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1.
F <span style="font-variant: small-caps" class="small-caps">igure</span>  3.—

F igure 3.—. From: Comparison of Constitutional and Replication Stress-Induced Genome Structural Variation by SNP Array and Mate-Pair Sequencing.

Array run correlation by CNV category. Scatter plots show the correlation of two different SNP array runs of 090. where the top panel shows all data and the bottom panel is magnified to the region near the origin, corresponding to predicted heterozygous events. Green circles are the array log2R values of CNV regions detected by both array and mate pairs, blue circles are CNVs detected only by array, and red circles are CNVs detected only by mate pairs for which array probes were present.

Martin F. Arlt, et al. Genetics. 2011 March;187(3):675-683.
2.
F <span style="font-variant: small-caps" class="small-caps">igure</span>  2.—

F igure 2.—. From: Comparison of Constitutional and Replication Stress-Induced Genome Structural Variation by SNP Array and Mate-Pair Sequencing.

Examples of constitutional CNVs. Major classes of constitutional CNVs observed in 090 are depicted similarly to Figure 1. Orange boxes highlight known human CNVs. (A) An 8.2-kb deletion on chromosome 2 evident in both array and mate-pair data. (B) A 6.5-kb gain on chromosome 18 evident in array but not mate-pair data. (C) A 6.5-kb deletion on chromosome 2 evident in mate-pair but not array data. (D) A 10.2-kb deletion on chromosome 12 evident in mate-pair data in a region with no array probes. A trace shows the relative density of normal ∼3-kb mate-pair mappings, and a cyan box highlights a HERVK element in the reference genome.

Martin F. Arlt, et al. Genetics. 2011 March;187(3):675-683.
3.
F <span style="font-variant: small-caps" class="small-caps">igure</span>  4.—

F igure 4.—. From: Comparison of Constitutional and Replication Stress-Induced Genome Structural Variation by SNP Array and Mate-Pair Sequencing.

Size distribution of SVs. Histograms show the fraction of events by event size within each of four groups. “Const. array”: constitutional CNVs observed in 090D2 by SNP array (blue circles). “Const. mate-pair”: constitutional SVs observed in 090 and/or 090D2 by mate-pair sequencing (red circles). “APH array”: new CNVs observed in a series of 23 independent aphidicolin-treated subclones of 090 or 090D2 by SNP array and/or aCGH (open circles). “APH mate-pair”: new CNVs observed in aphidicolin-treated subclones A3A2 and A1A1 by mate-pair sequencing (black circles). Also shown is a trace of the CNVs detected by microarray from two published compendia (green circles) (Conrad et al. 2010b; Park et al. 2010). Numbers in parentheses indicate the total number of events in each group. Array traces combine both gains and losses, while mate-pair traces combine deletion and duplication sets.

Martin F. Arlt, et al. Genetics. 2011 March;187(3):675-683.
4.
F <span style="font-variant: small-caps" class="small-caps">igure</span>  1.—

F igure 1.—. From: Comparison of Constitutional and Replication Stress-Induced Genome Structural Variation by SNP Array and Mate-Pair Sequencing.

Examples of aphidicolin-induced CNVs. Intensity data (log2R) from SNP arrays are at the top of each panel with mate pairs of the indicated type below. Array data are averaged over a five-probe window. Individual mate pairs are drawn as bars connecting the two reads as mapped to the reference genome. Blue denotes the reference 090 sample and magenta the aphidicolin-treated A3A2 sample. Chromosome coordinates are in megabases. (A) An induced deletion on chromosome 15 that overlaps a constitutional CNV. The orange box denotes the position of a known human population CNV. (B) A bi-allelic deletion on chromosome 3. (C) A complex inversion on chromosome 4 that creates two associated copy-number gains. One potential underlying allele is drawn as an event chain similar to Figure S7.

Martin F. Arlt, et al. Genetics. 2011 March;187(3):675-683.

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