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Volume 5(Suppl 9);  2011
Proceedings
Identifying rare variants from exome scans: the GAW17 experience
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, Elizabeth Pugh, Brian Suarez, Yan Sun, Alun Thomas, Nathan Tintle, Xiaofeng Zhu, Andreas Ziegler, Jean W MacCluer, Laura Almasy
BMC Proc. 2011; 5(Suppl 9): S1. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S1
PMCID:
PMC3287821
Abstract Full Text PDF–200K
Genetic Analysis Workshop 17 mini-exome simulation
Laura Almasy, Thomas D Dyer, Juan Manuel Peralta, Jack W Kent, Jr, Jac C Charlesworth, Joanne E Curran, John Blangero
BMC Proc. 2011; 5(Suppl 9): S2. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S2
PMCID:
PMC3287854
Abstract Full Text PDF–489K
Identifying influential regions in extremely rare variants using a fixed-bin approach
Michael Agne, Chien-Hsun Huang, Inchi Hu, Haitian Wang, Tian Zheng, Shaw-Hwa Lo
BMC Proc. 2011; 5(Suppl 9): S3. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S3
PMCID:
PMC3287865
Abstract Full Text PDF–470K
Identification of genes and variants associated with quantitative traits using Bayesian factor screening
Kith Pradhan, Seungtai Chris Yoon, Tao Wang, Kenny Ye
BMC Proc. 2011; 5(Suppl 9): S4. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S4
PMCID:
PMC3287876
Abstract Full Text PDF–290K
Genome-wide association analysis of GAW17 data using an empirical Bayes variable selection
Vitara Pungpapong, Libo Wang, Yanzhu Lin, Dabao Zhang, Min Zhang
BMC Proc. 2011; 5(Suppl 9): S5. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S5
PMCID:
PMC3287887
Abstract Full Text PDF–399K
A weighted accumulation test for associating rare genetic variation with quantitative phenotypes
Chuanhua Xing, Glen A Satten, Andrew S Allen
BMC Proc. 2011; 5(Suppl 9): S6. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S6
PMCID:
PMC3287898
Abstract Full Text PDF–202K
A gene-based approach for testing association of rare alleles
Hongyan Xu, Varghese George
BMC Proc. 2011; 5(Suppl 9): S7. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S7
PMCID:
PMC3287909
Abstract Full Text PDF–454K
Population structure analysis using rare and common functional variants
Tesfaye M Baye, Hua He, Lili Ding, Brad G Kurowski, Xue Zhang, Lisa J Martin
BMC Proc. 2011; 5(Suppl 9): S8. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S8
PMCID:
PMC3287920
Abstract Full Text PDF–478K
Pairwise shared genomic segment analysis in high-risk pedigrees: application to Genetic Analysis Workshop 17 exome-sequencing SNP data
Zheng Cai, Stacey Knight, Alun Thomas, Nicola J Camp
BMC Proc. 2011; 5(Suppl 9): S9. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S9
PMCID:
PMC3287931
Abstract Full Text PDF–234K
Detection of associations with rare and common SNPs for quantitative traits: a nonparametric Bayes-based approach
Lili Ding, Tesfaye M Baye, Hua He, Xue Zhang, Brad G Kurowski, Lisa J Martin
BMC Proc. 2011; 5(Suppl 9): S10. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S10
PMCID:
PMC3287822
Abstract Full Text PDF–360K
Successful identification of rare variants using oligogenic segregation analysis as a prioritizing tool for whole-exome sequencing studies
France Gagnon, Nicole M Roslin, Mathieu Lemire
BMC Proc. 2011; 5(Suppl 9): S11. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S11
PMCID:
PMC3287833
Abstract Full Text PDF–227K
Evaluation of a LASSO regression approach on the unrelated samples of Genetic Analysis Workshop 17
Wei Guo, Robert C Elston, Xiaofeng Zhu
BMC Proc. 2011; 5(Suppl 9): S12. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S12
PMCID:
PMC3287844
Abstract Full Text PDF–333K
Identification of functional genetic variation in exome sequence analysis
Andrew Jaffe, Genevieve Wojcik, Audrey Chu, Asieh Golozar, Ankit Maroo, Priya Duggal, Alison P Klein
BMC Proc. 2011; 5(Suppl 9): S13. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S13
PMCID:
PMC3287847
Abstract Full Text PDF–219K
Comparing nominal and real quality scores on next-generation sequencing genotype calls
Alexander H Stram
BMC Proc. 2011; 5(Suppl 9): S14. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S14
PMCID:
PMC3287848
Abstract Full Text PDF–195K
Comparison of results from tests of association in unrelated individuals with uncollapsed and collapsed sequence variants using tiled regression
Heejong Sung, Yoonhee Kim, Juanliang Cai, Cheryl D Cropp, Claire L Simpson, Qing Li, Brian C Perry, Alexa JM Sorant, Joan E Bailey-Wilson, Alexander F Wilson
BMC Proc. 2011; 5(Suppl 9): S15. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S15
PMCID:
PMC3287849
Abstract Full Text PDF–261K
Enhancing the discovery of rare disease variants through hierarchical modeling
Gary K Chen
BMC Proc. 2011; 5(Suppl 9): S16. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S16
PMCID:
PMC3287850
Abstract Full Text PDF–629K
Identifying rare disease variants in the Genetic Analysis Workshop 17 simulated data: a comparison of several statistical approaches
Ruixue Fan, Chien-Hsun Huang, Shaw-Hwa Lo, Tian Zheng, Iuliana Ionita-Laza
BMC Proc. 2011; 5(Suppl 9): S17. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S17
PMCID:
PMC3287851
Abstract Full Text PDF–223K
Pathway analysis following association study
Julius S Ngwa, Alisa K Manning, Jonna L Grimsby, Chen Lu, Wei V Zhuang, Anita L DeStefano
BMC Proc. 2011; 5(Suppl 9): S18. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S18
PMCID:
PMC3287852
Abstract Full Text PDF–288K
Gene-based partial least-squares approaches for detecting rare variant associations with complex traits
Asuman S Turkmen, Shili Lin
BMC Proc. 2011; 5(Suppl 9): S19. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S19
PMCID:
PMC3287853
Abstract Full Text PDF–298K
Incorporating predicted functions of nonsynonymous variants into gene-based analysis of exome sequencing data: a comparative study
Peng Wei, Xiaoming Liu, Yun-Xin Fu
BMC Proc. 2011; 5(Suppl 9): S20. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S20
PMCID:
PMC3287855
Abstract Full Text PDF–276K
Identifying causal rare variants of disease through family-based analysis of Genetics Analysis Workshop 17 data set
Wai-Ki Yip, Gourab De, Benjamin A Raby, Nan Laird
BMC Proc. 2011; 5(Suppl 9): S21. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S21
PMCID:
PMC3287856
Abstract Full Text PDF–256K
Pathway analysis for family data using nested random-effects models
Jeanine J Houwing-Duistermaat, Hae-Won Uh, Roula Tsonaka
BMC Proc. 2011; 5(Suppl 9): S22. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S22
PMCID:
PMC3287857
Abstract Full Text PDF–240K
An aggregating U-Test for a genetic association study of quantitative traits
Ming Li, Wenjiang Fu, Qing Lu
BMC Proc. 2011; 5(Suppl 9): S23. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S23
PMCID:
PMC3287858
Abstract Full Text PDF–250K
LASSO model selection with post-processing for a genome-wide association study data set
Allan J Motyer, Chris McKendry, Sally Galbraith, Susan R Wilson
BMC Proc. 2011; 5(Suppl 9): S24. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S24
PMCID:
PMC3287859
Abstract Full Text PDF–225K
Interrogating population structure and its impact on association tests
Huaizhen Qin, Robert C Elston, Xiaofeng Zhu
BMC Proc. 2011; 5(Suppl 9): S25. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S25
PMCID:
PMC3287860
Abstract Full Text PDF–389K
Testing gene-environment interactions in gene-based association studies
Xuefeng Wang, Huaizhen Qin, Nathan J Morris, Xiaofeng Zhu, Robert C Elston
BMC Proc. 2011; 5(Suppl 9): S26. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S26
PMCID:
PMC3287861
Abstract Full Text PDF–279K
Detecting functional rare variants by collapsing and incorporating functional annotation in Genetic Analysis Workshop 17 mini-exome data
Xiting Yan, Lun Li, Joon Sang Lee, Wei Zheng, John Ferguson, Hongyu Zhao
BMC Proc. 2011; 5(Suppl 9): S27. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S27
PMCID:
PMC3287862
Abstract Full Text PDF–298K
Exploration and comparison of methods for combining population- and family-based genetic association using the Genetic Analysis Workshop 17 mini-exome
David W Fardo, Anthony R Druen, Jinze Liu, Lucia Mirea, Claire Infante-Rivard, Patrick Breheny
BMC Proc. 2011; 5(Suppl 9): S28. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S28
PMCID:
PMC3287863
Abstract Full Text PDF–288K
Use of principal components to aggregate rare variants in case-control and family-based association studies in the presence of multiple covariates
Rémi Kazma, Thomas J Hoffmann, John S Witte
BMC Proc. 2011; 5(Suppl 9): S29. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S29
PMCID:
PMC3287864
Abstract Full Text PDF–1.3M
Challenges and directions: an analysis of Genetic Analysis Workshop 17 data by collapsing rare variants within family data
Peng Lin, Michael Hamm, Sarah Hartz, Zhehao Zhang, John P Rice
BMC Proc. 2011; 5(Suppl 9): S30. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S30
PMCID:
PMC3287866
Abstract Full Text PDF–279K
Identity by descent and association analysis of dichotomous traits based on large pedigrees
Tian Liu, Anbupalam Thalamuthu
BMC Proc. 2011; 5(Suppl 9): S31. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S31
PMCID:
PMC3287867
Abstract Full Text PDF–429K
Comparison of genetic association strategies in the presence of rare alleles
Jestinah M Mahachie John, Tom Cattaert, Lizzy De Lobel, François Van Lishout, Alain Empain, Kristel Van Steen
BMC Proc. 2011; 5(Suppl 9): S32. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S32
PMCID:
PMC3287868
Abstract Full Text PDF–232K Supplementary Material
Comparative study of statistical methods for detecting association with rare variants in exome-resequencing data
Mohamad Saad, Aude Saint Pierre, Nora Bohossian, Matthias Macé, Maria Martinez
BMC Proc. 2011; 5(Suppl 9): S33. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S33
PMCID:
PMC3287869
Abstract Full Text PDF–265K
Estimating heritability using family and unrelated individuals data
Priya B Shetty, Huaizhen Qin, Junghyun Namkung, Robert C Elston, Xiaofeng Zhu
BMC Proc. 2011; 5(Suppl 9): S34. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S34
PMCID:
PMC3287870
Abstract Full Text PDF–308K
Methods for adjusting population structure and familial relatedness in association test for collective effect of multiple rare variants on quantitative traits
Qunyuan Zhang, Doyoung Chung, Aldi Kraja, Ingrid I Borecki, Michael A Province
BMC Proc. 2011; 5(Suppl 9): S35. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S35
PMCID:
PMC3287871
Abstract Full Text PDF–287K
Family- and population-based designs identify different rare causal variants
Xue Zhang, Hua He, Lili Ding, Tesfaye M Baye, Brad G Kurowski, Lisa J Martin
BMC Proc. 2011; 5(Suppl 9): S36. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S36
PMCID:
PMC3287872
Abstract Full Text PDF–220K Supplementary Material
Use of Bayesian networks to dissect the complexity of genetic disease: application to the Genetic Analysis Workshop 17 simulated data
Jia Kang, Wei Zheng, Lun Li, Joon Sang Lee, Xiting Yan, Hongyu Zhao
BMC Proc. 2011; 5(Suppl 9): S37. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S37
PMCID:
PMC3287873
Abstract Full Text PDF–388K
Using the posterior distribution of deviance to measure evidence of association for rare susceptibility variants
Justo Lorenzo-Bermejo, Lars Beckmann, Jenny Chang-Claude, Christine Fischer
BMC Proc. 2011; 5(Suppl 9): S38. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S38
PMCID:
PMC3287874
Abstract Full Text PDF–395K
Rare variant density across the genome and across populations
Paola Raska, Xiaofeng Zhu
BMC Proc. 2011; 5(Suppl 9): S39. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S39
PMCID:
PMC3287875
Abstract Full Text PDF–690K
Prioritizing single-nucleotide variations that potentially regulate alternative splicing
Mingxiang Teng, Yadong Wang, Guohua Wang, Jeesun Jung, Howard J Edenberg, Jeremy R Sanford, Yunlong Liu
BMC Proc. 2011; 5(Suppl 9): S40. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S40
PMCID:
PMC3287877
Abstract Full Text PDF–704K
Comparison of SNP-based and gene-based association studies in detecting rare variants using unrelated individuals
Liping Tong, Bamidele Tayo, Jie Yang, Richard S Cooper
BMC Proc. 2011; 5(Suppl 9): S41. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S41
PMCID:
PMC3287878
Abstract Full Text PDF–324K
Collapsing ROC approach for risk prediction research on both common and rare variants
Changshuai Wei, Qing Lu
BMC Proc. 2011; 5(Suppl 9): S42. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S42
PMCID:
PMC3287879
Abstract Full Text PDF–318K
Region-based and pathway-based QTL mapping using a p-value combination method
Hsin-Chou Yang, Chia-Wei Chen
BMC Proc. 2011; 5(Suppl 9): S43. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S43
PMCID:
PMC3287880
Abstract Full Text PDF–441K
Combining effects from rare and common genetic variants in an exome-wide association study of sequence data
Hugues Aschard, Weiliang Qiu, Bogdan Pasaniuc, Noah Zaitlen, Michael H Cho, Vincent Carey
BMC Proc. 2011; 5(Suppl 9): S44. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S44
PMCID:
PMC3287881
Abstract Full Text PDF–485K
Pathway-based joint effects analysis of rare genetic variants using Genetic Analysis Workshop 17 exon sequence data
Pingzhao Hu, Wei Xu, Lu Cheng, Xiang Xing, Andrew D Paterson
BMC Proc. 2011; 5(Suppl 9): S45. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S45
PMCID:
PMC3287882
Abstract Full Text PDF–215K
Large-scale risk prediction applied to Genetic Analysis Workshop 17 mini-exome sequence data
Gengxin Li, John Ferguson, Wei Zheng, Joon Sang Lee, Xianghua Zhang, Lun Li, Jia Kang, Xiting Yan, Hongyu Zhao
BMC Proc. 2011; 5(Suppl 9): S46. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S46
PMCID:
PMC3287883
Abstract Full Text PDF–337K
Evaluating aggregate effects of rare and common variants in the 1000 Genomes Project exon sequencing data using latent variable structural equation modeling
NL Nock, LX Zhang
BMC Proc. 2011; 5(Suppl 9): S47. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S47
PMCID:
PMC3287884
Abstract Full Text PDF–5.3M
Evaluating methods for combining rare variant data in pathway-based tests of genetic association
Ashley Petersen, Alexandra Sitarik, Alexander Luedtke, Scott Powers, Airat Bekmetjev, Nathan L Tintle
BMC Proc. 2011; 5(Suppl 9): S48. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S48
PMCID:
PMC3287885
Abstract Full Text PDF–281K
Comparison of scoring methods for the detection of causal genes with or without rare variants
Markus Scholz, Holger Kirsten
BMC Proc. 2011; 5(Suppl 9): S49. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S49
PMCID:
PMC3287886
Abstract Full Text PDF–228K
New insights into old methods for identifying causal rare variants
Haitian Wang, Chien-Hsun Huang, Shaw-Hwa Lo, Tian Zheng, Inchi Hu
BMC Proc. 2011; 5(Suppl 9): S50. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S50
PMCID:
PMC3287888
Abstract Full Text PDF–264K
Methods for detecting associations between phenotype and aggregations of rare variants
Fan Yang, Chul Joo Kang, Paul Marjoram
BMC Proc. 2011; 5(Suppl 9): S51. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S51
PMCID:
PMC3287889
Abstract Full Text PDF–417K
Enrichment analysis of genetic association in genes and pathways by aggregating signals from both rare and common variants
Wei Yang, C Charles Gu
BMC Proc. 2011; 5(Suppl 9): S52. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S52
PMCID:
PMC3287890
Abstract Full Text PDF–418K
Two-stage analyses of sequence variants in association with quantitative traits
Jennifer H Barrett, Jérémie Nsengimana
BMC Proc. 2011; 5(Suppl 9): S53. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S53
PMCID:
PMC3287891
Abstract Full Text PDF–286K
Distance-based phenotypic association analysis of DNA sequence data
Doyoung Chung, Qunyuan Zhang, Aldi T Kraja, Ingrid B Borecki, Michael A Province
BMC Proc. 2011; 5(Suppl 9): S54. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S54
PMCID:
PMC3287892
Abstract Full Text PDF–410K
Mutational load analysis of unrelated individuals
Daniel P Howrigan, Matthew A Simonson, Helen M Kamens, Sarah H Stephens, Amanda G Wills, Marissa A Ehringer, Matthew C Keller, Matthew B McQueen
BMC Proc. 2011; 5(Suppl 9): S55. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S55
PMCID:
PMC3287893
Abstract Full Text PDF–243K
Identification of functional rare variants in genome-wide association studies using stability selection based on random collapsing
Xin Huang, Yixin Fang, Junhui Wang
BMC Proc. 2011; 5(Suppl 9): S56. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S56
PMCID:
PMC3287894
Abstract Full Text PDF–226K
Application of Bayesian regression with singular value decomposition method in association studies for sequence data
Soonil Kwon, Xiaofei Yan, Jinrui Cui, Jie Yao, Kai Yang, Donald Tsiang, Xiaohui Li, Jerome I Rotter, Xiuqing Guo
BMC Proc. 2011; 5(Suppl 9): S57. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S57
PMCID:
PMC3287895
Abstract Full Text PDF–304K
Confidence set of putative quantitative trait loci in whole genome scans with application to the Genetic Analysis Workshop 17 simulated data
Charalampos Papachristou
BMC Proc. 2011; 5(Suppl 9): S58. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S58
PMCID:
PMC3287896
Abstract Full Text PDF–209K
Resampling procedures to identify important SNPs using a consensus approach
Christopher Pardy, Allan Motyer, Susan Wilson
BMC Proc. 2011; 5(Suppl 9): S59. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S59
PMCID:
PMC3287897
Abstract Full Text PDF–296K
Treating phenotype as given: a simple resampling method for genome-wide association studies
Kai Wang, Jian Huang
BMC Proc. 2011; 5(Suppl 9): S60. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S60
PMCID:
PMC3287899
Abstract Full Text PDF–450K
Disease risk prediction with rare and common variants
Chengqing Wu, Kyle M Walsh, Andrew T DeWan, Josephine Hoh, Zuoheng Wang
BMC Proc. 2011; 5(Suppl 9): S61. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S61
PMCID:
PMC3287900
Abstract Full Text PDF–217K
Case-control association testing by graphical modeling for the Genetic Analysis Workshop 17 mini-exome sequence data
Haley J Abel, Alun Thomas
BMC Proc. 2011; 5(Suppl 9): S62. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S62
PMCID:
PMC3287901
Abstract Full Text PDF–1.1M
Power of association tests in the presence of multiple causal variants
Yanming Di, Gu Mi, Luna Sun, Rongrong Dong, Hong Zhu, Lili Peng
BMC Proc. 2011; 5(Suppl 9): S63. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S63
PMCID:
PMC3287902
Abstract Full Text PDF–306K
Two-stage study designs combining genome-wide association studies, tag single-nucleotide polymorphisms, and exome sequencing: accuracy of genetic effect estimates
Laura L Faye, Shelley B Bull
BMC Proc. 2011; 5(Suppl 9): S64. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S64
PMCID:
PMC3287903
Abstract Full Text PDF–238K
Gene-based Higher Criticism methods for large-scale exonic single-nucleotide polymorphism data
Shiquan He, Zheyang Wu
BMC Proc. 2011; 5(Suppl 9): S65. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S65
PMCID:
PMC3287904
Abstract Full Text PDF–393K Supplementary Material
Principal components ancestry adjustment for Genetic Analysis Workshop 17 data
Jing Jin, Jane E Cerise, Sun Jung Kang, Eun Jung Yoon, Seungtai Yoon, Nancy R Mendell, Stephen J Finch
BMC Proc. 2011; 5(Suppl 9): S66. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S66
PMCID:
PMC3287905
Abstract Full Text PDF–214K
Regularized regression method for genome-wide association studies
Jin Liu, Kai Wang, Shuangge Ma, Jian Huang
BMC Proc. 2011; 5(Suppl 9): S67. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S67
PMCID:
PMC3287906
Abstract Full Text PDF–414K
Identifying variants that contribute to linkage for dichotomous and quantitative traits in extended pedigrees
Wei-Min Chen, Ani Manichaikul, Stephen S Rich
BMC Proc. 2011; 5(Suppl 9): S68. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S68
PMCID:
PMC3287907
Abstract Full Text PDF–204K
Using LASSO regression to detect predictive aggregate effects in genetic studies
Joel B Fontanarosa, Yang Dai
BMC Proc. 2011; 5(Suppl 9): S69. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S69
PMCID:
PMC3287908
Abstract Full Text PDF–197K
Detecting rare functional variants using a wavelet-based test on quantitative and qualitative traits
Renfang Jiang, Jianping Dong
BMC Proc. 2011; 5(Suppl 9): S70. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S70
PMCID:
PMC3287910
Abstract Full Text PDF–233K
Propensity score analysis in the Genetic Analysis Workshop 17 simulated data set on independent individuals
Chen Min Lin, Fah J Sathirapongsasuti, Berit Kerner
BMC Proc. 2011; 5(Suppl 9): S71. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S71
PMCID:
PMC3287911
Abstract Full Text PDF–236K
Genetic signal maximization using environmental regression
Phillip E Melton, Jack W Kent, Jr, Thomas D Dyer, Laura Almasy, John Blangero
BMC Proc. 2011; 5(Suppl 9): S72. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S72
PMCID:
PMC3287912
Abstract Full Text PDF–723K
Integrating binary traits with quantitative phenotypes for association mapping of multivariate phenotypes
Indranil Mukhopadhyay, Sujayam Saha, Saurabh Ghosh
BMC Proc. 2011; 5(Suppl 9): S73. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S73
PMCID:
PMC3287913
Abstract Full Text PDF–218K
Joint association analysis of bivariate quantitative and qualitative traits
Mengdie Yuan, Guoqing Diao
BMC Proc. 2011; 5(Suppl 9): S74. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S74
PMCID:
PMC3287914
Abstract Full Text PDF–302K
Gene-based multiple trait analysis for exome sequencing data
Jingyuan Zhao, Anbupalam Thalamuthu
BMC Proc. 2011; 5(Suppl 9): S75. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S75
PMCID:
PMC3287915
Abstract Full Text PDF–267K
Identity-by-descent filtering as a tool for the identification of disease alleles in exome sequence data from distant relatives
Nirmala Akula, Sevilla Detera-Wadleigh, Yin Yao Shugart, Michael Nalls, Jo Steele, Francis J McMahon
BMC Proc. 2011; 5(Suppl 9): S76. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S76
PMCID:
PMC3287916
Abstract Full Text PDF–294K
Strategies for selection of subjects for sequencing after detection of a linkage peak
Kristina Allen-Brady, James Farnham, Lisa Cannon-Albright
BMC Proc. 2011; 5(Suppl 9): S77. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S77
PMCID:
PMC3287917
Abstract Full Text PDF–216K
Different approaches for dealing with rare variants in family-based genetic studies: application of a Genetic Analysis Workshop 17 problem
Marcio Augusto Alfonso de Almeida, Andrea Roseli Vançan Russo Horimoto, Paulo Sérgio Lopes de Oliveira, José Eduardo Krieger, Alexandre da Costa Pereira
BMC Proc. 2011; 5(Suppl 9): S78. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S78
PMCID:
PMC3287918
Abstract Full Text PDF–236K
Using linkage analysis of large pedigrees to guide association analyses
Seung-Hoan Choi, Chunyu Liu, Josée Dupuis, Mark W Logue, Gyungah Jun
BMC Proc. 2011; 5(Suppl 9): S79. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S79
PMCID:
PMC3287919
Abstract Full Text PDF–216K
A novel method to detect rare variants using both family and unrelated case-control data
Tao Feng, Robert C Elston, Xiaofeng Zhu
BMC Proc. 2011; 5(Suppl 9): S80. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S80
PMCID:
PMC3287921
Abstract Full Text PDF–255K
Linkage analysis merging replicate phenotypes: an application to three quantitative phenotypes in two African samples
Anthony L Hinrichs, Robert C Culverhouse, Brian K Suarez
BMC Proc. 2011; 5(Suppl 9): S81. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S81
PMCID:
PMC3287922
Abstract Full Text PDF–393K
Enriching rare variants using family-specific linkage information
Gang Shi, Jeannette Simino, Dabeeru C Rao
BMC Proc. 2011; 5(Suppl 9): S82. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S82
PMCID:
PMC3287923
Abstract Full Text PDF–225K
Old lessons learned anew: family-based methods for detecting genes responsible for quantitative and qualitative traits in the Genetic Analysis Workshop 17 mini-exome sequence data
Claire L Simpson, Cristina M Justice, Mera Krishnan, Robert Wojciechowski, Heejong Sung, Jerry Cai, Tiffany Green, Deyana Lewis, Dana Behneman, Alexander F Wilson, Joan E Bailey-Wilson
BMC Proc. 2011; 5(Suppl 9): S83. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S83
PMCID:
PMC3287924
Abstract Full Text PDF–230K
A method to detect single-nucleotide polymorphisms accounting for a linkage signal using covariate-based affected relative pair linkage analysis
Yeunjoo E Song, Junghyun Namkung, Robert W Shields, Daniel J Baechle, Sunah Song, Robert C Elston
BMC Proc. 2011; 5(Suppl 9): S84. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S84
PMCID:
PMC3287925
Abstract Full Text PDF–428K
A pathway-based association analysis model using common and rare variants
Lu Cheng, Pingzhao Hu, Jenna Sykes, Melania Pintilie, Geoffrey Liu, Wei Xu
BMC Proc. 2011; 5(Suppl 9): S85. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S85
PMCID:
PMC3287926
Abstract Full Text PDF–302K
Evaluation of association tests for rare variants using simulated data sets in the Genetic Analysis Workshop 17 data
Wenan Chen, Xi Gao, Jiexun Wang, Chuanyu Sun, Wen Wan, Degui Zhi, Nianjun Liu, Xiangning Chen, Guimin Gao
BMC Proc. 2011; 5(Suppl 9): S86. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S86
PMCID:
PMC3287927
Abstract Full Text PDF–204K
Do rare variant genotypes predict common variant genotypes?
Jack W Kent, Jr, Vidya Farook, Harald HH Göring, Thomas D Dyer, Laura Almasy, Ravindranath Duggirala, John Blangero
BMC Proc. 2011; 5(Suppl 9): S87. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S87
PMCID:
PMC3287928
Abstract Full Text PDF–236K
Capability of common SNPs to tag rare variants
Xiangqing Sun, Junghyun Namkung, Xiaofeng Zhu, Robert C Elston
BMC Proc. 2011; 5(Suppl 9): S88. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S88
PMCID:
PMC3287929
Abstract Full Text PDF–284K
Association tests for rare and common variants based on genotypic and phenotypic measures of similarity between individuals
Anbupalam Thalamuthu, Jingyuan Zhao, Garrett Teoh Hor Keong, Venkateswarlu Kondragunta, Indranil Mukhopadhyay
BMC Proc. 2011; 5(Suppl 9): S89. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S89
PMCID:
PMC3287930
Abstract Full Text PDF–374K
Does pathway analysis make it easier for common variants to tag rare ones?
Hae-Won Uh, Roula Tsonaka, Jeanine J Houwing-Duistermaat
BMC Proc. 2011; 5(Suppl 9): S90. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S90
PMCID:
PMC3287932
Abstract Full Text PDF–423K
SNP set analysis for detecting disease association using exon sequence data
Ru Wang, Jie Peng, Pei Wang
BMC Proc. 2011; 5(Suppl 9): S91. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S91
PMCID:
PMC3287933
Abstract Full Text PDF–309K
Penalized-regression-based multimarker genotype analysis of Genetic Analysis Workshop 17 data
Kristin L Ayers, Chrysovalanto Mamasoula, Heather J Cordell
BMC Proc. 2011; 5(Suppl 9): S92. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S92
PMCID:
PMC3287934
Abstract Full Text PDF–688K
Analysis of human mini-exome sequencing data from Genetic Analysis Workshop 17 using a Bayesian hierarchical mixture model
Julio S Bueno Filho, Gota Morota, Quoc Tran, Matthew J Maenner, Lina M Vera-Cala, Corinne D Engelman, Kristin J Meyers
BMC Proc. 2011; 5(Suppl 9): S93. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S93
PMCID:
PMC3287935
Abstract Full Text PDF–339K
Rare variant collapsing in conjunction with mean log p-value and gradient boosting approaches applied to Genetic Analysis Workshop 17 data
Yauheniya Cherkas, Nandini Raghavan, Stephan Francke, Frank DeFalco, Marsha A Wilcox
BMC Proc. 2011; 5(Suppl 9): S94. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S94
PMCID:
PMC3287936
Abstract Full Text PDF–308K
Search for compound heterozygous effects in exome sequence of unrelated subjects
G Bryce Christensen, Christophe G Lambert
BMC Proc. 2011; 5(Suppl 9): S95. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S95
PMCID:
PMC3287937
Abstract Full Text PDF–215K
Detecting disease rare alleles using single SNPs in families and haplotyping in unrelated subjects from the Genetic Analysis Workshop 17 data
Aldi T Kraja, Jacek Czajkowski, Mary F Feitosa, Ingrid B Borecki, Michael A Province
BMC Proc. 2011; 5(Suppl 9): S96. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S96
PMCID:
PMC3287938
Abstract Full Text PDF–1.2M
Addition of multiple rare SNPs to known common variants improves the association between disease and gene in the Genetic Analysis Workshop 17 data
Jenna Sykes, Lu Cheng, Wei Xu, Ming-Sound Tsao, Geoffrey Liu, Melania Pintilie
BMC Proc. 2011; 5(Suppl 9): S97. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S97
PMCID:
PMC3287939
Abstract Full Text PDF–383K
Finding genes that influence quantitative traits with tree-based clustering
Ian J Wilson, Richard AJ Howey, Darren T Houniet, Mauro Santibanez-Koref
BMC Proc. 2011; 5(Suppl 9): S98. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S98
PMCID:
PMC3287940
Abstract Full Text PDF–516K
Identifying rare variants using a Bayesian regression approach
Aimin Yan, Nan M Laird, Cheng Li
BMC Proc. 2011; 5(Suppl 9): S99. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S99
PMCID:
PMC3287941
Abstract Full Text PDF–265K
A LASSO-based approach to analyzing rare variants in genetic association studies
Jennifer S Brennan, Yunxiao He, Rose Calixte, Epiphanie Nyirabahizi, Yuan Jiang, Heping Zhang
BMC Proc. 2011; 5(Suppl 9): S100. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S100
PMCID:
PMC3287823
Abstract Full Text PDF–209K
Stratify or adjust? Dealing with multiple populations when evaluating rare variants
Robert C Culverhouse, Anthony L Hinrichs, Brian K Suarez
BMC Proc. 2011; 5(Suppl 9): S101. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S101
PMCID:
PMC3287824
Abstract Full Text PDF–218K
Novel tree-based method to generate markers from rare variant data
Yuan Jiang, Jennifer S Brennan, Rose Calixte, Yunxiao He, Epiphanie Nyirabahizi, Heping Zhang
BMC Proc. 2011; 5(Suppl 9): S102. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S102
PMCID:
PMC3287825
Abstract Full Text PDF–259K
Identification of multiple rare variants associated with a disease
Jeesun Jung, Jessica Dantzer, Yunlong Liu
BMC Proc. 2011; 5(Suppl 9): S103. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S103
PMCID:
PMC3287826
Abstract Full Text PDF–246K
Performance of random forests and logic regression methods using mini-exome sequence data
Yoonhee Kim, Qing Li, Cheryl D Cropp, Heejong Sung, Juanliang Cai, Claire L Simpson, Brian Perry, Abhijit Dasgupta, James D Malley, Alexander F Wilson, Joan E Bailey-Wilson
BMC Proc. 2011; 5(Suppl 9): S104. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S104
PMCID:
PMC3287827
Abstract Full Text PDF–296K Supplementary Material
Digging into the extremes: a useful approach for the analysis of rare variants with continuous traits?
Claudia Lamina
BMC Proc. 2011; 5(Suppl 9): S105. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S105
PMCID:
PMC3287828
Abstract Full Text PDF–1.7M
Association screening for genes with multiple potentially rare variants: an inverse-probability weighted clustering approach
Ying Liu, Chien Hsun Huang, Inchi Hu, Shaw-Hwa Lo, Tian Zheng
BMC Proc. 2011; 5(Suppl 9): S106. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S106
PMCID:
PMC3287829
Abstract Full Text PDF–1.9M
Assessing the impact of missing genotype data in rare variant association analysis
Reedik Mägi, Ashish Kumar, Andrew P Morris
BMC Proc. 2011; 5(Suppl 9): S107. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S107
PMCID:
PMC3287830
Abstract Full Text PDF–463K
Detection of rare functional variants using group ISIS
Yue S Niu, Ning Hao, Lingling An
BMC Proc. 2011; 5(Suppl 9): S108. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S108
PMCID:
PMC3287831
Abstract Full Text PDF–229K
Application of Bayesian network structure learning to identify causal variant SNPs from resequencing data
Christopher E Schlosberg, Tae-Hwi Schwantes-An, Weimin Duan, Nancy L Saccone
BMC Proc. 2011; 5(Suppl 9): S109. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S109
PMCID:
PMC3287832
Abstract Full Text PDF–342K
Genome-wide case-control study in GAW17 using coalesced rare variants
Libo Wang, Vitara Pungpapong, Yanzhu Lin, Min Zhang, Dabao Zhang
BMC Proc. 2011; 5(Suppl 9): S110. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S110
PMCID:
PMC3287834
Abstract Full Text PDF–223K
Are quantitative trait-dependent sampling designs cost-effective for analysis of rare and common variants?
Yildiz E Yilmaz, Shelley B Bull
BMC Proc. 2011; 5(Suppl 9): S111. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S111
PMCID:
PMC3287835
Abstract Full Text PDF–232K
Detection of rare variant effects in association studies: extreme values, iterative regression, and a hybrid approach
Zhaogong Zhang, Qiuying Sha, Xinli Wang, Shuanglin Zhang
BMC Proc. 2011; 5(Suppl 9): S112. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S112
PMCID:
PMC3287836
Abstract Full Text PDF–809K
Comparison of statistical approaches to rare variant analysis for quantitative traits
Han Chen, Audrey E Hendricks, Yansong Cheng, Adrienne L Cupples, Josée Dupuis, Ching-Ti Liu
BMC Proc. 2011; 5(Suppl 9): S113. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S113
PMCID:
PMC3287837
Abstract Full Text PDF–377K
Improved power by collapsing rare and common variants based on a data-adaptive forward selection strategy
Yilin Dai, Ling Guo, Jianping Dong, Renfang Jiang
BMC Proc. 2011; 5(Suppl 9): S114. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S114
PMCID:
PMC3287838
Abstract Full Text PDF–252K
Comparison of collapsing methods for the statistical analysis of rare variants
Carmen Dering, Andreas Ziegler, Inke R König, Claudia Hemmelmann
BMC Proc. 2011; 5(Suppl 9): S115. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S115
PMCID:
PMC3287839
Abstract Full Text PDF–243K
Effect of population stratification analysis on false-positive rates for common and rare variants
Hua He, Xue Zhang, Lili Ding, Tesfaye M Baye, Brad G Kurowski, Lisa J Martin
BMC Proc. 2011; 5(Suppl 9): S116. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S116
PMCID:
PMC3287840
Abstract Full Text PDF–452K
Collapsing-based and kernel-based single-gene analyses applied to Genetic Analysis Workshop 17 mini-exome data
Lun Li, Wei Zheng, Joon Sang Lee, Xianghua Zhang, John Ferguson, Xiting Yan, Hongyu Zhao
BMC Proc. 2011; 5(Suppl 9): S117. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S117
PMCID:
PMC3287841
Abstract Full Text PDF–344K
Evaluation of pooled association tests for rare variant identification
Wan-Yu Lin, Boshao Zhang, Nengjun Yi, Guimin Gao, Nianjun Liu
BMC Proc. 2011; 5(Suppl 9): S118. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S118
PMCID:
PMC3287842
Abstract Full Text PDF–476K
Evaluating methods for the analysis of rare variants in sequence data
Alexander Luedtke, Scott Powers, Ashley Petersen, Alexandra Sitarik, Airat Bekmetjev, Nathan L Tintle
BMC Proc. 2011; 5(Suppl 9): S119. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S119
PMCID:
PMC3287843
Abstract Full Text PDF–235K
Identification of genes associated with complex traits by testing the genetic dissimilarity between individuals
Yan V Sun, Wei Zhao, Kerby A Shedden, Sharon LR Kardia
BMC Proc. 2011; 5(Suppl 9): S120. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S120
PMCID:
PMC3287845
Abstract Full Text PDF–222K
Application of collapsing methods for continuous traits to the Genetic Analysis Workshop 17 exome sequence data
Yun Ju Sung, Treva K Rice, Dabeeru C Rao
BMC Proc. 2011; 5(Suppl 9): S121. Published online 2011 November 29. doi: 10.1186/1753-6561-5-S9-S121
PMCID:
PMC3287846
Abstract Full Text PDF–444K
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