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Volume 5 Supplement 9

Genetic Analysis Workshop 17: Unraveling Human Exome Data

Proceedings

Edited by S Ghosh, H Bickeböller, J Bailey, JE Bailey-Wilson, R Cantor, W Daw, AL DeStefano, CD Engelman, A Hinrichs, J Houwing-Duistermaat, IR König, J Kent Jr., N Pankratz, A Paterson, E Pugh, Y Sun, A Thomas, N Tintle, X Zhu, JW MacCluer and L Almasy

Genetic Analysis Workshop 17. Go to conference site.

Boston, MA, USA13-16 October 2010

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  1. 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

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  2. 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

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  3. 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

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  4. 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

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  5. 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

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  7. Rare genetic variants have been shown to be important to the susceptibility of common human diseases. Methods for detecting association of rare genetic variants are drawing much attention. In this report, we a...

    Authors: Hongyan Xu and Varghese George

    Citation: BMC Proceedings 2011 5(Suppl 9):S7

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  8. 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

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  9. 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

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  10. 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

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  11. 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

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  13. Recent technological advances have allowed us to study individual genomes at a base-pair resolution and have demonstrated that the average exome harbors more than 15,000 genetic variants. However, our ability ...

    Authors: Andrew Jaffe, Genevieve Wojcik, Audrey Chu, Asieh Golozar, Ankit Maroo, Priya Duggal and Alison P Klein

    Citation: BMC Proceedings 2011 5(Suppl 9):S13

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  15. 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

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  17. 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

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  18. 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

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  20. 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

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  21. 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

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  22. 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

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  24. Model selection procedures for simultaneous analysis of all single-nucleotide polymorphisms in genome-wide association studies are most suitable for making full use of the data for a complex disease study. In ...

    Authors: Allan J Motyer, Chris McKendry, Sally Galbraith and Susan R Wilson

    Citation: BMC Proceedings 2011 5(Suppl 9):S24

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  26. 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

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  27. 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

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  28. 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

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  29. 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

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  30. 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

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  32. 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

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  33. 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

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  34. For the family data from Genetic Analysis Workshop 17, we obtained heritability estimates of quantitative traits Q1 and Q4 using the ASSOC program in the S.A.G.E. software package. ASSOC is a family-based meth...

    Authors: Priya B Shetty, Huaizhen Qin, Junghyun Namkung, Robert C Elston and Xiaofeng Zhu

    Citation: BMC Proceedings 2011 5(Suppl 9):S34

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  35. Because of the low frequency of rare genetic variants in observed data, the statistical power of detecting their associations with target traits is usually low. The collapsing test of collective effect of mult...

    Authors: Qunyuan Zhang, Doyoung Chung, Aldi Kraja, Ingrid I Borecki and Michael A Province

    Citation: BMC Proceedings 2011 5(Suppl 9):S35

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  36. 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

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  37. 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

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  38. 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

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  39. 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

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  40. 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

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  41. 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

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  44. 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

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  45. 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

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  46. We consider the application of Efron’s empirical Bayes classification method to risk prediction in a genome-wide association study using the Genetic Analysis Workshop 17 (GAW17) data. A major advantage of usin...

    Authors: Gengxin Li, John Ferguson, Wei Zheng, Joon Sang Lee, Xianghua Zhang, Lun Li, Jia Kang, Xiting Yan and Hongyu Zhao

    Citation: BMC Proceedings 2011 5(Suppl 9):S46

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  47. 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

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  48. Analyzing sets of genes in genome-wide association studies is a relatively new approach that aims to capitalize on biological knowledge about the interactions of genes in biological pathways. This approach, ca...

    Authors: Ashley Petersen, Alexandra Sitarik, Alexander Luedtke, Scott Powers, Airat Bekmetjev and Nathan L Tintle

    Citation: BMC Proceedings 2011 5(Suppl 9):S48

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  50. The advance of high-throughput next-generation sequencing technology makes possible the analysis of rare variants. However, the investigation of rare variants in unrelated-individuals data sets faces the chall...

    Authors: Haitian Wang, Chien-Hsun Huang, Shaw-Hwa Lo, Tian Zheng and Inchi Hu

    Citation: BMC Proceedings 2011 5(Suppl 9):S50

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