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Volume 6 Supplement 1

Genetic Analysis Workshop 14: Microsatellite and single-nucleotide polymorphism

Proceedings

Edited by Joan E Bailey-Wilson, Laura Almasy, Mariza de Andrade, Julia Bailey, Heike Bickeböller, Heather J Cordell, E Warwick Daw, Lynn Goldin, Ellen L Goode, Courtney Gray-McGuire, Wayne Hening, Gail Jarvik, Brion S Maher, Nancy Mendell, Andrew D Paterson, John Rice, Glen Satten, Brian Suarez, Veronica Vieland, Marsha Wilcox, Heping Zhang, Andreas Ziegler and Jean W MacCluer

Genetic Analysis Workshop 14: Microsatellite and single-nucleotide polymorphism. Go to conference site.

Noordwijkerhout, The Netherlands7-10 September 2004

Page 1 of 4

  1. Authors: Joan E Bailey-Wilson, Laura Almasy, Mariza de Andrade, Julia Bailey, Heike Bickeböller, Heather J Cordell, E Warwick Daw, Lynn Goldin, Ellen L Goode, Courtney Gray-McGuire, Wayne Hening, Gail Jarvik, Brion S Maher, Nancy Mendell, Andrew D Paterson, John Rice…

    Citation: BMC Genetics 2005 6(Suppl 1):S1

    Content type: Introduction

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  2. The data provided to the Genetic Analysis Workshop 14 (GAW 14) was the result of a collaboration among several different groups, catalyzed by Elizabeth Pugh from The Center for Inherited Disease Research (CIDR...

    Authors: Howard J Edenberg, Laura J Bierut, Paul Boyce, Manqiu Cao, Simon Cawley, Richard Chiles, Kimberly F Doheny, Mark Hansen, Tony Hinrichs, Kevin Jones, Mark Kelleher, Giulia C Kennedy, Guoying Liu, Gregory Marcus, Celeste McBride, Sarah Shaw Murray…

    Citation: BMC Genetics 2005 6(Suppl 1):S2

    Content type: Proceedings

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  3. The Genetic Analysis Workshop 14 simulated dataset was designed 1) To test the ability to find genes related to a complex disease (such as alcoholism). Such a disease may be given a variety of definitions by d...

    Authors: David A Greenberg, Junying Zhang, Dvora Shmulewitz, Lisa J Strug, Regina Zimmerman, Veena Singh and Sudhir Marathe

    Citation: BMC Genetics 2005 6(Suppl 1):S3

    Content type: Proceedings

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  4. We analyzed 143 pedigrees (364 nuclear families) in the Collaborative Study on the Genetics of Alcoholism (COGA) data provided to the participants in the Genetic Analysis Workshop 14 (GAW14) with the goal of c...

    Authors: Guanjie Chen, Adebowale Adeyemo, Jie Zhou, Ao Yuan, Yuanxiu Chen and Charles Rotimi

    Citation: BMC Genetics 2005 6(Suppl 1):S4

    Content type: Proceedings

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  5. The feasibility of effectively analyzing high-density single nucleotide polymorphism (SNP) maps in whole genome scans of complex traits is not known. The purpose of this study was to compare variance component...

    Authors: Helen Kim, Carolyn M Hutter, Stephanie A Monks and Karen L Edwards

    Citation: BMC Genetics 2005 6(Suppl 1):S5

    Content type: Proceedings

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  6. We performed linkage and linkage disequilibrium (LD) mapping analyses to compare the power between microsatellite and single nucleotide polymorphism (SNP) markers. Chromosome-wide analyses were performed for a...

    Authors: Hsiu-Fen Lin, Suh-Hang Hank Juo and Rong Cheng

    Citation: BMC Genetics 2005 6(Suppl 1):S7

    Content type: Proceedings

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  7. Both theoretical and applied studies have proven that the utility of single nucleotide polymorphism (SNP) markers in linkage analysis is more powerful and cost-effective than current microsatellite marker assa...

    Authors: Qianli Ma, Yi Yu, Yan Meng, John Farrell, Lindsay A Farrer and Marsha A Wilcox

    Citation: BMC Genetics 2005 6(Suppl 1):S8

    Content type: Proceedings

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  8. The efficacy of linkage studies using microsatellites and single-nucleotide polymorphisms (SNPs) was evaluated. Analyzed data were supplied by the Collaborative Study on the Genetics of Alcoholism (COGA). Alco...

    Authors: Jérémie Nsengimana, Hélène Renard and David Goldgar

    Citation: BMC Genetics 2005 6(Suppl 1):S10

    Content type: Proceedings

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  9. We performed multipoint linkage analysis of the electrophysiological trait ECB21 on chromosome 4 in the full pedigrees provided by the Collaborative Study on the Genetics of Alcoholism (COGA). Three Markov cha...

    Authors: Weiva Sieh, Saonli Basu, Audrey Q Fu, Joseph H Rothstein, Paul A Scheet, William CL Stewart, Yun J Sung, Elizabeth A Thompson and Ellen M Wijsman

    Citation: BMC Genetics 2005 6(Suppl 1):S11

    Content type: Proceedings

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  10. Using the dataset provided for Genetic Analysis Workshop 14 by the Collaborative Study on the Genetics of Alcoholism, we performed genome-wide linkage analysis of age at onset of alcoholism to compare the util...

    Authors: Bamidele O Tayo, Yulan Liang, Saverio Stranges and Maurizio Trevisan

    Citation: BMC Genetics 2005 6(Suppl 1):S12

    Content type: Proceedings

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  11. Recent studies have suggested that a high-density single nucleotide polymorphism (SNP) marker set could provide equivalent or even superior information compared with currently used microsatellite (STR) marker ...

    Authors: Xiaohong (Rose) Yang, Kevin Jacobs, Kimberly F Kerstann, Andrew W Bergen, Alisa M Goldstein and Lynn R Goldin

    Citation: BMC Genetics 2005 6(Suppl 1):S14

    Content type: Proceedings

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  12. Alcohol dependence is a serious public health problem. We studied data from families participating in the Collaborative Study on the Genetics of Alcoholism (COGA) and made available to participants in the Gene...

    Authors: Yi Yu, Yan Meng, Qianli Ma, John Farrell, Lindsay A Farrer and Marsha A Wilcox

    Citation: BMC Genetics 2005 6(Suppl 1):S15

    Content type: Proceedings

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  13. The central issue for Genetic Analysis Workshop 14 (GAW14) is the question, which is the better strategy for linkage analysis, the use of single-nucleotide polymorphisms (SNPs) or microsatellite markers? To an...

    Authors: Qingqi Yue, Victor Apprey and George E Bonney

    Citation: BMC Genetics 2005 6(Suppl 1):S16

    Content type: Proceedings

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  14. The Collaborative Study on the Genetics of Alcoholism (COGA) is a large-scale family study designed to identify genes that affect the risk for alcoholism and alcohol-related phenotypes. We performed genome-wid...

    Authors: Chun Zhang, Simon Cawley, Guoying Liu, Manqiu Cao, Harley Gorrell and Giulia C Kennedy

    Citation: BMC Genetics 2005 6(Suppl 1):S17

    Content type: Proceedings

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  15. The objective of this study is to evaluate the efficacy of a model-free linkage statistics for finding evidence of linkage using two different maps and to illustrate how the comparison of results from several ...

    Authors: Marie-Claude Babron, Catherine Bourgain, Anne-Louise Leutenegger and Françoise Clerget-Darpoux

    Citation: BMC Genetics 2005 6(Suppl 1):S18

    Content type: Proceedings

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  16. Multivariate phenotypes underlie complex traits. Thus, instead of using the end-point trait, it may be statistically more powerful to use a multivariate phenotype correlated to the end-point trait for detectin...

    Authors: Saurabh Ghosh, Samsiddhi Bhattacharjee, Gourab Basu, Sandip Pal and Partha P Majumder

    Citation: BMC Genetics 2005 6(Suppl 1):S19

    Content type: Proceedings

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  17. Genome-wide linkage analysis using microsatellite markers has been successful in the identification of numerous Mendelian and complex disease loci. The recent availability of high-density single-nucleotide pol...

    Authors: Alison P Klein, Ya-Yu Tsai, Priya Duggal, Elizabeth M Gillanders, Michael Barnhart, Rasika A Mathias, Ian P Dusenberry, Amy Turiff, Peter S Chines, Janet Goldstein, Robert Wojciechowski, Wayne Hening, Elizabeth W Pugh and Joan E Bailey-Wilson

    Citation: BMC Genetics 2005 6(Suppl 1):S20

    Content type: Proceedings

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  18. Study design strategies are of critical importance in the search for genes underlying complex diseases. Two important design choices in planning gene mapping studies are the analytic strategy to be used, which...

    Authors: Sabine Plancoulaine, Alexandre Alcaïs, Yue Chen, Laurent Abel and France Gagnon

    Citation: BMC Genetics 2005 6(Suppl 1):S22

    Content type: Proceedings

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  19. The simultaneous testing of a large number of hypotheses in a genome scan, using individual thresholds for significance, inherently leads to inflated genome-wide false positive rates. There exist various appro...

    Authors: Ritwik Sinha, Moumita Sinha, George Mathew, Robert C Elston and Yuqun Luo

    Citation: BMC Genetics 2005 6(Suppl 1):S23

    Content type: Proceedings

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  20. Using the simulated data of Problem 2 for Genetic Analysis Workshop 14 (GAW14), we investigated the ability of three bootstrap-based resampling estimators (a shrinkage, an out-of-sample, and a weighted estimat...

    Authors: Long Yang Wu, Sophia SF Lee, Haijiang Steven Shi, Lei Sun and Shelley B Bull

    Citation: BMC Genetics 2005 6(Suppl 1):S24

    Content type: Proceedings

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  21. Single-nucleotide polymorphisms (SNPs) are a class of attractive genetic markers for population genetic studies and for identifying genetic variations underlying complex traits. However, the usefulness and eff...

    Authors: Nianjun Liu, Liang Chen, Shuang Wang, Cheongeun Oh and Hongyu Zhao

    Citation: BMC Genetics 2005 6(Suppl 1):S26

    Content type: Proceedings

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  22. Using the Genetic Analysis Workshop 14 (GAW14) simulated dataset, we compare microsatellite and single-nucleotide polymorphism (SNP) markers in terms of two measures of information content, the traditional ent...

    Authors: Anbupalam Thalamuthu, Indranil Mukhopadhyay, Amrita Ray and Daniel E Weeks

    Citation: BMC Genetics 2005 6(Suppl 1):S27

    Content type: Proceedings

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  23. There is currently a great interest in using single-nucleotide polymorphisms (SNPs) in genetic linkage and association studies because of the abundance of SNPs as well as the availability of high-throughput ge...

    Authors: Shuang Wang, Song Huang, Nianjun Liu, Liang Chen, Cheongeun Oh and Hongyu Zhao

    Citation: BMC Genetics 2005 6(Suppl 1):S28

    Content type: Proceedings

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  24. There is growing evidence that a map of dense single-nucleotide polymorphisms (SNPs) can outperform a map of sparse microsatellites for linkage analysis. There is also argument as to whether a clustered SNP ma...

    Authors: Chao Xing, Fredrick R Schumacher, Guan Xing, Qing Lu, Tao Wang and Robert C Elston

    Citation: BMC Genetics 2005 6(Suppl 1):S29

    Content type: Proceedings

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  25. A thorough genetic mapping study was performed to identify predisposing genes for alcoholism dependence using the Collaborative Study on the Genetics of Alcoholism (COGA) data. The procedure comprised whole-ge...

    Authors: Hsin-Chou Yang, Chien-Ching Chang, Chin-Yu Lin, Chun-Liang Chen, Chin-Yu Lin and Cathy SJ Fann

    Citation: BMC Genetics 2005 6(Suppl 1):S30

    Content type: Proceedings

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  26. Increasingly, single-nucleotide polymorphism (SNP) markers are being used in preference to microsatellite markers. However, methods developed for microsatellites may be problematic when applied to SNP markers....

    Authors: E Warwick Daw, Simon C Heath and Yue Lu

    Citation: BMC Genetics 2005 6(Suppl 1):S32

    Content type: Proceedings

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  27. Covariate-based linkage analyses using a conditional logistic model as implemented in LODPAL can increase the power to detect linkage by minimizing disease heterogeneity. However, each additional covariate ana...

    Authors: Betty Q Doan, Constantine E Frangakis, Yin Y Shugart and Joan E Bailey-Wilson

    Citation: BMC Genetics 2005 6(Suppl 1):S33

    Content type: Proceedings

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  28. We used the LOKI software to generate multipoint identity-by-descent matrices for a microsatellite map (with 31 markers) and two single-nucleotide polymorphism (SNP) maps to examine information content across ...

    Authors: Anthony L Hinrichs, Sarah Bertelsen, Laura J Bierut, Gerald Dunn, Carol H Jin, John S Kauwe and Brian K Suarez

    Citation: BMC Genetics 2005 6(Suppl 1):S34

    Content type: Proceedings

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  29. The basic idea of affected-sib-pair (ASP) linkage analysis is to test whether the inheritance pattern of a marker deviates from Mendelian expectation in a sample of ASPs. The test depends on an assumed Mendeli...

    Authors: Pei-Ying Shih, Tao Wang, Chao Xing, Moumita Sinha, Yeunjoo Song and Robert C Elston

    Citation: BMC Genetics 2005 6(Suppl 1):S36

    Content type: Proceedings

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  30. In this paper, we applied the nonparametric linkage regression approach to the Caucasian genome scan data from the Collaborative Study on the Genetics of Alcoholism to search for regions of the genome that exh...

    Authors: Adrienne H Williams, W Mark Brown and Carl D Langefeld

    Citation: BMC Genetics 2005 6(Suppl 1):S37

    Content type: Proceedings

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  31. We have developed a recursive-partitioning (RP) algorithm for identifying phenotype and covariate groupings that interact with the evidence for linkage. This data-mining approach for detecting gene × environme...

    Authors: Wei Xu, Chelsea Taylor, Justin Veenstra, Shelley B Bull, Mary Corey and Celia MT Greenwood

    Citation: BMC Genetics 2005 6(Suppl 1):S38

    Content type: Proceedings

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  32. The main goal of this paper is to couple the Haseman-Elston method with a simple yet effective Bayesian factor-screening approach. This approach selects markers by considering a set of multigenic models that i...

    Authors: Seungtai Yoon, Young Ju Suh, Nancy Role Mendell and Kenny Qian Ye

    Citation: BMC Genetics 2005 6(Suppl 1):S39

    Content type: Proceedings

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  33. The purposes of this study were 1) to examine the performance of a new multimarker regression approach for model-free linkage analysis in comparison to a conventional multipoint approach, and 2) to determine t...

    Authors: Mathew J Barber, Eleanor Wheeler and Heather J Cordell

    Citation: BMC Genetics 2005 6(Suppl 1):S40

    Content type: Proceedings

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  34. In order to detect linkage of the simulated complex disease Kofendrerd Personality Disorder across studies from multiple populations, we performed a genome scan meta-analysis (GSMA). Using the 7-cM microsatell...

    Authors: Margaret E Cooper, Toby H Goldstein, Brion S Maher and Mary L Marazita

    Citation: BMC Genetics 2005 6(Suppl 1):S42

    Content type: Proceedings

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  35. We present a meta-analysis procedure for genome-wide linkage studies (MAGS). The MAGS procedure combines genome-wide linkage results across studies with possibly distinct marker maps. We applied the MAGS proce...

    Authors: Carol J Etzel, Mei Liu and Tracy J Costello

    Citation: BMC Genetics 2005 6(Suppl 1):S43

    Content type: Proceedings

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  36. The calculation of multipoint likelihoods is computationally challenging, with the exact calculation of multipoint probabilities only possible on small pedigrees with many markers or large pedigrees with few m...

    Authors: Andrew W George, LaVonne A Mangin, Christopher W Bartlett, Mark W Logue, Alberto M Segre and Veronica J Vieland

    Citation: BMC Genetics 2005 6(Suppl 1):S44

    Content type: Proceedings

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  37. We evaluate a method for the incorporation of covariates into linkage analysis using the Genetic Analysis Workshop 14 simulated data. Focusing on a randomly chosen replicate (42) we investigated the effect of ...

    Authors: Marian L Hamshere, Stuart MacGregor, Valentina Moskvina, Ivan N Nikolov and Peter A Holmans

    Citation: BMC Genetics 2005 6(Suppl 1):S45

    Content type: Proceedings

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  38. For linkage analysis in affected sibling pairs, we propose a regression model to incorporate information from a disease-associated single-nucleotide polymorphism located under the linkage peak. This model can ...

    Authors: Jeanine J Houwing-Duistermaat, Hae-Won Uh, Jeremie JP Lebrec, Hein Putter and Li Hsu

    Citation: BMC Genetics 2005 6(Suppl 1):S46

    Content type: Proceedings

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  39. In this paper we investigate the power of finding linkage to a disease locus through analysis of the disease-related traits. We propose two family-based gene-model-free linkage statistics. Both involve conside...

    Authors: Heejong Sung, Stephen J Finch, Kenny Q Ye and Nancy R Mendell

    Citation: BMC Genetics 2005 6(Suppl 1):S47

    Content type: Proceedings

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  40. In the Haseman-Elston approach the squared phenotypic difference is regressed on the proportion of alleles shared identical by descent (IBD) to map a quantitative trait to a genetic marker. In applications the...

    Authors: Daniel Franke, André Kleensang, Robert C Elston and Andreas Ziegler

    Citation: BMC Genetics 2005 6(Suppl 1):S50

    Content type: Proceedings

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