(Q35554981)

8 August 2017

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title

Haplotype phasing: existing methods and new developments (English)

1 reference

8 August 2017

Sharon R Browning

1 reference

8 August 2017

Brian L Browning

series ordinal

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8 August 2017

publication date

16 September 2011

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8 August 2017

published in

Nature Reviews Genetics

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8 August 2017

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8 August 2017

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8 August 2017

page(s)

703-714

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A comprehensively molecular haplotype-resolved genome of a European individual

8 August 2017

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27 July 2018

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27 July 2018

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27 July 2018

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27 July 2018

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A combined long-range phasing and long haplotype imputation method to impute phase for SNP genotypes

27 July 2018

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A rare variant in MYH6 is associated with high risk of sick sinus syndrome

27 July 2018

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Imputation of low-frequency variants using the HapMap3 benefits from large, diverse reference sets

27 July 2018

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A fast, powerful method for detecting identity by descent

27 July 2018

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The importance of phase information for human genomics

27 July 2018

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Whole-genome molecular haplotyping of single cells

27 July 2018

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Haplotype-resolved genome sequencing of a Gujarati Indian individual.

27 July 2018

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MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes

27 July 2018

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A map of human genome variation from population-scale sequencing

27 July 2018

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SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples

27 July 2018

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A comparison of several algorithms for the single individual SNP haplotyping reconstruction problem

27 July 2018

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Optimal algorithms for haplotype assembly from whole-genome sequence data

27 July 2018

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Inferring combined CNV/SNP haplotypes from genotype data

27 July 2018

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Direct determination of molecular haplotypes by chromosome microdissection.

27 July 2018

1 reference

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High-resolution detection of identity by descent in unrelated individuals

27 July 2018

1 reference

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Analysis of genetic inheritance in a family quartet by whole-genome sequencing

27 July 2018

1 reference

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Parental origin of sequence variants associated with complex diseases

27 July 2018

1 reference

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Sequencing technologies - the next generation

27 July 2018

1 reference

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Simultaneous genotype calling and haplotype phasing improves genotype accuracy and reduces false-positive associations for genome-wide association studies

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Systematic haplotype analysis resolves a complex plasma plant sterol locus on the Micronesian Island of Kosrae

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

HI: haplotype improver using paired-end short reads

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

A flexible and accurate genotype imputation method for the next generation of genome-wide association studies

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Genotype determination for polymorphisms in linkage disequilibrium

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Global distribution of genomic diversity underscores rich complex history of continental human populations

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Genotype-imputation accuracy across worldwide human populations

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Detection of sharing by descent, long-range phasing and haplotype imputation

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Shape-IT: new rapid and accurate algorithm for haplotype inference

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Real-time DNA sequencing from single polymerase molecules

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Missing data imputation and haplotype phase inference for genome-wide association studies

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Linkage disequilibrium-based quality control for large-scale genetic studies

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Genome-wide detection and characterization of positive selection in human populations

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Understanding the accuracy of statistical haplotype inference with sequence data of known phase

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

The diploid genome sequence of an individual human

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

A new multipoint method for genome-wide association studies by imputation of genotypes

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

A comparison of phasing algorithms for trios and unrelated individuals

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

A survey of current software for haplotype phase inference

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

The frequent 5,10-methylenetetrahydrofolate reductase C677T polymorphism is associated with a common haplotype in whites, Japanese, and Africans

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Estimating recombination rates from population genetic data

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

A New Statistical Method for Haplotype Reconstruction from Population Data

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Initial sequencing and analysis of the human genome

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Complex promoter and coding region beta 2-adrenergic receptor haplotypes alter receptor expression and predict in vivo responsiveness

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Parametric and nonparametric linkage analysis: a unified multipoint approach

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Global patterns of linkage disequilibrium at the CD4 locus and modern human origins

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

HAPLO: a program using the EM algorithm to estimate the frequencies of multi-site haplotypes.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Inference of haplotypes from PCR-amplified samples of diploid populations

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Completely phased genome sequencing through chromosome sorting

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Integrating common and rare genetic variation in diverse human populations

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Uncovering the roles of rare variants in common disease through whole-genome sequencing

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

A partition-ligation-combination-subdivision EM algorithm for haplotype inference with multiallelic markers: update of the SHEsis (http://analysis.bio-x.cn).

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Genome-wide haplotype association study identifies the SLC22A3-LPAL2-LPA gene cluster as a risk locus for coronary artery disease

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Advantages and limitations of next-generation sequencing technologies: a comparison of electrophoresis and non-electrophoresis methods

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

HapCUT: an efficient and accurate algorithm for the haplotype assembly problem

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

A second generation human haplotype map of over 3.1 million SNPs

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Allele-specific KRT1 expression is a complex trait

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Approximating the coalescent with recombination

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

HAPLORE: a program for haplotype reconstruction in general pedigrees without recombination

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

A new algorithm for haplotype-based association analysis: the Stochastic-EM algorithm.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Incorporating genotyping uncertainty in haplotype inference for single-nucleotide polymorphisms

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Haplotype inference by maximum parsimony

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Partition-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Detecting recent positive selection in the human genome from haplotype structure

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Caution on pedigree haplotype inference with software that assumes linkage equilibrium

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Haplotyping and estimation of haplotype frequencies for closely linked biallelic multilocus genetic phenotypes including nuclear family information.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

An E-M algorithm and testing strategy for multiple-locus haplotypes

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3217888

Handling marker-marker linkage disequilibrium: pedigree analysis with clustered markers

26 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNRG3054

Confounding from cryptic relatedness in haplotype-based association studies

31 March 2020

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNRG3054

31 March 2020

Identifiers

DOI

10.1038/NRG3054

1 reference

8 August 2017

1 reference

8 August 2017

1 reference