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DELLY: structural variant discovery by integrated paired-end and split-read analysis
An SV discovery method that integrates short insert paired-ends, long-range mate-pairs and split-read alignments to accurately delineate genomic rearrangements at single-nucleotide resolution, called DELLY, which enables to ascertain the full spectrum of genomic rearrANGements, including complex events.
Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma
The presence of H3F3A/ATRX-DAXX/TP53 mutations was strongly associated with alternative lengthening of telomeres and specific gene expression profiles, suggesting that defects of the chromatin architecture underlie paediatric and young adult GBM pathogenesis.
An integrated map of structural variation in 2,504 human genomes
An integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which are constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations are described.
Mapping copy number variation by population scale genome sequencing
A map of unbalanced SVs is constructed based on whole genome DNA sequencing data from 185 human genomes, integrating evidence from complementary SV discovery approaches with extensive experimental validations, and serves as a resource for sequencing-based association studies.
Genome Sequencing of Pediatric Medulloblastoma Links Catastrophic DNA Rearrangements with TP53 Mutations
Dissecting the genomic complexity underlying medulloblastoma
An integrative deep-sequencing analysis of 125 tumour–normal pairs enhances the understanding of the genomic complexity and heterogeneity underlying medulloblastoma, and provides several potential targets for new therapeutics, especially for Group 3 and 4 patients.
Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition.
Assembly and diploid architecture of an individual human genome via single-molecule technologies
This work shows that it is now possible to integrate single-molecule and high-throughput sequence data to generate de novo assembled genomes that approach reference quality.
SeqAn An efficient, generic C++ library for sequence analysis
The design and content of SeqAn are described, which comprises implementations of existing, practical state-of-the-art algorithmic components to provide a sound basis for algorithm testing and development and greatly simplifies the rapid development of new bioinformatics tools.
The Genomic and Transcriptomic Landscape of a HeLa Cell Line
This study performed DNA and RNA sequencing of a HeLa Kyoto cell line and analyzed its mutational portfolio and gene expression profile, providing the first detailed account of genomic variants in the HeLa genome.