Haplotype phasing: existing methods and new developments.

PubWeight™: 4.66‹?› | Rank: Top 1%

🔗 View Article (PMC 3217888)

Published in Nat Rev Genet on September 16, 2011

Authors

Sharon R Browning1, Brian L Browning

Author Affiliations

1: Department of Biostatistics, University of Washington, Seattle, Washington 98195, USA. sguy@uw.edu

Articles citing this

(truncated to the top 100)

Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells. Nature (2012) 3.74

Phasing of many thousands of genotyped samples. Am J Hum Genet (2012) 2.47

Efficiency and power as a function of sequence coverage, SNP array density, and imputation. PLoS Comput Biol (2012) 2.29

Improving the accuracy and efficiency of identity-by-descent detection in population data. Genetics (2013) 2.26

Probing meiotic recombination and aneuploidy of single sperm cells by whole-genome sequencing. Science (2012) 2.14

Whole-genome haplotyping using long reads and statistical methods. Nat Biotechnol (2014) 2.11

The role of replicates for error mitigation in next-generation sequencing. Nat Rev Genet (2013) 1.66

HIBAG--HLA genotype imputation with attribute bagging. Pharmacogenomics J (2013) 1.66

Chromothripsis and beyond: rapid genome evolution from complex chromosomal rearrangements. Genes Dev (2013) 1.61

A new approach for efficient genotype imputation using information from relatives. BMC Genomics (2014) 1.59

Design of a bovine low-density SNP array optimized for imputation. PLoS One (2012) 1.59

Haplotype estimation using sequencing reads. Am J Hum Genet (2013) 1.56

Imputation of high-density genotypes in the Fleckvieh cattle population. Genet Sel Evol (2013) 1.48

Whole-genome haplotyping by dilution, amplification, and sequencing. Proc Natl Acad Sci U S A (2013) 1.44

Understanding the origin of species with genome-scale data: modelling gene flow. Nat Rev Genet (2013) 1.41

Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler. BMC Genomics (2016) 1.41

Identity by descent: variation in meiosis, across genomes, and in populations. Genetics (2013) 1.37

HapCompass: a fast cycle basis algorithm for accurate haplotype assembly of sequence data. J Comput Biol (2012) 1.31

Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing. Nat Genet (2014) 1.28

Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes. F1000Res (2015) 1.14

A field guide to whole-genome sequencing, assembly and annotation. Evol Appl (2014) 1.12

Strategies and utility of imputed SNP genotypes for genomic analysis in dairy cattle. BMC Genomics (2012) 1.10

Imputation-based genomic coverage assessments of current human genotyping arrays. G3 (Bethesda) (2013) 1.06

Haplotype assembly in polyploid genomes and identical by descent shared tracts. Bioinformatics (2013) 1.05

A coalescent model for genotype imputation. Genetics (2012) 1.04

Limited evidence for classic selective sweeps in African populations. Genetics (2012) 1.04

Assembly of a phased diploid Candida albicans genome facilitates allele-specific measurements and provides a simple model for repeat and indel structure. Genome Biol (2013) 1.04

DNA sequencing: clinical applications of new DNA sequencing technologies. Circulation (2012) 1.03

Testing for rare variant associations in the presence of missing data. Genet Epidemiol (2013) 1.01

Integrated view of genome structure and sequence of a single DNA molecule in a nanofluidic device. Proc Natl Acad Sci U S A (2013) 1.00

Fast and accurate long-range phasing in a UK Biobank cohort. Nat Genet (2016) 1.00

Reference-based phasing using the Haplotype Reference Consortium panel. Nat Genet (2016) 0.98

De novo assembly of a haplotype-resolved human genome. Nat Biotechnol (2015) 0.98

Genome-wide association study on detailed profiles of smoking behavior and nicotine dependence in a twin sample. Mol Psychiatry (2013) 0.96

A Phylogenomic Approach Based on PCR Target Enrichment and High Throughput Sequencing: Resolving the Diversity within the South American Species of Bartsia L. (Orobanchaceae). PLoS One (2016) 0.96

On the design of clone-based haplotyping. Genome Biol (2013) 0.95

Genomic evaluation of both purebred and crossbred performances. Genet Sel Evol (2014) 0.95

Conditionally fluorescent molecular probes for detecting single base changes in double-stranded DNA. Nat Chem (2013) 0.95

Species formation by host shifting in avian malaria parasites. Proc Natl Acad Sci U S A (2014) 0.95

Genotype Imputation for Latinos Using the HapMap and 1000 Genomes Project Reference Panels. Front Genet (2012) 0.94

Methods of tagSNP selection and other variables affecting imputation accuracy in swine. BMC Genet (2013) 0.93

Detection of recombination events, haplotype reconstruction and imputation of sires using half-sib SNP genotypes. Genet Sel Evol (2014) 0.90

Whole-genome haplotyping approaches and genomic medicine. Genome Med (2014) 0.90

Inference of identity by descent in population isolates and optimal sequencing studies. Eur J Hum Genet (2013) 0.89

Phasing of single DNA molecules by massively parallel barcoding. Nat Commun (2015) 0.88

Local host specialization, host-switching, and dispersal shape the regional distributions of avian haemosporidian parasites. Proc Natl Acad Sci U S A (2015) 0.87

A multi-locus likelihood method for assessing parent-of-origin effects using case-control mother-child pairs. Genet Epidemiol (2012) 0.86

Genome of The Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels. Nat Commun (2015) 0.86

Dating rare mutations from small samples with dense marker data. Genetics (2014) 0.86

Heterozygous Mapping Strategy (HetMappS) for High Resolution Genotyping-By-Sequencing Markers: A Case Study in Grapevine. PLoS One (2015) 0.86

HapFABIA: identification of very short segments of identity by descent characterized by rare variants in large sequencing data. Nucleic Acids Res (2013) 0.86

Mendel-GPU: haplotyping and genotype imputation on graphics processing units. Bioinformatics (2012) 0.86

Impact of pre-imputation SNP-filtering on genotype imputation results. BMC Genet (2014) 0.86

GenomeLaser: fast and accurate haplotyping from pedigree genotypes. Bioinformatics (2015) 0.86

Dominant sequences of human major histocompatibility complex conserved extended haplotypes from HLA-DQA2 to DAXX. PLoS Genet (2014) 0.85

MixSIH: a mixture model for single individual haplotyping. BMC Genomics (2013) 0.85

A bioinformatics workflow for detecting signatures of selection in genomic data. Front Genet (2014) 0.85

High-accuracy haplotype imputation using unphased genotype data as the references. Gene (2015) 0.85

Hierarchical molecular tagging to resolve long continuous sequences by massively parallel sequencing. Sci Rep (2013) 0.84

Genotype-based test in mapping cis-regulatory variants from allele-specific expression data. PLoS One (2012) 0.84

A systematic review of CD14 and toll-like receptors in relation to asthma in Caucasian children. Allergy Asthma Clin Immunol (2013) 0.84

Probabilistic single-individual haplotyping. Bioinformatics (2014) 0.84

GAGA: a new algorithm for genomic inference of geographic ancestry reveals fine level population substructure in Europeans. PLoS Comput Biol (2014) 0.84

References for Haplotype Imputation in the Big Data Era. Mol Biol (Los Angel) (2015) 0.83

hsphase: an R package for pedigree reconstruction, detection of recombination events, phasing and imputation of half-sib family groups. BMC Bioinformatics (2014) 0.83

Determination of haplotypes at structurally complex regions using emulsion haplotype fusion PCR. BMC Genomics (2012) 0.82

A fast and accurate algorithm for single individual haplotyping. BMC Syst Biol (2012) 0.82

A dynamic Bayesian Markov model for phasing and characterizing haplotypes in next-generation sequencing. Bioinformatics (2013) 0.82

A linear-time algorithm for reconstructing zero-recombinant haplotype configuration on a pedigree. BMC Bioinformatics (2012) 0.82

Disentangling homeologous contigs in allo-tetraploid assembly: application to durum wheat. BMC Bioinformatics (2013) 0.81

PediHaplotyper: software for consistent assignment of marker haplotypes in pedigrees. Mol Breed (2016) 0.81

Joint analysis of sequence data and single-nucleotide polymorphism data using pedigree information for imputation and recombination inference. BMC Proc (2014) 0.81

Conflation of Short Identity-by-Descent Segments Bias Their Inferred Length Distribution. G3 (Bethesda) (2016) 0.81

Mendelian sampling covariability of marker effects and genetic values. Genet Sel Evol (2016) 0.81

MAC: identifying and correcting annotation for multi-nucleotide variations. BMC Genomics (2015) 0.80

iXora: exact haplotype inferencing and trait association. BMC Genet (2013) 0.80

Concurrent whole-genome haplotyping and copy-number profiling of single cells. Am J Hum Genet (2015) 0.80

On combining reference data to improve imputation accuracy. PLoS One (2013) 0.80

Allele-Specific Quantification of Structural Variations in Cancer Genomes. Cell Syst (2016) 0.79

Polymorphisms and a haplotype in heparanase gene associations with the progression and prognosis of gastric cancer in a northern Chinese population. PLoS One (2012) 0.79

Introduction to deep sequencing and its application to drug addiction research with a focus on rare variants. Mol Neurobiol (2013) 0.79

Proof-of-principle rapid noninvasive prenatal diagnosis of autosomal recessive founder mutations. J Clin Invest (2015) 0.78

Haplotype phasing after joint estimation of recombination and linkage disequilibrium in breeding populations. J Anim Sci Biotechnol (2013) 0.78

Empirical prediction of genomic susceptibilities for multiple cancer classes. Proc Natl Acad Sci U S A (2014) 0.78

Heuristic exploitation of genetic structure in marker-assisted gene pyramiding problems. BMC Genet (2015) 0.78

Robust and scalable inference of population history from hundreds of unphased whole genomes. Nat Genet (2016) 0.78

InPhaDel: integrative shotgun and proximity-ligation sequencing to phase deletions with single nucleotide polymorphisms. Nucleic Acids Res (2016) 0.77

Direct chromosome-length haplotyping by single-cell sequencing. Genome Res (2016) 0.77

Evaluating allopolyploid origins in strawberries (Fragaria) using haplotypes generated from target capture sequencing. BMC Evol Biol (2017) 0.76

Read-based phasing of related individuals. Bioinformatics (2016) 0.76

Scaling probabilistic models of genetic variation to millions of humans. Nat Genet (2016) 0.76

A simple procedure for directly obtaining haplotype sequences of diploid genomes. BMC Genomics (2015) 0.76

Imputing Genotypes in Biallelic Populations from Low-Coverage Sequence Data. Genetics (2015) 0.76

High rates of phasing errors in highly polymorphic species with low levels of linkage disequilibrium. Mol Ecol Resour (2016) 0.76

scphaser: haplotype inference using single-cell RNA-seq data. Bioinformatics (2016) 0.76

Prevalence of avian haemosporidian parasites is positively related to the abundance of host species at multiple sites within a region. Parasitol Res (2016) 0.76

Comparing variant calling algorithms for target-exon sequencing in a large sample. BMC Bioinformatics (2015) 0.75

Role of TNF block genetic variants in HIV-associated sensory neuropathy in black Southern Africans. Eur J Hum Genet (2014) 0.75

CoVaMa: Co-Variation Mapper for disequilibrium analysis of mutant loci in viral populations using next-generation sequence data. Methods (2015) 0.75

Odintifier--A computational method for identifying insertions of organellar origin from modern and ancient high-throughput sequencing data based on haplotype phasing. BMC Bioinformatics (2015) 0.75

Articles cited by this

Initial sequencing and analysis of the human genome. Nature (2001) 212.86

Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature (2007) 144.95

A map of human genome variation from population-scale sequencing. Nature (2010) 121.13

The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res (2010) 97.51

A second generation human haplotype map of over 3.1 million SNPs. Nature (2007) 85.39

A new statistical method for haplotype reconstruction from population data. Am J Hum Genet (2001) 59.30

A new multipoint method for genome-wide association studies by imputation of genotypes. Nat Genet (2007) 52.68

The diploid genome sequence of an individual human. PLoS Biol (2007) 44.80

Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour (2010) 42.87

Sequencing technologies - the next generation. Nat Rev Genet (2009) 40.57

Parametric and nonparametric linkage analysis: a unified multipoint approach. Am J Hum Genet (1996) 39.80

Integrating common and rare genetic variation in diverse human populations. Nature (2010) 32.30

Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol (1995) 30.55

A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet (2009) 30.09

Real-time DNA sequencing from single polymerase molecules. Science (2008) 29.53

A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet (2006) 28.32

MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiol (2010) 26.41

Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet (2007) 24.68

Detecting recent positive selection in the human genome from haplotype structure. Nature (2002) 22.00

Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science (2010) 18.45

A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. Am J Hum Genet (2009) 17.80

Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics (2003) 17.73

Genome-wide detection and characterization of positive selection in human populations. Nature (2007) 17.27

Inference of haplotypes from PCR-amplified samples of diploid populations. Mol Biol Evol (1990) 16.18

Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. Am J Hum Genet (2005) 14.09

An E-M algorithm and testing strategy for multiple-locus haplotypes. Am J Hum Genet (1995) 13.84

HAPLO: a program using the EM algorithm to estimate the frequencies of multi-site haplotypes. J Hered (1995) 13.52

A comparison of phasing algorithms for trios and unrelated individuals. Am J Hum Genet (2006) 12.45

Complex promoter and coding region beta 2-adrenergic receptor haplotypes alter receptor expression and predict in vivo responsiveness. Proc Natl Acad Sci U S A (2000) 10.27

Partition-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms. Am J Hum Genet (2002) 10.12

Detection of sharing by descent, long-range phasing and haplotype imputation. Nat Genet (2008) 9.69

Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nat Rev Genet (2010) 9.53

Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet (2011) 8.34

Global patterns of linkage disequilibrium at the CD4 locus and modern human origins. Science (1996) 8.25

Genotype-imputation accuracy across worldwide human populations. Am J Hum Genet (2009) 7.28

Parental origin of sequence variants associated with complex diseases. Nature (2009) 7.21

Whole-genome molecular haplotyping of single cells. Nat Biotechnol (2010) 6.77

Estimating recombination rates from population genetic data. Genetics (2001) 5.95

Simultaneous genotype calling and haplotype phasing improves genotype accuracy and reduces false-positive associations for genome-wide association studies. Am J Hum Genet (2009) 5.65

Low-coverage sequencing: implications for design of complex trait association studies. Genome Res (2011) 5.34

Haplotype-resolved genome sequencing of a Gujarati Indian individual. Nat Biotechnol (2010) 5.32

Genome-wide haplotype association study identifies the SLC22A3-LPAL2-LPA gene cluster as a risk locus for coronary artery disease. Nat Genet (2009) 4.63

Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region. Nat Genet (2009) 4.61

A fast, powerful method for detecting identity by descent. Am J Hum Genet (2011) 4.26

A rare variant in MYH6 is associated with high risk of sick sinus syndrome. Nat Genet (2011) 3.94

Approximating the coalescent with recombination. Philos Trans R Soc Lond B Biol Sci (2005) 3.66

Missing data imputation and haplotype phase inference for genome-wide association studies. Hum Genet (2008) 3.65

High-resolution detection of identity by descent in unrelated individuals. Am J Hum Genet (2010) 3.41

A new algorithm for haplotype-based association analysis: the Stochastic-EM algorithm. Ann Hum Genet (2004) 3.24

SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples. Genome Res (2010) 2.97

HapCUT: an efficient and accurate algorithm for the haplotype assembly problem. Bioinformatics (2008) 2.96

A partition-ligation-combination-subdivision EM algorithm for haplotype inference with multiallelic markers: update of the SHEsis (http://analysis.bio-x.cn). Cell Res (2009) 2.86

Global distribution of genomic diversity underscores rich complex history of continental human populations. Genome Res (2009) 2.76

Caution on pedigree haplotype inference with software that assumes linkage equilibrium. Am J Hum Genet (2002) 2.51

The importance of phase information for human genomics. Nat Rev Genet (2011) 2.25

Direct determination of molecular haplotypes by chromosome microdissection. Nat Methods (2010) 2.21

HAPLORE: a program for haplotype reconstruction in general pedigrees without recombination. Bioinformatics (2004) 2.16

Optimal algorithms for haplotype assembly from whole-genome sequence data. Bioinformatics (2010) 1.98

A combined long-range phasing and long haplotype imputation method to impute phase for SNP genotypes. Genet Sel Evol (2011) 1.97

Completely phased genome sequencing through chromosome sorting. Proc Natl Acad Sci U S A (2010) 1.96

Understanding the accuracy of statistical haplotype inference with sequence data of known phase. Genet Epidemiol (2007) 1.87

A comprehensively molecular haplotype-resolved genome of a European individual. Genome Res (2011) 1.83

Imputation of low-frequency variants using the HapMap3 benefits from large, diverse reference sets. Eur J Hum Genet (2011) 1.68

Incorporating genotyping uncertainty in haplotype inference for single-nucleotide polymorphisms. Am J Hum Genet (2004) 1.66

Imputation of missing genotypes from sparse to high density using long-range phasing. Genetics (2011) 1.57

Haplotyping and estimation of haplotype frequencies for closely linked biallelic multilocus genetic phenotypes including nuclear family information. Hum Mutat (2001) 1.52

Haplotype inference by maximum parsimony. Bioinformatics (2003) 1.43

Advantages and limitations of next-generation sequencing technologies: a comparison of electrophoresis and non-electrophoresis methods. Electrophoresis (2008) 1.41

Allele-specific KRT1 expression is a complex trait. PLoS Genet (2006) 1.41

Inferring combined CNV/SNP haplotypes from genotype data. Bioinformatics (2010) 1.35

A comparison of several algorithms for the single individual SNP haplotyping reconstruction problem. Bioinformatics (2010) 1.27

The frequent 5,10-methylenetetrahydrofolate reductase C677T polymorphism is associated with a common haplotype in whites, Japanese, and Africans. Am J Hum Genet (2002) 1.23

HI: haplotype improver using paired-end short reads. Bioinformatics (2009) 1.20

Shape-IT: new rapid and accurate algorithm for haplotype inference. BMC Bioinformatics (2008) 1.17

Systematic haplotype analysis resolves a complex plasma plant sterol locus on the Micronesian Island of Kosrae. Proc Natl Acad Sci U S A (2009) 1.13

Linkage disequilibrium-based quality control for large-scale genetic studies. PLoS Genet (2008) 1.03

Genotype determination for polymorphisms in linkage disequilibrium. BMC Bioinformatics (2009) 0.94

A survey of current software for haplotype phase inference. Hum Genomics (2004) 0.94

Confounding from cryptic relatedness in haplotype-based association studies. Genetica (2010) 0.79

Articles by these authors

Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet (2007) 24.68

A recurrent 16p12.1 microdeletion supports a two-hit model for severe developmental delay. Nat Genet (2010) 6.62

Genome-wide meta-analysis identifies novel multiple sclerosis susceptibility loci. Ann Neurol (2011) 3.52

High-resolution detection of identity by descent in unrelated individuals. Am J Hum Genet (2010) 3.41

Evaluation of Nyholt's procedure for multiple testing correction. Hum Hered (2005) 2.50

Genetic loci associated with plasma phospholipid n-3 fatty acids: a meta-analysis of genome-wide association studies from the CHARGE Consortium. PLoS Genet (2011) 2.33

Performance of genotype imputation for rare variants identified in exons and flanking regions of genes. PLoS One (2011) 1.72

Detecting rare variant associations by identity-by-descent mapping in case-control studies. Genetics (2012) 1.71

Population structure can inflate SNP-based heritability estimates. Am J Hum Genet (2011) 1.54

Identity by descent between distant relatives: detection and applications. Annu Rev Genet (2012) 1.39

Interactions among genes in the ErbB-Neuregulin signalling network are associated with increased susceptibility to schizophrenia. Behav Brain Funct (2007) 1.19

Triallelic single nucleotide polymorphisms and genotyping error in genetic epidemiology studies: MDR1 (ABCB1) G2677/T/A as an example. Cancer Epidemiol Biomarkers Prev (2007) 1.15

Genome-wide association study identifies novel loci associated with concentrations of four plasma phospholipid fatty acids in the de novo lipogenesis pathway: results from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium. Circ Cardiovasc Genet (2013) 1.12

Additive genetic variation in schizophrenia risk is shared by populations of African and European descent. Am J Hum Genet (2013) 1.07

Exome sequencing reveals novel rare variants in the ryanodine receptor and calcium channel genes in malignant hyperthermia families. Anesthesiology (2013) 1.06

Identity-by-descent-based heritability analysis in the Northern Finland Birth Cohort. Hum Genet (2012) 1.05

Interactions among genes influencing bacterial recognition increase IBD risk in a population-based New Zealand cohort. Hum Immunol (2009) 0.97

On reducing the statespace of hidden Markov models for the identity by descent process. Theor Popul Biol (2002) 0.93

Genes, diet and inflammatory bowel disease. Mutat Res (2007) 0.91

Genetic analysis of MDR1 and inflammatory bowel disease reveals protective effect of heterozygous variants for ulcerative colitis. Inflamm Bowel Dis (2009) 0.82

Nucleotide-binding oligomerization domain containing 1 (NOD1) haplotypes and single nucleotide polymorphisms modify susceptibility to inflammatory bowel diseases in a New Zealand caucasian population: a case-control study. BMC Res Notes (2009) 0.79

Efficient clustering of identity-by-descent between multiple individuals. Bioinformatics (2013) 0.79