Results 1 - 10 of 46

Marchini J: A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet 2009

by Bryan N. Howie, Peter Donnelly, Jonathan Marchini
"... 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 - Cited by 449 (5 self) - Add to MetaCart
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

MaCH-Admix: Genotype Imputation for Admixed Populations

by Eric Yi Liu, Mingyao Li, Wei Wang, Yun Li , 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 - Cited by 23 (3 self) - Add to MetaCart
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

INVESTIGATION Genotype Imputation with Thousands of Genomes

by Bryan Howie, Jonathan Marchini, Matthew Stephens
"... 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 - Cited by 34 (1 self) - Add to MetaCart
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 Epidemiology 00: 1–13 (2012) MaCH-Admix: Genotype Imputation for Admixed Populations

by Eric Yi Liu, Mingyao Li, Wei Wang, Yun Li
"... 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 populations ..."
Abstract - Add to MetaCart
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

DEVELOPMENT OF MODERN EDIT AND IMPUTATION METHODS AT

by unknown authors , 2002
"... Abstract: The development of modern edit and imputation (E&I) methods and software is one of the spearheads of the Methods and Informatics Department of Statistics Netherlands. Many aspects of E&I are covered by the work that is currently being carried out. Software development focuses on th ..."
Abstract - Add to MetaCart
Abstract: The development of modern edit and imputation (E&I) methods and software is one of the spearheads of the Methods and Informatics Department of Statistics Netherlands. Many aspects of E&I are covered by the work that is currently being carried out. Software development focuses

Reconstructing DNA Copy Number by Penalized Estimation and Imputation

by Zhongyang Zhang, Kenneth Lange, Chiara Sabatti , 2009
"... Recent advances in genomics have underscored the surprising ubiquity of DNA copy number variation (CNV). Fortunately, modern genotyping platforms also detect CNVs with fairly high reliability. Hidden Markov models and algorithms have played a dominant role in the interpretation of CNV data. Here we ..."
Abstract - Cited by 4 (1 self) - Add to MetaCart
Recent advances in genomics have underscored the surprising ubiquity of DNA copy number variation (CNV). Fortunately, modern genotyping platforms also detect CNVs with fairly high reliability. Hidden Markov models and algorithms have played a dominant role in the interpretation of CNV data. Here we

Practical issues in imputation-based association mapping

by Yongtao Guan, Matthew Stephens - PLoS Genet , 2008
"... Imputation-based association methods provide a powerful framework for testing untyped variants for association with phenotypes and for combining results from multiple studies that use different genotyping platforms. Here, we consider several issues that arise when applying these methods in practice, ..."
Abstract - Cited by 42 (7 self) - Add to MetaCart
Imputation-based association methods provide a powerful framework for testing untyped variants for association with phenotypes and for combining results from multiple studies that use different genotyping platforms. Here, we consider several issues that arise when applying these methods in practice

MaCH: Using Sequence and Genotype Data to Estimate Haplotypes and Unobserved Genotypes

by Yun Li, Cristen J. Willer, Jun Ding, Paul Scheet, Gonc-alo R. Abecasis
"... Genome-wide association studies (GWAS) can identify common alleles that contribute to complex disease susceptibility. Despite the large number of SNPs assessed in each study, the effects of most common SNPs must be evaluated indirectly using either genotyped markers or haplotypes thereof as proxies. ..."
Abstract - Cited by 69 (9 self) - Add to MetaCart
. We have previously implemented a computationally efficient Markov Chain framework for genotype imputation and haplotyping in the freely available MaCH software package. The approach describes sampled chromosomes as mosaics of each other and uses available genotype and shotgun sequence data

Breakdown of Methods for Phasing and Imputation in the Presence of Double Genotype Sharing

by Carl Nettelblad , 2012
"... In genome-wide association studies, results have been improved through imputation of a denser marker set based on reference haplotypes and phasing of the genotype data. To better handle very large sets of reference haplotypes, prephasing with only study individuals has been suggested. We present a p ..."
Abstract - Add to MetaCart
In genome-wide association studies, results have been improved through imputation of a denser marker set based on reference haplotypes and phasing of the genotype data. To better handle very large sets of reference haplotypes, prephasing with only study individuals has been suggested. We present a

1 Breakdown of methods for phasing and imputation in the presence of double genotype sharing

by Carl Nettelblad
"... In genome-wide association studies, results have been improved through imputation of a denser marker set based on reference haplotypes and phasing of the genotype data. To better handle very large sets of reference haplotypes, pre-phasing with only study individuals has been suggested. We present a ..."
Abstract - Add to MetaCart
In genome-wide association studies, results have been improved through imputation of a denser marker set based on reference haplotypes and phasing of the genotype data. To better handle very large sets of reference haplotypes, pre-phasing with only study individuals has been suggested. We present a
Results 1 - 10 of 46