#### DMCA

## Analyses and comparison of accuracy of different genotype imputation methods (2008)

Venue: | PLoS ONE |

Citations: | 13 - 0 self |

### Citations

408 | A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase.
- Scheet, Stephens
- 2006
(Show Context)
Citation Context ...Ps) can provide partial solutions for recovering missing or untyped genotype data [7,8,9,10,11]. Several imputation methods using various statistical models such as the haplotype-clustering algorithm =-=[12]-=-, the hidden Markov model (HMM) [5], and the Markov Chain model [13], have been proposed. Imputed genotypes, generated with these methods, have been used, successfully, to improve power in association... |

248 |
NJ, Donnelly P (2001) A new statistical method for haplotype reconstruction from population data
- Stephens, Smith
(Show Context)
Citation Context ...es based on known information (e.g. linkage disequilibrium between missing or untyped SNPs and their flanking typed SNPs) can provide partial solutions for recovering missing or untyped genotype data =-=[7,8,9,10,11]-=-. Several imputation methods using various statistical models such as the haplotype-clustering algorithm [12], the hidden Markov model (HMM) [5], and the Markov Chain model [13], have been proposed. I... |

190 |
A second generation human haplotype map of over 3.1 million SNPs.
- KA, DG, et al.
- 2007
(Show Context)
Citation Context ...vances in genotyping have increased the ability to detect dense single nucleotide polymorphisms (SNPs) in the human genome. To date, over three million SNPs have been documented by the HapMap Project =-=[1,2]-=-. The availability of high-throughput genotyping has benefited biological researchers in several ways, including, improved power for genetic association analyses [3,4]. However, challenges exist curre... |

146 |
Donnelly P (2003) A comparison of Bayesian methods for haplotype reconstruction from population genotype data
- Stephens
(Show Context)
Citation Context ...es based on known information (e.g. linkage disequilibrium between missing or untyped SNPs and their flanking typed SNPs) can provide partial solutions for recovering missing or untyped genotype data =-=[7,8,9,10,11]-=-. Several imputation methods using various statistical models such as the haplotype-clustering algorithm [12], the hidden Markov model (HMM) [5], and the Markov Chain model [13], have been proposed. I... |

144 |
A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants.
- LJ, KL, et al.
- 2007
(Show Context)
Citation Context ...en Markov model (HMM) [5], and the Markov Chain model [13], have been proposed. Imputed genotypes, generated with these methods, have been used, successfully, to improve power in association analyses =-=[5,14,15,16,17,18,19]-=-, to facilitate meta-analyses, and to replicate significant findings in follow-up studies [6]. As new methods for genotype imputation are developed, the relative performance of these methods must be a... |

141 |
Efficiency and power in genetic association studies. Nat Genet.
- PI, Yelensky, et al.
- 2005
(Show Context)
Citation Context ...documented by the HapMap Project [1,2]. The availability of high-throughput genotyping has benefited biological researchers in several ways, including, improved power for genetic association analyses =-=[3,4]-=-. However, challenges exist currently. For example, although the popular Affymetrix 500K Array Set contains approximately 500,000 SNPs, this only represents one sixth of the approximately three millio... |

108 |
Donnelly P (2007) A new multipoint method for genome-wide association studies by imputation of genotypes. Nat Genet 39: 906â€“913
- Marchini, Howie, et al.
(Show Context)
Citation Context ...to low call rates, deviations from Hardy-Weinberg equilibrium, rare alleles, and etc. As a result, genotype data is often missing, and this missing data results in a power loss in association studies =-=[5]-=-. Additionally, different platforms usually contain distinct sets of SNPs, making it difficult to replicate significant findings or to perform follow-up meta-analysis [6]. Imputation methods, used to ... |

72 |
Scuteri A, Bonnycastle LL, et al. (2008) Newly identified loci that influence lipid concentrations and risk of coronary artery disease. Nat Genet 40
- CJ, Sanna, et al.
(Show Context)
Citation Context ...th strategies, selecting the most likely genotype and selecting the posterior distribution of all possible genotypes, have demonstrated the capacity to improve power in follow-up association analysis =-=[5,6,16]-=-. However, comprehensive analyses appear to be warranted to better evaluate this issue. Materials and Methods Data Simulations Haplotypes covering a 250 kb chromosomal region were simulated with unifo... |

64 | Model-based inference of haplotype block variation. - Greenspan, Geiger - 2004 |

57 |
R: GERBIL: Genotype resolution and block identification using likelihood
- Kimmel, Shamir
(Show Context)
Citation Context ...es based on known information (e.g. linkage disequilibrium between missing or untyped SNPs and their flanking typed SNPs) can provide partial solutions for recovering missing or untyped genotype data =-=[7,8,9,10,11]-=-. Several imputation methods using various statistical models such as the haplotype-clustering algorithm [12], the hidden Markov model (HMM) [5], and the Markov Chain model [13], have been proposed. I... |

55 |
Browning BL (2007) Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering
- SR
(Show Context)
Citation Context |

51 |
Common variants in the GDF5-UQCC region are associated with variation in human height.
- Sanna, Jackson, et al.
- 2008
(Show Context)
Citation Context ...en Markov model (HMM) [5], and the Markov Chain model [13], have been proposed. Imputed genotypes, generated with these methods, have been used, successfully, to improve power in association analyses =-=[5,14,15,16,17,18,19]-=-, to facilitate meta-analyses, and to replicate significant findings in follow-up studies [6]. As new methods for genotype imputation are developed, the relative performance of these methods must be a... |

48 |
Abecasis GR (2006) Mach 1.0: Rapid haplotype reconstruction and missing genotype inference.
- Li
- 2009
(Show Context)
Citation Context ...imputation methods were investigated in this study: MACH, IMPUTE, fastPHASE, PLINK and Beagle. These methods are briefly described below. MACH. MACH v 1.0.10 implements a Markov Chain based algorithm =-=[13,27]-=- to infer possible pairs of haplotypes for each individualâ€™s genotypes (including untyped genotypes). It defines a series of indicators (S) to denote unobserved states underlying unphased genotypes an... |

37 |
Stephens M (2007) Imputation-based analysis of association studies: candidate regions and quantitative traits. PLoS genetics 3: e114
- Servin
(Show Context)
Citation Context ...en Markov model (HMM) [5], and the Markov Chain model [13], have been proposed. Imputed genotypes, generated with these methods, have been used, successfully, to improve power in association analyses =-=[5,14,15,16,17,18,19]-=-, to facilitate meta-analyses, and to replicate significant findings in follow-up studies [6]. As new methods for genotype imputation are developed, the relative performance of these methods must be a... |

11 |
Evaluation of genome-wide power of genetic association studies based on empirical data from the HapMap project.
- Nannya, Taura, et al.
- 2007
(Show Context)
Citation Context ...documented by the HapMap Project [1,2]. The availability of high-throughput genotyping has benefited biological researchers in several ways, including, improved power for genetic association analyses =-=[3,4]-=-. However, challenges exist currently. For example, although the popular Affymetrix 500K Array Set contains approximately 500,000 SNPs, this only represents one sixth of the approximately three millio... |