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## Variable-Length Haplotype Construction for Gene-Gene Interaction Studies

### Citations

1202 |
A new statistical method for haplotype reconstruction from population data
- Stephens, Smith, et al.
- 2001
(Show Context)
Citation Context ...s. For example, genotype 0102 leads to haplotypes 0001 and 0101 while genotype 0112 leads to two possible haplotype pairs: 0001/0111 and 0011/0101. Many algorithms exist for haplotype inference [15], =-=[16]-=-, [17]. In this paper, an expectation-maximisation algorithm [15] is the chosen technique due to its simplicity and implementation efficacy. Regardless of the inference technique employed, the usual r... |

473 | Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. - Excoffier, Slatkin - 1995 |

229 | Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms.
- Niu, Qin, et al.
- 2002
(Show Context)
Citation Context ... example, genotype 0102 leads to haplotypes 0001 and 0101 while genotype 0112 leads to two possible haplotype pairs: 0001/0111 and 0011/0101. Many algorithms exist for haplotype inference [15], [16], =-=[17]-=-. In this paper, an expectation-maximisation algorithm [15] is the chosen technique due to its simplicity and implementation efficacy. Regardless of the inference technique employed, the usual result ... |

77 |
Trimming, weighting, and grouping SNPs in human case-control association studies,”
- Hoh, Wille, et al.
- 2001
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Citation Context ...metric methods. Examples of parametric method cover logistic regression techniques [4] and neural networks [5]. On the other hand, examples of non-parametric method include a set association approach =-=[6]-=-, combinatorial techniques [7], [8], [9] and recursive partitioning techniques [10], [11]. In some of mentioned parametric [4], [5] and non-parametric [9] methods, pattern recognition and classificati... |

71 |
Identifying SNPs predictive of phenotype using Random Forests. Genetic Epidemiology 28
- Bureau, Dupuis, et al.
- 2005
(Show Context)
Citation Context ...nd neural networks [5]. On the other hand, examples of non-parametric method include a set association approach [6], combinatorial techniques [7], [8], [9] and recursive partitioning techniques [10], =-=[11]-=-. In some of mentioned parametric [4], [5] and non-parametric [9] methods, pattern recognition and classification approaches have been successfully implemented as their core engines. In addition to si... |

71 |
Mendelian proportions in a mixed population,”
- Hardy
- 1908
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Citation Context ...ntains 600 case samples and 600 control samples. Each sample consists of 10 total SNPs from two genes where five SNPs exist in each gene. All SNPs in control samples are in Hardy-Weinberg equilibrium =-=[20]-=-. Only one SNP from each gene is interacted with one another. The two-locus interaction models are illustrated in Table I. The epistatic models Ep-1–Ep-6 and the heterogeneity models Het-1–Het-3 have ... |

69 |
Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interaction
- HAHN, RITCHIE, et al.
- 2003
(Show Context)
Citation Context ...ethod cover logistic regression techniques [4] and neural networks [5]. On the other hand, examples of non-parametric method include a set association approach [6], combinatorial techniques [7], [8], =-=[9]-=- and recursive partitioning techniques [10], [11]. In some of mentioned parametric [4], [5] and non-parametric [9] methods, pattern recognition and classification approaches have been successfully imp... |

51 |
A powerful strategy to account for multiple testing in the context of haplotype analysis
- Becker, Knapp
(Show Context)
Citation Context ...from possible SNPs is the one with minimum p-value and is said to be the best model for interaction explanation. This statistics-based procedure can be found as an integral part of the FAMHAP program =-=[18]-=-. III. VARHAP VarHAP is proposed for case-control interaction studies. Similar to MDR, the technique is also a classifier-based technique. However, instead of using a genotype data analysis as a means... |

43 |
Screening large-scale association study data: exploiting interactions using Random Forests
- Lunetta, Hayward, et al.
- 2004
(Show Context)
Citation Context ... [4] and neural networks [5]. On the other hand, examples of non-parametric method include a set association approach [6], combinatorial techniques [7], [8], [9] and recursive partitioning techniques =-=[10]-=-, [11]. In some of mentioned parametric [4], [5] and non-parametric [9] methods, pattern recognition and classification approaches have been successfully implemented as their core engines. In addition... |

40 |
A combinatorial partitioning method to identify multilocus genotypic partitions that predict quantitative trait variation
- Nelson, Kardia, et al.
- 2001
(Show Context)
Citation Context ...rametric method cover logistic regression techniques [4] and neural networks [5]. On the other hand, examples of non-parametric method include a set association approach [6], combinatorial techniques =-=[7]-=-, [8], [9] and recursive partitioning techniques [10], [11]. In some of mentioned parametric [4], [5] and non-parametric [9] methods, pattern recognition and classification approaches have been succes... |

40 |
W: Detecting epistatic interactions contributing to quantitative traits. Genet Epidemiol 2004; 27: 141–152
- Culverhouse, Klein, et al.
(Show Context)
Citation Context ...ric method cover logistic regression techniques [4] and neural networks [5]. On the other hand, examples of non-parametric method include a set association approach [6], combinatorial techniques [7], =-=[8]-=-, [9] and recursive partitioning techniques [10], [11]. In some of mentioned parametric [4], [5] and non-parametric [9] methods, pattern recognition and classification approaches have been successfull... |

31 |
On measures of gametic disequilibrium
- Lewontin
- 1988
(Show Context)
Citation Context ...eed to be explored: strong LD and weak LD cases. In the strong LD case, the susceptibility-causative SNP in each gene and its two adjacent SNPs are in linkage disequilibrium where Lewontin’s D′ value =-=[24]-=- is in the range of 0.80–0.95. In contrast, the Lewontin’s D′ value for each pairwise LD measurement between susceptibility-causative SNP and its adjacent SNPs is in the range of 0.50–0.60 in the weak... |

30 |
Genetic association studies: design, analysis and interpretation.
- Lewis
- 2002
(Show Context)
Citation Context ...r 2007. Traditional techniques for identification of relationship between a single SNP and disease susceptibility status involve various univariate statistical tests including χ2 and odds ratio tests =-=[1]-=-, [2]. However, many complementary computational techniques have been developed in the past decade to handle problems that involve multiple SNPs. Heidema et al. [3] have categorised these multi-locus ... |

26 |
Optimization of neural network architecture using genetic programming improves detection and modeling of gene-gene interactions in studies of human diseases
- Ritchie, White, et al.
(Show Context)
Citation Context ...e capable of identifying a candidate SNP set from possible SNPs, into parametric and non-parametric methods. Examples of parametric method cover logistic regression techniques [4] and neural networks =-=[5]-=-. On the other hand, examples of non-parametric method include a set association approach [6], combinatorial techniques [7], [8], [9] and recursive partitioning techniques [10], [11]. In some of menti... |

24 | Data simulation software for whole-genome association and other studies in human genetics
- Dudek, Motsinger, et al.
- 2006
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Citation Context ...rance. Penetrance of a genotype with a specific number of disease alleles is the probability that a subject with this genotype has the disease. The test data sets are simulated by a genomeSIM package =-=[23]-=- with the default setting. As a result, it is also possible to vary the LD pattern among SNPs in the same gene. This leads to two main case studies that need to be explored: strong LD and weak LD case... |

16 |
Two-trait-locus linkage analysis: a powerful strategy for mapping complex genetic traits.
- NJ, Boehnke, et al.
- 1993
(Show Context)
Citation Context ...and Rice [21], who also provide examples of diseases for which these models may be applicable. The heterogeneity models S-1 and S-2 and the epistatic model S-3 have been investigated by Schork et al. =-=[22]-=-. From Table I, if the frequency of the disease allele at a locus is greater than 0.5, the major allele is the disease allele. Otherwise, the minor allele is the disease allele. These interaction mode... |

13 |
The Challenge for Genetic Epidemiologists: How to Analyze Large Numbers of SNPs in Relation to Complex Diseases. BioMed Central Genetics
- Heidema, Boer, et al.
- 2006
(Show Context)
Citation Context ...s including χ2 and odds ratio tests [1], [2]. However, many complementary computational techniques have been developed in the past decade to handle problems that involve multiple SNPs. Heidema et al. =-=[3]-=- have categorised these multi-locus techniques, which are capable of identifying a candidate SNP set from possible SNPs, into parametric and non-parametric methods. Examples of parametric method cover... |

11 |
Haplotype interaction analysis of unlinked regions, Genetic Epidemiology
- Becker, Schumacher, et al.
- 2005
(Show Context)
Citation Context ... from multiple SNPs, as problem inputs. For instance, Sham et al. [13] proposes a logistic regression technique that produces a mapping model between haplotypes and disease status while Becker et al. =-=[14]-=- combine haplotype explanation probabilities of given genotypes from multiple gene or unlinked region data into a scalar statistic for a univariate test. Nonetheless, haplotypes have rarely been used ... |

10 |
MP: Two-locus disease models with two marker loci: The power of affected-sib-pair tests
- Knapp, SA, et al.
- 1994
(Show Context)
Citation Context ...sed VarHAP technique is evaluated through benchmark trials. 12 simulated data sets, which represent various gene-gene interaction phenomena including epistasis and heterogeneity, are considered [14], =-=[19]-=-. Each data set contains 600 case samples and 600 control samples. Each sample consists of 10 total SNPs from two genes where five SNPs exist in each gene. All SNPs in control samples are in Hardy-Wei... |

10 |
Simulation of LD block-structured SNP haplotype data and its use for the analysis of case-control data by supervised learning methods
- Nothnagel
- 2002
(Show Context)
Citation Context ...ulated data sets used in the article are available upon request (email: nchl@kmutnb.ac.th). In addition to the use of the genomeSIM package [23], the data sets can also be generated by a SNaP package =-=[25]-=-. Readers might also be interested in applying the techniques discussed in this article to examples of case-control data sets, which are publicly available from the Wellcome Trust Case Control Consort... |

7 |
Haplotype association analysis of discrete and continuous traits using mixture of regression models
- Sham, Rijsdijk, et al.
- 2004
(Show Context)
Citation Context ...is should also be considered in addition to direct genotype analysis. Many computational techniques use haplotypes, which are inferred from multiple SNPs, as problem inputs. For instance, Sham et al. =-=[13]-=- proposes a logistic regression technique that produces a mapping model between haplotypes and disease status while Becker et al. [14] combine haplotype explanation probabilities of given genotypes fr... |

6 | Statistical methods in genetics
- Montana
- 2006
(Show Context)
Citation Context ...7. Traditional techniques for identification of relationship between a single SNP and disease susceptibility status involve various univariate statistical tests including χ2 and odds ratio tests [1], =-=[2]-=-. However, many complementary computational techniques have been developed in the past decade to handle problems that involve multiple SNPs. Heidema et al. [3] have categorised these multi-locus techn... |

6 |
Two-locus models of disease
- Neuman, Rice
- 1992
(Show Context)
Citation Context ...nteracted with one another. The two-locus interaction models are illustrated in Table I. The epistatic models Ep-1–Ep-6 and the heterogeneity models Het-1–Het-3 have been discussed by Neuman and Rice =-=[21]-=-, who also provide examples of diseases for which these models may be applicable. The heterogeneity models S-1 and S-2 and the epistatic model S-3 have been investigated by Schork et al. [22]. From Ta... |

2 |
Testing the Goodness-of-Fit of the Logistic Regression Model in CaseControl Studies Using Sample Reweighting
- Nagelkerke, Smits, et al.
(Show Context)
Citation Context ...cus techniques, which are capable of identifying a candidate SNP set from possible SNPs, into parametric and non-parametric methods. Examples of parametric method cover logistic regression techniques =-=[4]-=- and neural networks [5]. On the other hand, examples of non-parametric method include a set association approach [6], combinatorial techniques [7], [8], [9] and recursive partitioning techniques [10]... |

1 |
Haplotype thinking in lung disease
- Silverman
- 2007
(Show Context)
Citation Context ...ted in close proximity tend to travel together—in genome more accurately. Therefore, haplotypes may enable susceptibility gene identification in complex diseases more effectively than individual SNPs =-=[12]-=-. In lieu of this evidence, haplotype analysis should also be considered in addition to direct genotype analysis. Many computational techniques use haplotypes, which are inferred from multiple SNPs, a... |