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Article
Open AccessMap** recurrent mosaic copy number variation in human neurons
When somatic cells acquire complex karyotypes, they often are removed by the immune system. Mutant somatic cells that evade immune surveillance can lead to cancer. Neurons with complex karyotypes arise during ...
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Article
Open AccessGenomic data resources of the Brain Somatic Mosaicism Network for neuropsychiatric diseases
Somatic mosaicism is defined as an occurrence of two or more populations of cells having genomic sequences differing at given loci in an individual who is derived from a single zygote. It is a characteristic o...
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Article
Open AccessSquiggleNet: real-time, direct classification of nanopore signals
We present SquiggleNet, the first deep-learning model that can classify nanopore reads directly from their electrical signals. SquiggleNet operates faster than DNA passes through the pore, allowing real-time c...
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Article
Open AccessCas9 targeted enrichment of mobile elements using nanopore sequencing
Mobile element insertions (MEIs) are repetitive genomic sequences that contribute to genetic variation and can lead to genetic disorders. Targeted and whole-genome approaches using short-read sequencing have b...
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Article
Open AccessComprehensive identification of somatic nucleotide variants in human brain tissue
Post-zygotic mutations incurred during DNA replication, DNA repair, and other cellular processes lead to somatic mosaicism. Somatic mosaicism is an established cause of various diseases, including cancers. How...
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Article
Author Correction: A robust benchmark for detection of germline large deletions and insertions
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Article
A robust benchmark for detection of germline large deletions and insertions
New technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution and comprehensiveness. To help translate these methods to routine r...
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Article
Open AccessAssociation of CNVs with methylation variation
Germline copy number variants (CNVs) and single-nucleotide polymorphisms (SNPs) form the basis of inter-individual genetic variation. Although the phenotypic effects of SNPs have been extensively investigated,...
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Article
Structural variation in the sequencing era
Identifying structural variation (SV) is essential for genome interpretation but has been historically difficult due to limitations inherent to available genome technologies. Detection methods that use ensembl...
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Article
Open AccessTranslation of upstream open reading frames in a model of neuronal differentiation
Upstream open reading frames (uORFs) initiate translation within mRNA 5′ leaders, and have the potential to alter main coding sequence (CDS) translation on transcripts in which they reside. Ribosome profiling ...
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Article
Open AccessMulti-platform discovery of haplotype-resolved structural variation in human genomes
The incomplete identification of structural variants (SVs) from whole-genome sequencing data limits studies of human genetic diversity and disease association. Here, we apply a suite of long-read, short-read, ...
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Article
Open AccessFusorSV: an algorithm for optimally combining data from multiple structural variation detection methods
Comprehensive and accurate identification of structural variations (SVs) from next generation sequencing data remains a major challenge. We develop FusorSV, which uses a data mining approach to assess performance...
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Article
Open AccessSPECtre: a spectral coherence-based classifier of actively translated transcripts from ribosome profiling sequence data
Active protein translation can be assessed and measured using ribosome profiling sequencing strategies. Prevailing analytical approaches applied to this technology make use of sequence fragment length profilin...
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Article
Open AccessResolving complex structural genomic rearrangements using a randomized approach
Complex chromosomal rearrangements are structural genomic alterations involving multiple instances of deletions, duplications, inversions, or translocations that co-occur either on the same chromosome or repre...
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Article
Open AccessAn integrated map of structural variation in 2,504 human genomes
Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising bo...
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Open AccessCopy number variation genoty** using family information
In recent years there has been a growing interest in the role of copy number variations (CNV) in genetic diseases. Though there has been rapid development of technologies and statistical methods devoted to det...
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Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration
Michael Talkowski and colleagues examine karyotypically balanced genomic rearrangement landscapes in the germline at single-nucleotide resolution. They find predominant roles for complex reorganization and non...
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Article
Open AccessRefinement of primate copy number variationhotspots identifies candidate genomic regions evolving under positive selection
Copy number variants (CNVs), defined as losses and gains of segments of genomic DNA, are a major source of genomic variation.
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Article
Map** copy number variation by population-scale genome sequencing
Genomic structural variants (SVs) are abundant in humans, differing from other forms of variation in extent, origin and functional impact. Despite progress in SV characterization, the nucleotide resolution arc...
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Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing
Jeong-Sun Seo and colleagues report a catalog of common CNVs in Asians. The authors integrated high-resolution array CGH data with next-generation DNA sequencing data to discover 3,568 putative Asian-specific ...
