Haplotype phasing: existing methods and new developments

A Fast, Powerful Method for Detecting Identity by Descent

(2011) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2011) Luke Jostins et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Low-coverage sequencing: Implications for design of complex trait association studies

(2011) Y. Li et al.   GENOME RESEARCH

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

(2011) Hilma Holm et al.   NATURE GENETICS

The importance of phase information for human genomics

(2011) Ryan Tewhey et al.   NATURE REVIEWS GENETICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

High-Resolution Detection of Identity by Descent in Unrelated Individuals

(2010) Sharon R. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Inferring combined CNV/SNP haplotypes from genotype data

(2010) Shu-Yi Su et al.   BIOINFORMATICS

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

(2010) F. Geraci   BIOINFORMATICS

Optimal algorithms for haplotype assembly from whole-genome sequence data

(2010) D. He et al.   BIOINFORMATICS

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

(2010) Yun Li et al.   GENETIC EPIDEMIOLOGY

Confounding from cryptic relatedness in haplotype-based association studies

(2010) Feng Zhang et al.   GENETICA

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

(2010) S. Q. Le et al.   GENOME RESEARCH

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

(2010) A. McKenna et al.   GENOME RESEARCH

Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows

(2010) LAURENT EXCOFFIER et al.   Molecular Ecology Resources

Integrating common and rare genetic variation in diverse human populations

(2010)   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Whole-genome molecular haplotyping of single cells

(2010) H Christina Fan et al.   NATURE BIOTECHNOLOGY

Haplotype-resolved genome sequencing of a Gujarati Indian individual

(2010) Jacob O Kitzman et al.   NATURE BIOTECHNOLOGY

Direct determination of molecular haplotypes by chromosome microdissection

(2010) Li Ma et al.   NATURE METHODS

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

(2010) Elizabeth T. Cirulli et al.   NATURE REVIEWS GENETICS

Completely phased genome sequencing through chromosome sorting

(2010) H. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing

(2010) J. C. Roach et al.   SCIENCE

Simultaneous Genotype Calling and Haplotype Phasing Improves Genotype Accuracy and Reduces False-Positive Associations for Genome-wide Association Studies

(2009) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated Individuals

(2009) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genotype-Imputation Accuracy across Worldwide Human Populations

(2009) Lucy Huang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

HI: haplotype improver using paired-end short reads

(2009) Q. Long et al.   BIOINFORMATICS

Genotype determination for polymorphisms in linkage disequilibrium

(2009) Zhaoxia Yu et al.   BMC BIOINFORMATICS

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

(2009) Zhiqiang Li et al.   CELL RESEARCH

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

(2009) A. Auton et al.   GENOME RESEARCH

Parental origin of sequence variants associated with complex diseases

(2009) Augustine Kong et al.   NATURE

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

(2009) Jeffrey C Barrett et al.   NATURE GENETICS

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

(2009) David-Alexandre Trégouët et al.   NATURE GENETICS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

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

(2009) E. E. Kenny et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies

(2009) Bryan N. Howie et al.   PLoS Genetics

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

(2008) V. Bansal et al.   BIOINFORMATICS

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

(2008) Olivier Delaneau et al.   BMC BIOINFORMATICS

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

(2008) Daniel G. Hert et al.   ELECTROPHORESIS

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

(2008) Sharon R. Browning   HUMAN GENETICS

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

(2008) Augustine Kong et al.   NATURE GENETICS

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE

Linkage Disequilibrium-Based Quality Control for Large-Scale Genetic Studies

(2008) Paul Scheet et al.   PLoS Genetics