Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies

Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program

(2021) Daniel Taliun et al.   NATURE

A structural variation reference for medical and population genetics

(2020) Ryan L. Collins et al.   NATURE

The mutational constraint spectrum quantified from variation in 141,456 humans

(2020) Konrad J. Karczewski et al.   NATURE

Mapping and characterization of structural variation in 17,795 human genomes

(2020) Haley J. Abel et al.   NATURE

A long-read RNA-seq approach to identify novel transcripts of very large genes

(2020) Prech Uapinyoying et al.   GENOME RESEARCH

Whole-genome sequencing of patients with rare diseases in a national health system

(2020) Ernest Turro et al.   NATURE

Telomere-to-telomere assembly of a complete human X chromosome

(2020) Karen H. Miga et al.   NATURE

A robust benchmark for detection of germline large deletions and insertions

(2020) Justin M. Zook et al.   NATURE BIOTECHNOLOGY

Characterizing the Major Structural Variant Alleles of the Human Genome

(2019) Peter A. Audano et al.   CELL

Insights into genetics, human biology and disease gleaned from family based genomic studies

(2019) Jennifer E. Posey et al.   GENETICS IN MEDICINE

Using long-read sequencing to detect imprinted DNA methylation

(2019) Scott Gigante et al.   NUCLEIC ACIDS RESEARCH

Genetic Variation, Comparative Genomics, and the Diagnosis of Disease

(2019) Evan E. Eichler   NEW ENGLAND JOURNAL OF MEDICINE

Multi-platform discovery of haplotype-resolved structural variation in human genomes

(2019) Mark J. P. Chaisson et al.   Nature Communications

MsPAC: a tool for haplotype-phased structural variant detection

(2019) Oscar L Rodriguez et al.   BIOINFORMATICS

The “All of Us” Research Program

(2019)   NEW ENGLAND JOURNAL OF MEDICINE

Latest techniques to study DNA methylation

(2019) Quentin Gouil et al.   Essays in Biochemistry

Identification and characterization of occult human-specific LINE-1 insertions using long-read sequencing technology

(2019) Weichen Zhou et al.   NUCLEIC ACIDS RESEARCH

An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder

(2018) Donna M. Werling et al.   NATURE GENETICS

Human copy number variants are enriched in regions of low mappability

(2018) Jean Monlong et al.   NUCLEIC ACIDS RESEARCH

Paternally inherited cis-regulatory structural variants are associated with autism

(2018) William M. Brandler et al.   SCIENCE

Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects

(2018) Allison A. Regier et al.   Nature Communications

The UK Biobank

(2018) Nicole Rusk   NATURE METHODS

The impact of structural variation on human gene expression

(2017) Colby Chiang et al.   NATURE GENETICS

Single-cell template strand sequencing by Strand-seq enables the characterization of individual homologs

(2017) Ashley D Sanders et al.   Nature Protocols

Mapping and phasing of structural variation in patient genomes using nanopore sequencing

(2017) Mircea Cretu Stancu et al.   Nature Communications

A recurrence-based approach for validating structural variation using long-read sequencing technology

(2017) Xuefang Zhao et al.   GigaScience

Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA

(2016) Tychele N. Turner et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Characterizing polymorphic inversions in human genomes by single-cell sequencing

(2016) Ashley D. Sanders et al.   GENOME RESEARCH

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data

(2015) Caroline F Wright et al.   LANCET

An integrated map of structural variation in 2,504 human genomes

(2015) Peter H. Sudmant et al.   NATURE

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

(2015) Matthew Pendleton et al.   NATURE METHODS

The Intolerance of Regulatory Sequence to Genetic Variation Predicts Gene Dosage Sensitivity

(2015) Slavé Petrovski et al.   PLoS Genetics

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

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

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

A framework for the interpretation of de novo mutation in human disease

(2014) Kaitlin E Samocha et al.   NATURE GENETICS

The UCSC genome browser and associated tools

(2012) R. M. Kuhn et al.   BRIEFINGS IN BIOINFORMATICS

An informatics approach to analyzing the incidentalome

(2012) Jonathan S. Berg et al.   GENETICS IN MEDICINE

Mapping copy number variation by population-scale genome sequencing

(2011) Ryan E. Mills et al.   NATURE

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

(2011) A. P. Jason de Koning et al.   PLoS Genetics

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

(2010) A. McKenna et al.   GENOME RESEARCH

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The DNA replication FoSTeS/MMBIR mechanism can generate genomic, genic and exonic complex rearrangements in humans

(2009) Feng Zhang et al.   NATURE GENETICS

Natural Selection on Genes that Underlie Human Disease Susceptibility

(2008) Ran Blekhman et al.   CURRENT BIOLOGY