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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
    Content type: Proceedings Published on:

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

  2. We used our newly developed linkage disequilibrium (LD) plotting software, JLIN, to plot linkage disequilibrium between pairs of single-nucleotide polymorphisms (SNPs) for three chromosomes of the Genetic Anal...

    Authors: Pamela A McCaskie, Kim W Carter, Simon R McCaskie and Lyle J Palmer
    Citation: BMC Genetics 2005 6(Suppl 1):S151
    Content type: Proceedings Published on:

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

  3. Simulated Genetic Analysis Workshop14 data were analyzed by jointly testing linkage and association and by accounting for epistasis using a candidate gene approach. Our group was unblinded to the "answers." Th...

    Authors: Joshua Millstein, Kimberly D Siegmund, David V Conti and W James Gauderman
    Citation: BMC Genetics 2005 6(Suppl 1):S147
    Content type: Proceedings Published on:

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

  4. The multifactor dimensionality reduction (MDR) is a model-free approach that can identify gene × gene or gene × environment effects in a case-control study. Here we explore several modifications of the MDR met...

    Authors: Hao Mei, Deqiong Ma, Allison Ashley-Koch and Eden R Martin
    Citation: BMC Genetics 2005 6(Suppl 1):S145
    Content type: Proceedings Published on:

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

  5. 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
    Content type: Proceedings Published on:

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

  6. 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
    Content type: Proceedings Published on:

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

  7. 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
    Content type: Proceedings Published on:

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

  8. 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
    Content type: Proceedings Published on:

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

  9. 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
    Content type: Proceedings Published on:

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

  10. 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
    Content type: Proceedings Published on:

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

  12. 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
    Content type: Proceedings Published on:

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

  13. 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
    Content type: Proceedings Published on:

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

  14. 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
    Content type: Proceedings Published on:

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

  15. 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
    Content type: Proceedings Published on:

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

  16. 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
    Content type: Proceedings Published on:

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

  17. 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
    Content type: Proceedings Published on:

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

  18. 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
    Content type: Proceedings Published on:

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

  19. 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
    Content type: Proceedings Published on:

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

  20. 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
    Content type: Proceedings Published on:

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

  21. 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
    Content type: Proceedings Published on:

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

  22. 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
    Content type: Proceedings Published on:

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

  23. 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
    Content type: Proceedings Published on:

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

  24. 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
    Content type: Proceedings Published on:

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

  25. 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
    Content type: Proceedings Published on:

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

  26. 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
    Content type: Proceedings Published on:

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

  27. 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
    Content type: Proceedings Published on:

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

  28. 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
    Content type: Proceedings Published on:

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

  29. 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
    Content type: Proceedings Published on:

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

  30. 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
    Content type: Proceedings Published on:

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

  31. 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
    Content type: Proceedings Published on:

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

  32. 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
    Content type: Proceedings Published on:

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

  33. 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
    Content type: Proceedings Published on:

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

  34. 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
    Content type: Proceedings Published on:

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

  35. 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
    Content type: Proceedings Published on:

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

  36. 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 Published on:

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

  37. 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 Published on:

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

  38. 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 Published on:

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

  39. 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 Published on:

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

  40. 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 Published on:

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

  41. 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 Published on:

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

  42. 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
    Content type: Proceedings Published on:

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

  43. 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 Published on:

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

  44. 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
    Content type: Proceedings Published on:

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

  45. 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 Published on:

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

  46. 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 Published on:

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

  47. 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 Published on:

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

  48. 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 Published on:

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

  49. 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
    Content type: Proceedings Published on:

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

  50. 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 Published on:

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

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