Segmental duplications and copy-number variation in the human genome.

By A. Sharp, Devin P. Locke, S. McGrath, Ze Cheng, J. Bailey, Rhea U. Vallente, Lisa M. Pertz, Royden A. Clark, S. Schwartz, R. Segraves and 4 more. American Journal of Human Genetics, 2005

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Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/4ac8d3cbc041ce5e2326ff118c05a9b0180117f6

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Citations in the corpus

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly (2016, positive): “Although a subset of missing sequences is associated with gaps deemed recalcitrant to cloning, segmental duplications or other complex genomic architectures are implicated in most remaining gaps or misassemblies (Bailey et al. 2001; Sharp et al. 2005; Chaisson et al. 2015a).”
Human and chimpanzee Luteinizing hormone/ Chorionic Gonadotropin beta (LHB/CGB) gene clusters: diversity and divergence of young duplicated genes (2009, background): “CNVs range from kilobases to megabases in size and include deletion, insertion and duplication variations between individuals (Iafrate et al. 2004; Sebat et al. 2004; Sharp et al. 2005).”
PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. (2007, background): “Multiple genome-wide studies using array-CGH have shown that chromosome rearrangements tend to occur in genomic regions exhibiting segmental duplication (Iafrate et al. 2004; Sebat et al. 2004; Sharp et al. 2005; Locke et al. 2006).”
MODEL SELECTION FOR HIGH-DIMENSIONAL, MULTI-SEQUENCE CHANGE-POINT PROBLEMS (2012, methodology): “However, some inherited CNV reside in highly mutable regions of the genome, e.g., regions containing segmental duplications (Sharp et al. (2005)).”
Mapping and sequencing of structural variation from eight human genomes (2008, background): “Heterozygous submicroscopic inversions involving olfactory receptor-gene clusters mediate the recurrent t(4;8)(p16;p23) translocation.”
Discovery and statistical genotyping of copy-number variation from whole-exome sequencing depth. (2012, background): “Copy-number variants (CNVs) have emerged in the last decade as a category of structural genetic diversity that plays a key role in human health and common disease.(1) A number of studies have implicated deletion and duplication CNVs in cancer susceptibility, metastasis, gene expression, and treatmen”
De novo assembly and genotyping of variants using colored de Bruijn graphs (2012, methodology): “Fifth, although there are methods for detecting large structural variants, such as using array comparative genomic hybridization (aCGH) 22–25 and mapped reads 11,12,14,26 , these cannot determine the exact location, size or allelic sequence of variants.”
Copy number variation: new insights in genome diversity. (2006, background): “Since a significant portion of CNVs was identified in regions containing known segmental duplications, Sharp et al. (2005) reasoned that a custom array, containing DNA clones targeting these known duplicated regions of the human genome (which are also speculated to serve as potential rearrangement…”