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273
Marchini J: A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet 2009
"... Genotype imputation methods are now being widely used in the analysis of genome-wide association studies. Most imputation analyses to date have used the HapMap as a reference dataset, but new reference panels (such as controls genotyped on multiple SNP chips and densely typed samples from the 1,000 ..."
Abstract
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Cited by 449 (5 self)
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Genotype imputation methods are now being widely used in the analysis of genome-wide association studies. Most imputation analyses to date have used the HapMap as a reference dataset, but new reference panels (such as controls genotyped on multiple SNP chips and densely typed samples from the 1
A new multipoint method for genome-wide association studies by imputation of genotypes. Nature genetics.
, 2007
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A fast and flexible statistical model for large-scale population genotype data: Applications to inferring missing genotypes and haplotype phase
- American Journal of Human Genetics
, 2005
"... We present a statistical model for patterns of genetic variation in samples of unrelated individuals from natural populations. This model is based on the idea that, over short regions, haplotypes in a population tend to cluster into groups of similar haplotypes. To capture the fact that, because of ..."
Abstract
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Cited by 408 (10 self)
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missing genotypes and estimating haplotypic phase. For imputing missing genotypes, methods based on this model are as accurate or more accurate than existing methods. For haplotype estimation, the point estimates are slightly less accurate than those from the best existing methods (e.g., for unrelated
Analyses and comparison of accuracy of different genotype imputation methods
- PLoS ONE
, 2008
"... The power of genetic association analyses is often compromised by missing genotypic data which contributes to lack of significant findings, e.g., in in silico replication studies. One solution is to impute untyped SNPs from typed flanking markers, based on known linkage disequilibrium (LD) relations ..."
Abstract
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Cited by 13 (0 self)
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) relationships. Several imputation methods are available and their usefulness in association studies has been demonstrated, but factors affecting their relative performance in accuracy have not been systematically investigated. Therefore, we investigated and compared the performance of five popular genotype
INVESTIGATION Genotype Imputation with Thousands of Genomes
"... ABSTRACT Genotype imputation is a statistical technique that is often used to increase the power and resolution of genetic association studies. Imputation methods work by using haplotype patterns in a reference panel to predict unobserved genotypes in a study dataset, and a number of approaches have ..."
Abstract
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Cited by 34 (1 self)
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ABSTRACT Genotype imputation is a statistical technique that is often used to increase the power and resolution of genetic association studies. Imputation methods work by using haplotype patterns in a reference panel to predict unobserved genotypes in a study dataset, and a number of approaches
Genetic EpidemiologyRESEARCH ARTICLE Imputation Without Doing Imputation: A New Method for the Detection of Non-Genotyped Causal Variants
"... ABSTRACT: Genome-wide association studies allow detection of non-genotyped disease-causing variants through testing of nearby genotyped SNPs. This approach may fail when there are no genotyped SNPs in strong LD with the causal variant. Several genotyped SNPs in weak LD with the causal variant may, h ..."
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, however, considered together, provide equivalent information. This observationmotivates popular but computationally intensive approaches based on imputation or haplotyping. Here we present a new method and accompanying software designed for this scenario. Our approach proceeds by selecting, for each
Analyses and Comparison of Imputation-Based Association Methods
, 2010
"... Genotype imputation methods have become increasingly popular for recovering untyped genotype data. An important application with imputed genotypes is to test genetic association for diseases. Imputation-based association test can provide additional insight beyond what is provided by testing on typed ..."
Abstract
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Cited by 2 (0 self)
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Genotype imputation methods have become increasingly popular for recovering untyped genotype data. An important application with imputed genotypes is to test genetic association for diseases. Imputation-based association test can provide additional insight beyond what is provided by testing
MaCH-Admix: Genotype Imputation for Admixed Populations
, 2012
"... ABSTRACT: Imputation in admixed populations is an important problem but challenging due to the complex linkage disequilibrium (LD) pattern. The emergence of large reference panels such as that from the 1,000 Genomes Project enables more accurate imputation in general, and in particular for admixed p ..."
Abstract
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Cited by 23 (3 self)
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populations and for uncommon variants. To efficiently benefit from these large reference panels, one key issue to consider in modern genotype imputation framework is the selection of effective reference panels. In this work, we consider a number of methods for effective reference panel construction inside a
Imputing Missing Genotypes with Weighted k Nearest
"... Motivation: Missing values are a common problem in genetic association studies concerned with single nucleotide polymorphisms (SNPs). Since most statistical methods cannot handle missing values, they have to be removed prior to the actual analysis. Considering only complete observations, however, of ..."
Abstract
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Cited by 2 (0 self)
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, often leads to an immense loss of information. Therefore, procedures are needed that can be used to replace such missing values. In this article, we propose a method based on weighted k nearest neighbors that can be employed for imputing such missing genotypes. Results: In a comparison to other
Utilizing Genotype Imputation for the Augmentation of Sequence Data
"... Background: In recent years, capabilities for genotyping large sets of single nucleotide polymorphisms (SNPs) has increased considerably with the ability to genotype over 1 million SNP markers across the genome. This advancement in technology has led to an increase in the number of genome-wide assoc ..."
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Cited by 3 (0 self)
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expensive. A more cost effective approach would be to sequence a portion of the individuals, followed by the application of genotype imputation methods for imputing markers in the remaining individuals. A potentially attractive alternative option would be to impute based on the 1000 Genomes Project; however
Results 1 - 10
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273
