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  1. Genetic Analysis Workshop 14 provided re-genotyped single-nucleotide polymorphism (SNP) data. Specifically, both Center for Inherited Disease Research (CIDR) and Affymetrix genotyped the same 11,560 SNPs from ...

    Authors: Nathan L Tintle, Kwangmi Ahn, Nancy Role Mendell, Derek Gordon and Stephen J Finch
    Citation: BMC Genetics 2005 6(Suppl 1):S154

    This article is part of a Supplement: Volume 6 Supplement 1

  2. Linkage analysis methods that incorporate etiological heterogeneity of complex diseases are likely to demonstrate greater power than traditional linkage analysis methods. Several such methods use covariates to...

    Authors: Brian H Reck, Nandita Mukhopadhyay, Hui-Ju Tsai and Daniel E Weeks
    Citation: BMC Genetics 2005 6(Suppl 1):S143

    This article is part of a Supplement: Volume 6 Supplement 1

  3. The Genetic Analysis Workshop 14 simulated data presents an interesting, challenging, and plausible example of a complex disease interaction in a dataset. This paper summarizes the ease of detection for each o...

    Authors: Mark W Logue, Andrew W George, M Anne Spence and Veronica J Vieland
    Citation: BMC Genetics 2005 6(Suppl 1):S141

    This article is part of a Supplement: Volume 6 Supplement 1

  4. We explored the utility of selecting a genetically predisposed subgroup to increase the finding of a genetic signal in the Genetic Analysis Workshop 14 Collaborative Study on the Genetics of Alcoholism dataset...

    Authors: Kelly S Benke, Gary A Chase and Daniele M Fallin
    Citation: BMC Genetics 2005 6(Suppl 1):S137

    This article is part of a Supplement: Volume 6 Supplement 1

  5. Genetic mechanisms underlying alcoholism are complex. Understanding the etiology of alcohol dependence and its comorbid conditions such as smoking is important because of the significant health concerns. In th...

    Authors: Yuanqing Ye, Xiaoyun Zhong and Heping Zhang
    Citation: BMC Genetics 2005 6(Suppl 1):S135

    This article is part of a Supplement: Volume 6 Supplement 1

  6. Alcoholism is a serious public health problem. It has both genetic and environmental causes. In an effort to gain understanding of the underlying genetic susceptibility to alcoholism, a long-term study has bee...

    Authors: Catherine T Falk
    Citation: BMC Genetics 2005 6(Suppl 1):S131

    This article is part of a Supplement: Volume 6 Supplement 1

  7. The problem of estimating haplotype frequencies from population data has been considered by numerous investigators, resulting in a wide variety of possible algorithmic and statistical solutions. We propose a r...

    Authors: Kevin C Cartier and Daniel Baechle
    Citation: BMC Genetics 2005 6(Suppl 1):S129

    This article is part of a Supplement: Volume 6 Supplement 1

  8. In this paper we apply two novel quantitative trait linkage statistics based on the posterior probability of linkage (PPL) to chromosome 4 from the GAW 14 COGA dataset. Our approaches are advantageous since th...

    Authors: Christopher W Bartlett and Veronica J Vieland
    Citation: BMC Genetics 2005 6(Suppl 1):S121

    This article is part of a Supplement: Volume 6 Supplement 1

  9. A genetic analysis of age of onset of alcoholism was performed on the Collaborative Study on the Genetics of Alcoholism data released for Genetic Analysis Workshop 14. Our study illustrates an application of t...

    Authors: Victor Apprey, Joseph Afful, Jules P Harrell, Robert E Taylor and George E Bonney
    Citation: BMC Genetics 2005 6(Suppl 1):S119

    This article is part of a Supplement: Volume 6 Supplement 1

  10. Complex diseases are often reported along with disease-related traits (DRT). Sometimes investigators consider both disease and DRT phenotypes separately and sometimes they consider individuals as affected if t...

    Authors: Fei Ji, Dayoung Lee and Nancy Role Mendell
    Citation: BMC Genetics 2005 6(Suppl 1):S113

    This article is part of a Supplement: Volume 6 Supplement 1

  11. We report the analysis results of the Genetic Analysis Workshop 14 simulated microsatellite marker dataset, using replicate 50 from the Danacaa population. We applied several methods for association analysis o...

    Authors: Rachid El Galta, Li Hsu and Jeanine J Houwing-Duistermaat
    Citation: BMC Genetics 2005 6(Suppl 1):S101

    This article is part of a Supplement: Volume 6 Supplement 1

  12. 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

    This article is part of a Supplement: Volume 6 Supplement 1

  13. 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

    This article is part of a Supplement: Volume 6 Supplement 1

  14. 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

    This article is part of a Supplement: Volume 6 Supplement 1

  15. 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

    This article is part of a Supplement: Volume 6 Supplement 1

  16. 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

    This article is part of a Supplement: Volume 6 Supplement 1

  17. We studied several methods for selecting single-nucleotide polymorphisms (SNPs) in a disease association study. Two major categories for analytical strategy are the univariate and the set selection approaches....

    Authors: Jungnam Joo, Xin Tian, Gang Zheng, Jing-Ping Lin and Nancy L Geller
    Citation: BMC Genetics 2005 6(Suppl 1):S93

    This article is part of a Supplement: Volume 6 Supplement 1

  18. 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

    This article is part of a Supplement: Volume 6 Supplement 1

  19. 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

    This article is part of a Supplement: Volume 6 Supplement 1

  20. 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

    This article is part of a Supplement: Volume 6 Supplement 1

  21. 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

    This article is part of a Supplement: Volume 6 Supplement 1

  22. Haplotype data contain signatures of ancestral alleles and increased information for mapping genes associated with complex traits. The motivation of this paper is to test the feasibility of a recently develope...

    Authors: Dajun Qian
    Citation: BMC Genetics 2005 6(Suppl 1):S79

    This article is part of a Supplement: Volume 6 Supplement 1

  23. 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

    This article is part of a Supplement: Volume 6 Supplement 1

  24. 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

    This article is part of a Supplement: Volume 6 Supplement 1

  25. We present a new method for fine-mapping a disease susceptibility locus using a case-control design. The new method, termed the weighted average (WA) statistic, averages the Cochran-Armitage (CA) trend test st...

    Authors: Kijoung Song, Mohammed S Orloff, Qing Lu and Robert C Elston
    Citation: BMC Genetics 2005 6(Suppl 1):S67

    This article is part of a Supplement: Volume 6 Supplement 1

  26. 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

    This article is part of a Supplement: Volume 6 Supplement 1

  27. 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

    This article is part of a Supplement: Volume 6 Supplement 1

  28. 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

    This article is part of a Supplement: Volume 6 Supplement 1

  29. 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

    This article is part of a Supplement: Volume 6 Supplement 1

  30. 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

    This article is part of a Supplement: Volume 6 Supplement 1

  31. 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

    This article is part of a Supplement: Volume 6 Supplement 1

  32. 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

    This article is part of a Supplement: Volume 6 Supplement 1

  33. 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

    This article is part of a Supplement: Volume 6 Supplement 1

  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

    This article is part of a Supplement: Volume 6 Supplement 1

  35. 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

    This article is part of a Supplement: Volume 6 Supplement 1

  36. 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

    This article is part of a Supplement: Volume 6 Supplement 1

  37. 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

    This article is part of a Supplement: Volume 6 Supplement 1

  38. Several simulation studies have suggested that a high-density single-nucleotide polymorphisms (SNPs) marker set may be as useful as a traditional microsatellites (MS) marker set in performing whole-genome link...

    Authors: Jennifer Lin and Kuang-Yu Liu
    Citation: BMC Genetics 2005 6(Suppl 1):S25

    This article is part of a Supplement: Volume 6 Supplement 1

  39. 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

    This article is part of a Supplement: Volume 6 Supplement 1

  40. 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

    This article is part of a Supplement: Volume 6 Supplement 1

  41. Three variants of the confidence set inference (CSI) procedure were proposed and applied to both the simulated and the Collaborative Study on the Genetics of Alcoholism (COGA) data. For each of the two applica...

    Authors: Charalampos Papachristou and Shili Lin
    Citation: BMC Genetics 2005 6(Suppl 1):S21

    This article is part of a Supplement: Volume 6 Supplement 1

  42. 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

    This article is part of a Supplement: Volume 6 Supplement 1

  43. 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

    This article is part of a Supplement: Volume 6 Supplement 1

  44. 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

    This article is part of a Supplement: Volume 6 Supplement 1

  45. 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

    This article is part of a Supplement: Volume 6 Supplement 1

  46. 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

    This article is part of a Supplement: Volume 6 Supplement 1

  47. 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

    This article is part of a Supplement: Volume 6 Supplement 1

  48. Dense SNP maps can be highly informative for linkage studies. But when parental genotypes are missing, multipoint linkage scores can be inflated in regions with substantial marker-marker linkage disequilibrium...

    Authors: Douglas F Levinson and Peter Holmans
    Citation: BMC Genetics 2005 6(Suppl 1):S6

    This article is part of a Supplement: Volume 6 Supplement 1

  49. 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

    This article is part of a Supplement: Volume 6 Supplement 1

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