Haplotype-resolved genome sequencing: experimental methods and applications

Integrative analysis of haplotype-resolved epigenomes across human tissues

(2015) Danny Leung et al.   NATURE

A Rapid Molecular Approach for Chromosomal Phasing

(2015) John F. Regan et al.   PLoS One

Probabilistic single-individual haplotyping

(2014) V. Kuleshov   BIOINFORMATICS

Programming and Inheritance of Parental DNA Methylomes in Mammals

(2014) Lu Wang et al.   CELL

Single haplotype assembly of the human genome from a hydatidiform mole

(2014) Karyn Meltz Steinberg et al.   GENOME RESEARCH

In vitro, long-range sequence information for de novo genome assembly via transposase contiguity

(2014) Andrew Adey et al.   GENOME RESEARCH

The genomic landscape of Neanderthal ancestry in present-day humans

(2014) Sriram Sankararaman et al.   NATURE

Resolving the complexity of the human genome using single-molecule sequencing

(2014) Mark J. P. Chaisson et al.   NATURE

Decoding long nanopore sequencing reads of natural DNA

(2014) Andrew H Laszlo et al.   NATURE BIOTECHNOLOGY

Whole-genome haplotyping using long reads and statistical methods

(2014) Volodymyr Kuleshov et al.   NATURE BIOTECHNOLOGY

Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping

(2014) Paula J P de Vree et al.   NATURE BIOTECHNOLOGY

Large-scale meta-analysis of genome-wide association data identifies six new risk loci for Parkinson's disease

(2014) Mike A Nalls et al.   NATURE GENETICS

Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing

(2014) Sasan Amini et al.   NATURE GENETICS

Inferring human population size and separation history from multiple genome sequences

(2014) Stephan Schiffels et al.   NATURE GENETICS

A Quantitative Comparison of Single-Cell Whole Genome Amplification Methods

(2014) Charles F. A. de Bourcy et al.   PLoS One

Resurrecting Surviving Neandertal Lineages from Modern Human Genomes

(2014) B. Vernot et al.   SCIENCE

Multiple haplotype-resolved genomes reveal population patterns of gene and protein diplotypes

(2014) Margret R. Hoehe et al.   Nature Communications

Haplotype Estimation Using Sequencing Reads

(2013) Olivier Delaneau et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Joint haplotype phasing and genotype calling of multiple individuals using haplotype informative reads

(2013) Kui Zhang et al.   BIOINFORMATICS

Leveraging reads that span multiple single nucleotide polymorphisms for haplotype inference from sequencing data

(2013) W.-Y. Yang et al.   BIOINFORMATICS

Haplotype assembly in polyploid genomes and identical by descent shared tracts

(2013) Derek Aguiar et al.   BIOINFORMATICS

Identification of gene fusions from human lung cancer mass spectrometry data

(2013) Han Sun et al.   BMC GENOMICS

Genome Analyses of Single Human Oocytes

(2013) Yu Hou et al.   CELL

Sequencing of isolated sperm cells for direct haplotyping of a human genome

(2013) E. F. Kirkness et al.   GENOME RESEARCH

The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line

(2013) Andrew Adey et al.   NATURE

The complete genome sequence of a Neanderthal from the Altai Mountains

(2013) Kay Prüfer et al.   NATURE

Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing

(2013) Siddarth Selvaraj et al.   NATURE BIOTECHNOLOGY

Truncating mutations of MAGEL2 cause Prader-Willi phenotypes and autism

(2013) Christian P Schaaf et al.   NATURE GENETICS

Genome-wide association analysis identifies 13 new risk loci for schizophrenia

(2013) Stephan Ripke et al.   NATURE GENETICS

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

Whole-genome haplotyping by dilution, amplification, and sequencing

(2013) F. Kaper et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Erythroid Enhancer of BCL11A Subject to Genetic Variation Determines Fetal Hemoglobin Level

(2013) D. E. Bauer et al.   SCIENCE

The genome sequence of the colonial chordate, Botryllus schlosseri

(2013) Ayelet Voskoboynik et al.   eLife

On the design of clone-based haplotyping

(2013) Christine Lo et al.   GENOME BIOLOGY

Genomic Patterns of Homozygosity in Worldwide Human Populations

(2012) Trevor J. Pemberton et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Base-Resolution Analyses of Sequence and Parent-of-Origin Dependent DNA Methylation in the Mouse Genome

(2012) Wei Xie et al.   CELL

Genome-wide Single-Cell Analysis of Recombination Activity and De Novo Mutation Rates in Human Sperm

(2012) Jianbin Wang et al.   CELL

The Life History of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

HapCompass: A Fast Cycle Basis Algorithm for Accurate Haplotype Assembly of Sequence Data

(2012) Derek Aguiar et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Non-invasive prenatal measurement of the fetal genome

(2012) H. Christina Fan et al.   NATURE

Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells

(2012) Brock A. Peters et al.   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

The expanding scope of DNA sequencing

(2012) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Extremely low-coverage sequencing and imputation increases power for genome-wide association studies

(2012) Bogdan Pasaniuc et al.   NATURE GENETICS

Identification of 15 new psoriasis susceptibility loci highlights the role of innate immunity

(2012) Lam C Tsoi et al.   NATURE GENETICS

Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell

(2012) C. Zong et al.   SCIENCE

Probing Meiotic Recombination and Aneuploidy of Single Sperm Cells by Whole-Genome Sequencing

(2012) S. Lu et al.   SCIENCE

Noninvasive Whole-Genome Sequencing of a Human Fetus

(2012) J. O. Kitzman et al.   Science Translational Medicine

Strobe sequence design for haplotype assembly

(2011) Christine Lo et al.   BMC BIOINFORMATICS

Relationship between Single Nucleotide Polymorphisms and Haplotypes in DPYD and Toxicity and Efficacy of Capecitabine in Advanced Colorectal Cancer

(2011) M. J. Deenen et al.   CLINICAL CANCER RESEARCH

A comprehensively molecular haplotype-resolved genome of a European individual

(2011) E.-K. Suk et al.   GENOME RESEARCH

An autosomal locus that controls chromosome-wide replication timing and mono-allelic expression

(2011) Eric P. Stoffregen et al.   HUMAN MOLECULAR GENETICS

Haplotype phasing: existing methods and new developments

(2011) Sharon R. Browning et al.   NATURE REVIEWS GENETICS

Fosmid-based whole genome haplotyping of a HapMap trio child: evaluation of Single Individual Haplotyping techniques

(2011) Jorge Duitama et al.   NUCLEIC ACIDS RESEARCH

Targeted isolation of cloned genomic regions by recombineering for haplotype phasing and isogenic targeting

(2011) Marta Nedelkova et al.   NUCLEIC ACIDS RESEARCH

A three-dimensional model of the yeast genome

(2010) Zhijun Duan 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

Parallel, tag-directed assembly of locally derived short sequence reads

(2010) Joseph B Hiatt et al.   NATURE METHODS

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

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Maternal Plasma DNA Sequencing Reveals the Genome-Wide Genetic and Mutational Profile of the Fetus

(2010) Y. M. D. Lo et al.   Science Translational Medicine

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding

(2009) K. J. McKernan et al.   GENOME RESEARCH

Direct determination of haplotypes from single DNA molecules

(2009) Ming Xiao et al.   NATURE METHODS

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Reduced Neutrophil Count in People of African Descent Is Due To a Regulatory Variant in the Duffy Antigen Receptor for Chemokines Gene

(2009) David Reich et al.   PLoS Genetics

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

(2008) V. Bansal et al.   BIOINFORMATICS

An MCMC algorithm for haplotype assembly from whole-genome sequence data

(2008) V. Bansal et al.   GENOME RESEARCH