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  1. A simple multipoint procedure to test for parent-of-origin effects in samples of affected siblings is discussed. The procedure consists of artificially changing all full sibs to half-sibs, with distinct mother...

    Authors: Mathieu Lemire
    Citation: BMC Genetics 2005 6(Suppl 1):S159
    Content type: Proceedings Published on:

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

  2. We report a simple and rapid method for detecting additive genetic variance due to X-linked loci in the absence of marker data for this chromosome. We examined the interaction of this method with an establishe...

    Authors: Jack W Kent Jr, Loren R Lease, Michael C Mahaney, Thomas D Dyer, Laura Almasy and John Blangero
    Citation: BMC Genetics 2005 6(Suppl 1):S157
    Content type: Proceedings Published on:

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

  3. Homozygosity outlier loci, which show patterns of variation that are extremely divergent from the rest of the genome, can be evaluated by comparison of the homozygosity under Hardy-Weinberg proportions (the su...

    Authors: Ke-Sheng Wang, Michelle Liu and Andrew D Paterson
    Citation: BMC Genetics 2005 6(Suppl 1):S155
    Content type: Proceedings Published on:

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

  4. Errors while genotyping are inevitable and can reduce the power to detect linkage. However, does genotyping error have the same impact on linkage results for single-nucleotide polymorphism (SNP) and microsatel...

    Authors: Cheryl L Thompson, Dan Baechle, Qing Lu, George Mathew, Yeunjoo Song, Sudha K Iyengar, Courtney Gray-McGuire and Katrina AB Goddard
    Citation: BMC Genetics 2005 6(Suppl 1):S153
    Content type: Proceedings Published on:

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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. Alcoholism is a complex disease. As with other common diseases, genetic variants underlying alcoholism have been illusive, possibly due to the small effect from each individual susceptible variant, gene × envi...

    Authors: Liang Chen, Nianjun Liu, Shuang Wang, Cheongeun Oh, Nicholas J Carriero and Hongyu Zhao
    Citation: BMC Genetics 2005 6(Suppl 1):S130
    Content type: Proceedings Published on:

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

  13. Using data provided by the Collaborative Study on the Genetics of Alcoholism we studied the genetics of a quantitative trait: the maximum number of drinks consumed in a 24-hour period. A two-stage method was u...

    Authors: Scott F Saccone, Nancy L Saccone, Rosalind J Neuman and John P Rice
    Citation: BMC Genetics 2005 6(Suppl 1):S124
    Content type: Proceedings Published on:

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

  14. Studies have shown that genetic and environmental factors and their interactions affect several alcoholism phenotypes. Genotype × alcoholism (G×A) interaction refers to the environmental (alcoholic and non-alc...

    Authors: Rector Arya, Thomas D Dyer, Diane M Warren, Christopher P Jenkinson, Ravindranath Duggirala and Laura Almasy
    Citation: BMC Genetics 2005 6(Suppl 1):S120
    Content type: Proceedings Published on:

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

  15. Common human disorders, such as alcoholism, may be the result of interactions of many genes as well as environmental risk factors. Therefore, it is important to incorporate gene × gene and gene × environment i...

    Authors: Cheongeun Oh, Shuang Wang, Nianjun Liu, Liang Chen and Hongyu Zhao
    Citation: BMC Genetics 2005 6(Suppl 1):S116
    Content type: Proceedings Published on:

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

  16. 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

  17. 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

  18. 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

  19. 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

  20. The transmission/disequilibrium test was introduced to test for linkage disequilibrium between a marker and a putative disease locus using case-parent trios. However, parental genotypes may be incomplete in su...

    Authors: Chao-Yu Guo, Jing Cui and L Adrienne Cupples
    Citation: BMC Genetics 2005 6(Suppl 1):S90
    Content type: Proceedings Published on:

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

  21. 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
    Content type: Proceedings Published on:

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

  22. 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
    Content type: Proceedings Published on:

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

  23. Current genome-wide linkage-mapping single-nucleotide polymorphism (SNP) panels with densities of 0.3 cM are likely to have increased intermarker linkage disequilibrium (LD) compared to 5-cM microsatellite pan...

    Authors: Ellen L Goode, Michael D Badzioch and Gail P Jarvik
    Citation: BMC Genetics 2005 6(Suppl 1):S82
    Content type: Proceedings Published on:

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

  24. We compared the accuracy of haplotype inferences at a 6 Mb region on chromosome 7 where significant linkage between a brain oscillation phenotype and a cholinergic muscarinic receptor gene was previously repor...

    Authors: Christy L Avery, Lisa J Martin, Jeff T Williams and Kari E North
    Citation: BMC Genetics 2005 6(Suppl 1):S80
    Content type: Proceedings Published on:

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

  25. 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
    Content type: Proceedings Published on:

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

  26. 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

  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. 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

  30. 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

  31. 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

  32. 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

  33. 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

  34. 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
    Content type: Proceedings Published on:

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

  35. 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
    Content type: Proceedings Published on:

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

  36. 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 Published on:

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

  37. 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 Published on:

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

  38. 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

  39. 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

  40. 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

  41. 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

  42. 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

  43. 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 Published on:

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

  44. 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

  45. 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 Published on:

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

  46. 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 Published on:

    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
    Content type: Proceedings Published on:

    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
    Content type: Proceedings Published on:

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

  49. 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 Published on:

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

  50. 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 Published on:

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

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