Haplotyping germline and cancer genomes with high-throughput linked-read sequencing

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Assembly and diploid architecture of an individual human genome via single-molecule technologies

(2015) Matthew Pendleton et al.   NATURE METHODS

Phasing of single DNA molecules by massively parallel barcoding

(2015) Erik Borgström et al.   Nature Communications

A Rapid Molecular Approach for Chromosomal Phasing

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

Joint Variant and De Novo Mutation Identification on Pedigrees from High-Throughput Sequencing Data

(2014) John G. Cleary et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

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

(2014) Sasan Amini et al.   NATURE GENETICS

A programmable method for massively parallel targeted sequencing

(2014) Erik S. Hopmans et al.   NUCLEIC ACIDS RESEARCH

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

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

(2013) Andrew Adey et al.   NATURE

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

(2013) Siddarth Selvaraj et al.   NATURE BIOTECHNOLOGY

Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing

(2013) Garrett M Frampton et al.   NATURE BIOTECHNOLOGY

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

Gene Copy-Number Polymorphism Caused by Retrotransposition in Humans

(2013) Daniel R. Schrider et al.   PLoS Genetics

Change-point model on nonhomogeneous Poisson processes with application in copy number profiling by next-generation DNA sequencing

(2012) Jeremy J. Shen et al.   Annals of Applied Statistics

Discovery of ALK-PTPN3 gene fusion from human non-small cell lung carcinoma cell line using next generation RNA sequencing

(2012) Yeonjoo Jung et al.   GENES CHROMOSOMES & CANCER

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

(2012) Brock A. Peters et al.   NATURE

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Identification of new ALK and RET gene fusions from colorectal and lung cancer biopsies

(2012) Doron Lipson et al.   NATURE MEDICINE

Chromosomal Haplotypes by Genetic Phasing of Human Families

(2011) Jared C. Roach et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A comprehensively molecular haplotype-resolved genome of a European individual

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

Mapping copy number variation by population-scale genome sequencing

(2011) Ryan E. Mills et al.   NATURE

Efficient targeted resequencing of human germline and cancer genomes by oligonucleotide-selective sequencing

(2011) Samuel Myllykangas et al.   NATURE BIOTECHNOLOGY

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

(2011) Jorge Duitama et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Haplotype-resolved genome sequencing of a Gujarati Indian individual

(2010) Jacob O Kitzman et al.   NATURE BIOTECHNOLOGY

Beating Poisson encapsulation statistics using close-packed ordering

(2009) Adam R. Abate et al.   LAB ON A CHIP

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

Identification of Novel Isoforms of the EML4-ALK Transforming Gene in Non-Small Cell Lung Cancer

(2008) Y. L. Choi et al.   CANCER RESEARCH

EML4-ALK Fusion Gene and Efficacy of an ALK Kinase Inhibitor in Lung Cancer

(2008) J. P. Koivunen et al.   CLINICAL CANCER RESEARCH

Mapping and sequencing of structural variation from eight human genomes

(2008) Jeffrey M. Kidd et al.   NATURE