Assembly of microarrays for genome-wide measurement of DNA copy number

By Antoine Snijders, N. Nowak, R. Segraves, S. Blackwood, Nils Brown, J. Conroy, G. Hamilton, A. K. Hindle, B. Huey, Karen Kimura and 9 more. Nature Genetics, 2001

1,027 citations recorded by the source corpus.

Subfields: Cell Biology, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ecbe7b41b6412d4af05739b0735f7ba034fe0b54

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Citations in the corpus

Hidden Markov models approach to the analysis of array CGH data (2004, background): “[19].”
bcp: An R Package for Performing a Bayesian Analysis of Change Point Problems (2007, methodology): “A commercial program, SPROC, was used to map the data to its location in the genome, and as a ﬁlter to remove measurements based on a number of criteria including low reference/signal intensity (Snijders et al. 2001).”
Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives (2013, background): “(SNP) array approaches [10]; these approaches, however, have suffered from several inherent drawbacks, including hybridization noise, limited coverage for genome, low resolution, and difficulty in detecting novel and rare mutations [11,12].”
Development of query strategies to identify a histologic lymphoma subtype in a large linked database system. (2006, positive): “In contrast, genome wide arrays that sample copy number status of loci at megabase intervals have facilitated rapid survey for regions of loss and gain (Fiegler et al. 2003; Greshock et al. 2004; Snijders et al. 2001).”
ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. (2004, methodology): “Mapped cosmids and BAC clones have been used to build microarrays [46], and these arrays could be used to assay ChIP-chip experiments, but the resolution would be correspondingly low.”
MODEL SELECTION FOR HIGH-DIMENSIONAL, MULTI-SEQUENCE CHANGE-POINT PROBLEMS (2012, background): “…have enabled the genome-wide fine scale profiling of DNA copy number in high throughput experiments (Pinkel et al. (1988); Pollack et al. (1999); Snijders et al. (2001); Bignell et al. (2004); Peiffer et al. (2006)), leading to systematic studies aimed at using copy number polymorphisms to…”
A tiling resolution DNA microarray with complete coverage of the human genome (2004, methodology): “Efforts to construct DNA arrays spanning the human genome consisted of spotting 2,460 (ref”
Autophagy suppresses tumor progression by limiting chromosomal instability. (2007, methodology): “Briefly, genomic DNA from beclin1 and beclin1 iBMK cells and the normal mouse tissue was isolated, fluorescent-labeled, and hybridized to a BAC array (Snijders et al. 2001) in triplicate.”
Fine-scale structural variation of the human genome (2005, methodology): “We labeled test and reference DNAs (from an anonymous male donor) with Cy3 or Cy5 by random priming and hybridized them to a BAC microarra”
Analysis of array CGH data: from signal ratio to gain and loss of DNA regions (2004, methodology): “We present here the results obtained with our methodology applied to a public data set (Snijders et al., 2001).”
Determinants of BRAF mutations in primary melanomas. (2003, methodology): “We analyzed specimens from 68 case patients (19 with mutations) with array comparative genomic hybridization ( 8 ,9) to determine whether the mutant BRAF allele was preferentially gained.”
A Modified Bayes Information Criterion with Applications to the Analysis of Comparative Genomic Hybridization Data (2007, methodology): “Like the previous studies, we first use the Coriel data set featured in Snijders et al. (2001) to test the modified BIC.”
Circular binary segmentation for the analysis of array-based DNA copy number data. (2004, methodology): “Finally, for chromosome 15 on GM07081, our result is consistent with Snijders et al. (2001) in that no evidence of an alteration is seen in the aCGH data.”