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

By Peter J. Campbell, P. Stephens, E. Pleasance, Sarah O 'meara, Heng Li, T. Santarius, L. Stebbings, Catherine Leroy, S. Edkins, Claire W. Hardy and 14 more. Nature Genetics, 2008

907 citations recorded by the source corpus.

Subfields: Cancer Research, Genetics, Plant Science

View Paper: https://www.semanticscholar.org/paper/5c543beb331255796f61b6b7826f8b21b2cd64fa

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Citations in the corpus

Frequent pathway mutations of splicing machinery in myelodysplasia (2011, neutral): “240 aa Zn S34F(20) S34Y(5) Q157R(7) Q157P(4)”
Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives (2013, methodology): “Earlier methods such as mrCaNaVar and CNV-seq are implemented in a model-free style [31,35,36].”
High-resolution mapping of copy-number alterations with massively parallel sequencing (2008, background): “Recently, a new generation of DNA sequencers has enabled massively parallel sequencing of millions of short sequence reads at dramatically lower cost”
Mechanisms and insights into drug resistance in cancer (2013, background): “The second mechanism involves the acquisition of stochastic alterations within the cancer cells which provide a survival advantage (Campbell et al., 2008; Stratton et al., 2009; Negrini et al., 2010; The International Cancer Genome Consortium, 2010; Shen, 2011).”
cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate (2012, background): “:3) ik and new i to zero according to Equation (6) and Equation (7).”
Genome structural variation discovery and genotyping (2011, methodology): “Read-depth approaches using NGS data were first applied to define rearrangements in cance”
Discovery and statistical genotyping of copy-number variation from whole-exome sequencing depth. (2012, background): “The read depth of exome sequencing for an exon target is a function of a number of biochemical properties of the genome, in addition to experimental and bioinformatic steps including genomic fragmentation, array hybridization (‘‘capture’’), PCR,(23) sequencing,(24) and in silico alignment to the ref”
DELLY: structural variant discovery by integrated paired-end and split-read analysis (2012, background): “DELLY, thus, enables to ascertain the full spectrum of genomic rearrangements, including complex events.”
CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. (2011, methodology): “Previous approaches using RD were limited to only unique regions of the genome (Bentley et al. 2008; Campbell et al. 2008; Chiang et al. 2009), discovered only large CNVs with poor breakpoint resolution (Bentley et al. 2008; Campbell et al. 2008; Alkan et al. 2009; Chiang et al. 2009), or could not…”
COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer (2009, neutral): “More recently, CGP data includes low coverage whole genome resequencing screens (2), utilizing nextgeneration sequencing technologies which can precisely identify genome-level rearrangements previously invisible in both karyotypic and candidate gene screen procedures.”
A census of amplified and overexpressed human cancer genes (2010, background): “This distinction is important because activation of cancer genes by mutation or translocation can also be associated with their amplificatio”
Mutational Processes Molding the Genomes of 21 Breast Cancers (2012, methodology): “Structural variants were called from the short insert data by using MAQ alignments as previously described (Campbell et al., 2008; Stephens et al., 2009).”