Genome structural variation discovery and genotyping

Mapping copy number variation by population-scale genome sequencing

(2011) Ryan E. Mills et al.   NATURE

Mosaic Uniparental Disomies and Aneuploidies as Large Structural Variants of the Human Genome

(2010) Benjamín Rodríguez-Santiago et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Rare Deletions at 16p13.11 Predispose to a Diverse Spectrum of Sporadic Epilepsy Syndromes

(2010) Erin L. Heinzen et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Consensus Statement: Chromosomal Microarray Is a First-Tier Clinical Diagnostic Test for Individuals with Developmental Disabilities or Congenital Anomalies

(2010) David T. Miller et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Detection and characterization of novel sequence insertions using paired-end next-generation sequencing

(2010) Iman Hajirasouliha et al.   BIOINFORMATICS

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery

(2010) Fereydoun Hormozdiari et al.   BIOINFORMATICS

Multiplex Amplicon Quantification (MAQ), a fast and efficient method for the simultaneous detection of copy number alterations in neuroblastoma.

(2010) Candy Kumps et al.   BMC GENOMICS

A Human Genome Structural Variation Sequencing Resource Reveals Insights into Mutational Mechanisms

(2010) Jeffrey M. Kidd et al.   CELL

De novo rates and selection of large copy number variation

(2010) A. Itsara et al.   GENOME RESEARCH

Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome

(2010) A. R. Quinlan et al.   GENOME RESEARCH

Assembly of large genomes using second-generation sequencing

(2010) M. C. Schatz et al.   GENOME RESEARCH

Detecting copy number variation with mated short reads

(2010) P. Medvedev et al.   GENOME RESEARCH

Mechanisms of mosaicism, chimerism and uniparental disomy identified by single nucleotide polymorphism array analysis

(2010) Laura K. Conlin et al.   HUMAN MOLECULAR GENETICS

Digital PCR on a SlipChip

(2010) Feng Shen et al.   LAB ON A CHIP

Taking qPCR to a higher level: Analysis of CNV reveals the power of high throughput qPCR to enhance quantitative resolution

(2010) Suzanne Weaver et al.   METHODS

Human genome: Genomes by the thousand

(2010)   NATURE

Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls

(2010)   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Haplotype-resolved genome sequencing of a Gujarati Indian individual

(2010) Jacob O Kitzman et al.   NATURE BIOTECHNOLOGY

A large and complex structural polymorphism at 16p12.1 underlies microdeletion disease risk

(2010) Francesca Antonacci et al.   NATURE GENETICS

Mutation spectrum revealed by breakpoint sequencing of human germline CNVs

(2010) Donald F Conrad et al.   NATURE GENETICS

Public data archives for genomic structural variation

(2010) Deanna M Church et al.   NATURE GENETICS

Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing

(2010) Hansoo Park et al.   NATURE GENETICS

Characterization of missing human genome sequences and copy-number polymorphic insertions

(2010) Jeffrey M Kidd et al.   NATURE METHODS

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

FACADE : a fast and sensitive algorithm for the segmentation and calling of high resolution array CGH data

(2010) Bradley P. Coe et al.   NUCLEIC ACIDS RESEARCH

Comparative analyses of seven algorithms for copy number variant identification from single nucleotide polymorphism arrays

(2010) Andrew E. Dellinger et al.   NUCLEIC ACIDS RESEARCH

Single molecule linear analysis of DNA in nano-channel labeled with sequence specific fluorescent probes

(2010) S. K. Das et al.   NUCLEIC ACIDS RESEARCH

High-resolution human genome structure by single-molecule analysis

(2010) B. Teague et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diversity of Human Copy Number Variation and Multicopy Genes

(2010) Peter H. Sudmant et al.   SCIENCE

Systematic Inference of Copy-Number Genotypes from Personal Genome Sequencing Data Reveals Extensive Olfactory Receptor Gene Content Diversity

(2010) Sebastian M. Waszak et al.   PLoS Computational Biology

Towards a comprehensive structural variation map of an individual human genome

(2010) Andy W Pang et al.   GENOME BIOLOGY

Population Analysis of Large Copy Number Variants and Hotspots of Human Genetic Disease

(2009) Andy Itsara et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Microfluidic digital PCR enables rapid prenatal diagnosis of fetal aneuploidy

(2009) H. Christina Fan et al.   AMERICAN JOURNAL OF OBSTETRICS AND GYNECOLOGY

Targeted interrogation of copy number variation using SCIMMkit

(2009) Troy Zerr et al.   BIOINFORMATICS

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

The pitfalls of platform comparison: DNA copy number array technologies assessed

(2009) Christina Curtis et al.   BMC GENOMICS

A method for rapid, targeted CNV genotyping identifies rare variants associated with neurocognitive disease

(2009) H. C. Mefford et al.   GENOME RESEARCH

Mobile elements create structural variation: Analysis of a complete human genome

(2009) J. Xing et al.   GENOME RESEARCH

Sensitive and accurate detection of copy number variants using read depth of coverage

(2009) S. Yoon et al.   GENOME RESEARCH

Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes

(2009) F. Hormozdiari et al.   GENOME RESEARCH

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

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Origins and functional impact of copy number variation in the human genome

(2009) Donald F. Conrad et al.   NATURE

Single-molecule sequencing of an individual human genome

(2009) Dmitry Pushkarev et al.   NATURE BIOTECHNOLOGY

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library

(2009) Hugo Y K Lam et al.   NATURE BIOTECHNOLOGY

Personalized copy number and segmental duplication maps using next-generation sequencing

(2009) Can Alkan et al.   NATURE GENETICS

Direct determination of haplotypes from single DNA molecules

(2009) Ming Xiao et al.   NATURE METHODS

MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions

(2009) Seunghak Lee et al.   NATURE METHODS

Computational methods for discovering structural variation with next-generation sequencing

(2009) Paul Medvedev et al.   NATURE METHODS

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

(2009) Ken Chen et al.   NATURE METHODS

PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data

(2009) Jan O Korbel et al.   GENOME BIOLOGY

The Fine-Scale and Complex Architecture of Human Copy-Number Variation

(2008) George H. Perry et al.   AMERICAN JOURNAL OF HUMAN GENETICS

De novo fragment assembly with short mate-paired reads: Does the read length matter?

(2008) M. J. Chaisson et al.   GENOME RESEARCH

Whole population, genome-wide mapping of hidden relatedness

(2008) A. Gusev et al.   GENOME RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

The complete genome of an individual by massively parallel DNA sequencing

(2008) David A. Wheeler et al.   NATURE

Genotype, haplotype and copy-number variation in worldwide human populations

(2008) Mattias Jakobsson et al.   NATURE

Mapping and sequencing of structural variation from eight human genomes

(2008) Jeffrey M. Kidd et al.   NATURE

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

Evolutionary toggling of the MAPT 17q21.31 inversion region

(2008) Michael C Zody et al.   NATURE GENETICS

Systematic assessment of copy number variant detection via genome-wide SNP genotyping

(2008) Gregory M Cooper et al.   NATURE GENETICS

Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing

(2008) Peter J Campbell et al.   NATURE GENETICS

Integrated detection and population-genetic analysis of SNPs and copy number variation

(2008) Steven A McCarroll et al.   NATURE GENETICS

Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs

(2008) Joshua M Korn et al.   NATURE GENETICS

High-resolution mapping of copy-number alterations with massively parallel sequencing

(2008) Derek Y Chiang et al.   NATURE METHODS

Rare Structural Variants Disrupt Multiple Genes in Neurodevelopmental Pathways in Schizophrenia

(2008) T. Walsh et al.   SCIENCE