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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

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  1. Content type: Proceedings

    Recombination during meiosis is one of the most important biological processes, and the level of recombination rates for a given individual is under genetic control. In this study, we conducted genome-wide ass...

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

    Citation: BMC Genetics 2005 6(Suppl 1):S51

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  2. Content type: Proceedings

    Association studies of quantitative traits have often relied on methods in which a normal distribution of the trait is assumed. However, quantitative phenotypes from complex human diseases are often censored, ...

    Authors: Yi-Ju Li, Eden R Martin, Ling Zhang and Andrew S Allen

    Citation: BMC Genetics 2005 6(Suppl 1):S53

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  3. Content type: Proceedings

    By analyzing a "pseudo-trait," a trait not linked or associated with any of the markers tested, the distribution of the test statistic under the null hypothesis can provide the critical value for the appropria...

    Authors: George J Papanicolaou, Cristina M Justice, Illija M Kovac, Alexa JM Sorant and Alexander F Wilson

    Citation: BMC Genetics 2005 6(Suppl 1):S54

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  4. Content type: Proceedings

    For the identification of susceptibility loci in complex diseases the choice of the target phenotype is very important. We compared results of genome-wide searches for linkage or for association related to thr...

    Authors: Albert Rosenberger, Nico Janicke, Karola Köhler, Katrin Korb, Bettina Kulle and Heike Bickeböller

    Citation: BMC Genetics 2005 6(Suppl 1):S55

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  5. Content type: Proceedings

    The beta 2 electroencephalogram (EEG) phenotype is used as a quantitative measure related to alcoholism, and evidence of linkage and association has previously been reported in the Collaborative Study on the G...

    Authors: Marie-Hélène Roy-Gagnon, Rasika A Mathias and Alexander F Wilson

    Citation: BMC Genetics 2005 6(Suppl 1):S56

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  6. Content type: Proceedings

    The information content of a continuous variable exceeds that of its categorical counterpart. The parameterization of a model may diminish the benefit of using a continuous variable. We explored the use of con...

    Authors: Kevin R Viel, Diane M Warren, Alfonso Buil, Thomas D Dyer, Tom E Howard and Laura Almasy

    Citation: BMC Genetics 2005 6(Suppl 1):S57

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  7. Content type: Proceedings

    The transmission/disequilibrium test statistic has been used for assessing genetic association in affected-parent trios. In the presence of multiple tightly linked marker loci where local dependency may exist,...

    Authors: Li Hsu, Xuesong Yu, Jeanine J Houwing-Duistermaat, Hae-Won Uh, Rachid El Galta, Jeremie JP Lebrec and Hua Tang

    Citation: BMC Genetics 2005 6(Suppl 1):S60

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  8. Content type: Proceedings

    We developed a new marker-reordering algorithm to find the best order of fine-mapping markers for multipoint linkage analysis. The algorithm searches for the best order of fine-mapping markers such that the su...

    Authors: Gyungah Jun, Yeunjoo Song, Sudha K Iyengar and Robert C Elston

    Citation: BMC Genetics 2005 6(Suppl 1):S61

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  9. Content type: Proceedings

    We use the Genetic Analysis Workshop 14 simulated data to explore the effectiveness of a two-stage strategy for mapping complex disease loci consisting of an initial genome scan with confidence interval constr...

    Authors: Juan Pablo Lewinger, Sophia SF Lee, Joanna Biernacka, Long Yang Wu, Haijiang Steven Shi and Shelley B Bull

    Citation: BMC Genetics 2005 6(Suppl 1):S62

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  10. Content type: Proceedings

    There is great interest in the use of computationally intensive methods for fine mapping of marker data. In this paper we develop methods based upon ideas originally proposed 100 years ago in the context of sp...

    Authors: John Molitor, Keyan Zhao and Paul Marjoram

    Citation: BMC Genetics 2005 6(Suppl 1):S63

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  11. Content type: Proceedings

    Bayesian spatial modeling has become important in disease mapping and has also been suggested as a useful tool in genetic fine mapping. We have implemented the Potts model and applied it to the Genetic Analysi...

    Authors: Elena V Moltchanova, Janne Pitkäniemi and Laura Haapala

    Citation: BMC Genetics 2005 6(Suppl 1):S64

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  12. Content type: Proceedings

    It is generally assumed that the detection of disease susceptibility genes via fine-mapping association study is facilitated by consideration of marker haplotypes. In this study, we compared the performance of...

    Authors: Dushanthi Pinnaduwage and Laurent Briollais

    Citation: BMC Genetics 2005 6(Suppl 1):S65

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  13. Content type: Proceedings

    A common dilemma arising in linkage studies of complex genetic diseases is the selection of positive signals, their follow-up with association studies and discrimination between true and false positive results...

    Authors: Neil Shephard, Sally John, Lon Cardon, Mark I McCarthy and Eleftheria Zeggini

    Citation: BMC Genetics 2005 6(Suppl 1):S66

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  14. Content type: Proceedings

    We used the FBAT (family-based association test) software to test for association between 300 individual single-nucleotide polymorphisms and P1 (a latent trait of Kofendred Personality Disorder) in 100 simulat...

    Authors: Ming-Hsi Wang, Mitchell Guo and Yin Y Shugart

    Citation: BMC Genetics 2005 6(Suppl 1):S68

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  15. Content type: Proceedings

    Haplotypes, the combination of closely linked alleles that fall on the same chromosome, show great promise for studying the genetic components of complex diseases. However, when only multilocus genotype data a...

    Authors: Andrew S Allen and Glen A Satten

    Citation: BMC Genetics 2005 6(Suppl 1):S69

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  16. Content type: Proceedings

    We applied a new approach based on Mantel statistics to analyze the Genetic Analysis Workshop 14 simulated data with prior knowledge of the answers. The method was developed in order to improve the power of a ...

    Authors: Lars Beckmann, Christine Fischer, Markus Obreiter, Michael Rabes and Jenny Chang-Claude

    Citation: BMC Genetics 2005 6(Suppl 1):S70

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  17. Content type: Proceedings

    Our goal was to compare methods for tagging single-nucleotide polymorphisms (tagSNPs) with respect to the power to detect disease association under differing haplotype-disease association models. We were also ...

    Authors: Kelly M Burkett, Mercedeh Ghadessi, Brad McNeney, Jinko Graham and Denise Daley

    Citation: BMC Genetics 2005 6(Suppl 1):S71

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  18. Content type: Proceedings

    In genetic association studies, linkage disequilibrium (LD) within a region can be exploited to select a subset of single-nucleotide polymorphisms (SNPs) to genotype with minimal loss of information. A novel e...

    Authors: Joe M Butler, D Timothy Bishop and Jennifer H Barrett

    Citation: BMC Genetics 2005 6(Suppl 1):S72

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  19. Content type: Proceedings

    We compared seven different tagging single-nucleotide polymorphism (SNP) programs in 10 regions with varied amounts of linkage disequilibrium (LD) and physical distance. We used the Collaborative Studies on th...

    Authors: Priya Duggal, Elizabeth M Gillanders, Rasika A Mathias, Grace P Ibay, Alison P Klein, Agnes B Baffoe-Bonnie, Liang Ou, Ian P Dusenberry, Ya-Yu Tsai, Peter S Chines, Betty Q Doan and Joan E Bailey-Wilson

    Citation: BMC Genetics 2005 6(Suppl 1):S73

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  20. Content type: Proceedings

    Haplotype-based methods have become increasingly popular in the last decade because shared lengths in haplotypes can be used for disease localization. In this contribution, we propose a novel linkage-based hap...

    Authors: Andre Kleensang, Daniel Franke, Inke R König and Andreas Ziegler

    Citation: BMC Genetics 2005 6(Suppl 1):S75

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  21. Content type: Proceedings

    We compare and contrast the performance of SIMPLE, a Monte Carlo based software, with that of several other methods for linkage and haplotype analyses, focusing on the simulated data from the New York City pop...

    Authors: Shili Lin, Jie Ding, Crystal Dong, Zhenqiu Liu, Zhenxu J Ma, Shuyan Wan and Yan Xu

    Citation: BMC Genetics 2005 6(Suppl 1):S76

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  22. Content type: Proceedings

    The haplotypes of the X chromosome are accessible to direct count in males, whereas the diplotypes of the females may be inferred knowing the haplotype of their sons or fathers. Here, we investigated: 1) the p...

    Authors: Fabio Marroni, Chiara Toni, Benedetto Pennato, Ya-Yu Tsai, Pryia Duggal, Joan E Bailey-Wilson and Silvano Presciuttini

    Citation: BMC Genetics 2005 6(Suppl 1):S77

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  23. Content type: Proceedings

    Although permutation testing has been the gold standard for assessing significance levels in studies using multiple markers, it is time-consuming. A Bonferroni correction to the nominal p-value that uses the unde...

    Authors: Kristin K Nicodemus, Wenlei Liu, Gary A Chase, Ya-Yu Tsai and M Daniele Fallin

    Citation: BMC Genetics 2005 6(Suppl 1):S78

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  24. Content type: Proceedings

    This paper explores the decay of linkage disequilibrium (LD) on the autosomes and chromosome X. The extent of marker-marker LD is important for both linkage and association studies. The analysis of the Caucasi...

    Authors: Miranda E Cox, Joel K Campbell and Carl D Langefeld

    Citation: BMC Genetics 2005 6(Suppl 1):S81

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  25. Content type: Proceedings

    Accurately resolving population structure in a sample is important for both linkage and association studies. In this study we investigated the power of single-nucleotide polymorphisms (SNPs) in detecting popul...

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

    Citation: BMC Genetics 2005 6(Suppl 1):S84

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  26. Content type: Proceedings

    Genotype data from the Illumina Linkage III SNP panel (n = 4,720 SNPs) and the Affymetrix 10 k mapping array (n = 11,120 SNPs) were used to test the effects of linkage disequilibrium (LD) between SNPs in a linkag...

    Authors: Sarah Shaw Murray

    Citation: BMC Genetics 2005 6(Suppl 1):S85

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  27. Content type: Proceedings

    Linkage disequilibrium (LD) content was calculated for the Genetic Analysis Workshop 14 Affymetrix and Illumina single-nucleotide polymorphism (SNP) genome scans of the Collaborative Study on the Genetics of A...

    Authors: Juan Manuel Peralta, Thomas D Dyer, Diane M Warren, John Blangero and Laura Almasy

    Citation: BMC Genetics 2005 6(Suppl 1):S86

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  28. Content type: Proceedings

    Genetic Analysis Workshop 14 simulated data have been analyzed with MASC(marker association segregation chi-squares) in which we implemented a bootstrap procedure to provide the variation intervals of paramete...

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

    Citation: BMC Genetics 2005 6(Suppl 1):S87

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  29. Content type: Proceedings

    We applied three approaches for the identification of polymorphisms explaining the linkage evidence to the Genetic Analysis Workshop 14 simulated data: 1) the genotype-IBD sharing test (GIST); 2) an approach s...

    Authors: Ming-Huei Chen, Paul Van Eerdewegh and Josée Dupuis

    Citation: BMC Genetics 2005 6(Suppl 1):S88

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  30. Content type: Proceedings

    We conducted genome-wide linkage scans using both microsatellite and single-nucleotide polymorphism (SNP) markers. Regions showing the strongest evidence of linkage to alcoholism susceptibility genes were iden...

    Authors: Yen-Feng Chiu, Su-Yun Liu and Ya-Yu Tsai

    Citation: BMC Genetics 2005 6(Suppl 1):S89

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  31. Content type: Proceedings

    Linkage analysis based on identity-by-descent allele-sharing can be used to identify a chromosomal region harboring a quantitative trait locus (QTL), but lacks the resolution required for gene identification. ...

    Authors: Lorena M Havill, Thomas D Dyer, Dawn K Richardson, Michael C Mahaney and John Blangero

    Citation: BMC Genetics 2005 6(Suppl 1):S91

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  32. Content type: Proceedings

    This study, part of the Genetic Analysis Workshop 14 (GAW14), explored real Collaborative Study on the Genetics of Alcoholism data for linkage and association mapping between genetic polymorphisms (microsatell...

    Authors: Aldi T Kraja, Ingrid B Borecki and Michael A Province

    Citation: BMC Genetics 2005 6(Suppl 1):S94

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  33. Content type: Proceedings

    In this analysis we applied a regression based transmission disequilibrium test to the binary trait presence or absence of Kofendred Personality Disorder in the Genetic Analysis Workshop 14 (GAW14) simulated d...

    Authors: Emma K Larkin, Kevin C Cartier and Courtney Gray-McGuire

    Citation: BMC Genetics 2005 6(Suppl 1):S95

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  34. Content type: Proceedings

    Genome scans using dense single-nucleotide polymorphism (SNP) data have recently become a reality. It is thought that the increase in information content for linkage analysis as a result of the denser scans wi...

    Authors: Matthew B McQueen, Amy Murphy, Peter Kraft, Jessica Su, Ross Lazarus, Nan M Laird, Christoph Lange and Kristel Van Steen

    Citation: BMC Genetics 2005 6(Suppl 1):S96

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  35. Content type: Proceedings

    We explored the power and consistency to detect linkage and association with meta-analysis and pooled data analysis using Genetic Analysis Workshop 14 simulated data. The first 10 replicates from Aipotu popula...

    Authors: Xiaodong Wu, Donghui Kan, Richard S Cooper and Xiaofeng Zhu

    Citation: BMC Genetics 2005 6(Suppl 1):S97

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  36. Content type: Proceedings

    We consider 12 event-related potentials and one electroencephalogram measure as disease-related traits to compare alcohol-dependent individuals (cases) to unaffected individuals (controls). We use two approach...

    Authors: Tao Duan, Stephen J Finch, Kenny Q Ye, Gary A Chase and Nancy R Mendell

    Citation: BMC Genetics 2005 6(Suppl 1):S99

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  37. Content type: Proceedings

    We recently described a method for linkage disequilibrium (LD) mapping, using cladistic analysis of phased single-nucleotide polymorphism (SNP) haplotypes in a logistic regression framework. However, haplotype...

    Authors: Caroline Durrant and Andrew P Morris

    Citation: BMC Genetics 2005 6(Suppl 1):S100

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