng Wang
    Citation: BMC Proceedings 2011 5(Suppl 9):S61
    Content type: Proceedings Published on:

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

  27. Our goal is to identify common single-nucleotide polymorphisms (SNPs) (minor allele frequency > 1%) that add predictive accuracy above that gained by knowledge of easily measured clinical variables. We take an...

    Authors: Christopher Pardy, Allan Motyer and Susan Wilson
    Citation: BMC Proceedings 2011 5(Suppl 9):S59
    Content type: Proceedings Published on:

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

  28. Genetic association studies usually involve a large number of single-nucleotide polymorphisms (SNPs) (k) and a relative small sample size (n), which produces the situation that k is much greater than n. Because c...

    Authors: Soonil Kwon, Xiaofei Yan, Jinrui Cui, Jie Yao, Kai Yang, Donald Tsiang, Xiaohui Li, Jerome I Rotter and Xiuqing Guo
    Citation: BMC Proceedings 2011 5(Suppl 9):S57
    Content type: Proceedings Published on:

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

  29. Evolutionary genetic models predict that the cumulative effect of rare deleterious mutations across the genome—known as mutational load burden—increases the susceptibility to complex disease. To test the mutat...

    Authors: Daniel P Howrigan, Matthew A Simonson, Helen M Kamens, Sarah H Stephens, Amanda G Wills, Marissa A Ehringer, Matthew C Keller and Matthew B McQueen
    Citation: BMC Proceedings 2011 5(Suppl 9):S55
    Content type: Proceedings Published on:

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

  30. We propose a two-stage design for the analysis of sequence variants in which a proportion of genes that show some evidence of association are identified initially and then followed up in an independent data se...

    Authors: Jennifer H Barrett and Jérémie Nsengimana
    Citation: BMC Proceedings 2011 5(Suppl 9):S53
    Content type: Proceedings Published on:

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

  31. Although genome-wide association studies have uncovered variants associated with more than 150 traits, the percentage of phenotypic variation explained by these associations remains small. This has led to the ...

    Authors: Fan Yang, Chul Joo Kang and Paul Marjoram
    Citation: BMC Proceedings 2011 5(Suppl 9):S51
    Content type: Proceedings Published on:

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

  32. Rare causal variants are believed to significantly contribute to the genetic basis of common diseases or quantitative traits. Appropriate statistical methods are required to discover the highest possible numbe...

    Authors: Markus Scholz and Holger Kirsten
    Citation: BMC Proceedings 2011 5(Suppl 9):S49
    Content type: Proceedings Published on:

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

  33. Recent breakthroughs in next-generation sequencing technologies allow cost-effective methods for measuring a growing list of cellular properties, including DNA sequence and structural variation. Next-generatio...

    Authors: Hugues Aschard, Weiliang Qiu, Bogdan Pasaniuc, Noah Zaitlen, Michael H Cho and Vincent Carey
    Citation: BMC Proceedings 2011 5(Suppl 9):S44
    Content type: Proceedings Published on:

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

  34. Risk prediction that capitalizes on emerging genetic findings holds great promise for improving public health and clinical care. However, recent risk prediction research has shown that predictive tests formed ...

    Authors: Changshuai Wei and Qing Lu
    Citation: BMC Proceedings 2011 5(Suppl 9):S42
    Content type: Proceedings Published on:

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

  35. Recent evidence suggests that many complex diseases are caused by genetic variations that play regulatory roles in controlling gene expression. Most genetic studies focus on nonsynonymous variations that can a...

    Authors: Mingxiang Teng, Yadong Wang, Guohua Wang, Jeesun Jung, Howard J Edenberg, Jeremy R Sanford and Yunlong Liu
    Citation: BMC Proceedings 2011 5(Suppl 9):S40
    Content type: Proceedings Published on:

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

  36. Aitkin recently proposed an integrated Bayesian/likelihood approach that he claims is general and simple. We have applied this method, which does not rely on informative prior probabilities or large-sample res...

    Authors: Justo Lorenzo-Bermejo, Lars Beckmann, Jenny Chang-Claude and Christine Fischer
    Citation: BMC Proceedings 2011 5(Suppl 9):S38
    Content type: Proceedings Published on:

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

  37. Both family- and population-based samples are used to identify genetic variants associated with phenotypes. Each strategy has demonstrated advantages, but their ability to identify rare variants and genes cont...

    Authors: Xue Zhang, Hua He, Lili Ding, Tesfaye M Baye, Brad G Kurowski and Lisa J Martin
    Citation: BMC Proceedings 2011 5(Suppl 9):S36
    Content type: Proceedings Published on:

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

  38. In the quest for the missing heritability of most complex diseases, rare variants have received increased attention. Advances in large-scale sequencing have led to a shift from the common disease/common varian...

    Authors: Jestinah M Mahachie John, Tom Cattaert, Lizzy De Lobel, François Van Lishout, Alain Empain and Kristel Van Steen
    Citation: BMC Proceedings 2011 5(Suppl 9):S32
    Content type: Proceedings Published on:

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

  39. Recent studies suggest that the traditional case-control study design does not have sufficient power to discover rare risk variants. Two different methods—collapsing and family data—are suggested as alternativ...

    Authors: Peng Lin, Michael Hamm, Sarah Hartz, Zhehao Zhang and John P Rice
    Citation: BMC Proceedings 2011 5(Suppl 9):S30
    Content type: Proceedings Published on:

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

  40. We examine the performance of various methods for combining family- and population-based genetic association data. Several approaches have been proposed for situations in which information is collected from bo...

    Authors: David W Fardo, Anthony R Druen, Jinze Liu, Lucia Mirea, Claire Infante-Rivard and Patrick Breheny
    Citation: BMC Proceedings 2011 5(Suppl 9):S28
    Content type: Proceedings Published on:

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

  41. Gene-based and single-nucleotide polymorphism (SNP) set association studies provide an important complement to SNP analysis. Kernel-based nonparametric regression has recently emerged as a powerful and flexibl...

    Authors: Xuefeng Wang, Huaizhen Qin, Nathan J Morris, Xiaofeng Zhu and Robert C Elston
    Citation: BMC Proceedings 2011 5(Suppl 9):S26
    Content type: Proceedings Published on:

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

  42. Recently we proposed a novel two-step approach to test for pathway effects in disease progression. The goal of this approach is to study the joint effect of multiple single-nucleotide polymorphisms that belong...

    Authors: Jeanine J Houwing-Duistermaat, Hae-Won Uh and Roula Tsonaka
    Citation: BMC Proceedings 2011 5(Suppl 9):S22
    Content type: Proceedings Published on:

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

  43. Next-generation sequencing has opened up new avenues for the genetic study of complex traits. However, because of the small number of observations for any given rare allele and high sequencing error, it is a c...

    Authors: Peng Wei, Xiaoming Liu and Yun-Xin Fu
    Citation: BMC Proceedings 2011 5(Suppl 9):S20
    Content type: Proceedings Published on:

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

  44. Genome-wide association studies often emphasize single-nucleotide polymorphisms with the smallest p-values with less attention given to single-nucleotide polymorphisms not ranked near the top. We suggest that gen...

    Authors: Julius S Ngwa, Alisa K Manning, Jonna L Grimsby, Chen Lu, Wei V Zhuang and Anita L DeStefano
    Citation: BMC Proceedings 2011 5(Suppl 9):S18
    Content type: Proceedings Published on:

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

  45. Advances in next-generation sequencing technology are enabling researchers to capture a comprehensive picture of genomic variation across large numbers of individuals with unprecedented levels of efficiency. T...

    Authors: Gary K Chen
    Citation: BMC Proceedings 2011 5(Suppl 9):S16
    Content type: Proceedings Published on:

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

  46. We aim to identify rare variants that have large effects on trait variance using a cost-efficient strategy. We use an oligogenic segregation analysis as a prioritizing tool for whole-exome sequencing studies t...

    Authors: France Gagnon, Nicole M Roslin and Mathieu Lemire
    Citation: BMC Proceedings 2011 5(Suppl 9):S11
    Content type: Proceedings Published on:

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

  47. We applied our method of pairwise shared genomic segment (pSGS) analysis to high-risk pedigrees identified from the Genetic Analysis Workshop 17 (GAW17) mini-exome sequencing data set. The original shared geno...

    Authors: Zheng Cai, Stacey Knight, Alun Thomas and Nicola J Camp
    Citation: BMC Proceedings 2011 5(Suppl 9):S9
    Content type: Proceedings Published on:

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

  48. Next-generation sequencing technologies enable us to explore rare functional variants. However, most current statistical techniques are too underpowered to capture signals of rare variants in genome-wide assoc...

    Authors: Vitara Pungpapong, Libo Wang, Yanzhu Lin, Dabao Zhang and Min Zhang
    Citation: BMC Proceedings 2011 5(Suppl 9):S5
    Content type: Proceedings Published on:

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

  49. In this study, we analyze the Genetic Analysis Workshop 17 data to identify regions of single-nucleotide polymorphisms (SNPs) that exhibit a significant influence on response rate (proportion of subjects with ...

    Authors: Michael Agne, Chien-Hsun Huang, Inchi Hu, Haitian Wang, Tian Zheng and Shaw-Hwa Lo
    Citation: BMC Proceedings 2011 5(Suppl 9):S3
    Content type: Proceedings Published on:

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

  50. Genetic Analysis Workshop 17 (GAW17) provided a platform for evaluating existing statistical genetic methods and for developing novel methods to analyze rare variants that modulate complex traits. In this arti...

    Authors: Saurabh Ghosh, Heike Bickeböller, Julia Bailey, Joan E Bailey-Wilson, Rita Cantor, Robert Culverhouse, Warwick Daw, Anita L DeStefano, Corinne D Engelman, Anthony Hinrichs, Jeanine Houwing-Duistermaat, Inke R König, Jack Kent Jr, Nan Laird, Nathan Pankratz, Andrew Paterson…
    Citation: BMC Proceedings 2011 5(Suppl 9):S1
    Content type: Proceedings Published on:

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

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