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Results: 5

1.
Figure 4

Figure 4. From: Population Analysis of Large Copy Number Variants and Hotspots of Human Genetic Disease.

CNV Length, Gene Content, and Frequency Distributions
CNVs were plotted according to event type (color), length (y axis), frequency in the population (x axis, number of individuals from n = 2493), and number of RefSeq genes affected (circle size). To facilitate comparison across different platforms, events from different individuals were considered the same if their putative breakpoints were within 50 kb of one another. CNVs related to previously reported disease-causing variants are highlighted.

Andy Itsara, et al. Am J Hum Genet. 2009 February 13;84(2):148-161.
2.
Figure 2

Figure 2. From: Population Analysis of Large Copy Number Variants and Hotspots of Human Genetic Disease.

Autosomal Landscape of Large CNVs
Large CNVs are >100 kbp. Duplications (blue), deletions (red), and homozygous deletions (black) are depicted based on analysis of 2493 individuals. Chromosomes are drawn to scale (tick marks indicate 10 Mb), with the position of centromeres (gray) and predicted rearrangement hotspots (green lines connected by a diagonal) indicated. Those hotspots associated with disease are highlighted in purple. CNVs observed ten or more times for a given locus are cropped.

Andy Itsara, et al. Am J Hum Genet. 2009 February 13;84(2):148-161.
3.
Figure 3

Figure 3. From: Population Analysis of Large Copy Number Variants and Hotspots of Human Genetic Disease.

Cumulative Distributions of the Largest CNV per Individual According to Study
For 10 kb to 1 Mb in 10 kb intervals, the fraction of individuals containing one or more CNVs (y axis) of size greater or equal to a given size (x axis) is plotted according to study. Note that probe density has a significant impact at smaller CNV sizes, but that the cumulative distributions for blood-derived (PARC-PRINCE) and cell-line (PARC-CAP) DNA are similar. The average number of CNVs per individual varies by study from 3 to 7 (Figure S2).

Andy Itsara, et al. Am J Hum Genet. 2009 February 13;84(2):148-161.
4.
Figure 1

Figure 1. From: Population Analysis of Large Copy Number Variants and Hotspots of Human Genetic Disease.

Examples of CNVs by Location and Type
Typical examples of duplications (top row), heterozygous deletions (middle row), and homozygous deletions (bottom row) as detected by using SNP arrays classified as rearrangement hotspot mediated (A), hotspot associated (B), or nonhotspot (C) (see Material and Methods for definitions). The plots show LogR ratio (vertical bars), b-allele frequency (solid points), segmental duplications in the reference assembly (green blocks), and the locations of rearrangement hotspots (purple brackets). 4,35 CNVs are highlighted by gray rectangles, contrasting the LogR ratio (red) and b-allele frequency (blue) with flanking regions (black). Duplications are characterized by increased LogR ratio and heterozygous b-allele frequencies in multiple clusters, corresponding to “AAB” and “ABB” SNP genotypes, instead of a single cluster at 0.5 (“AB”). Heterozygous deletions have decreased LogR ratio and display a loss of heterozygosity. Homozygous deletions have an extremely low LogR ratio and display b-allele frequencies that fail to cluster.

Andy Itsara, et al. Am J Hum Genet. 2009 February 13;84(2):148-161.
5.
Figure 5

Figure 5. From: Population Analysis of Large Copy Number Variants and Hotspots of Human Genetic Disease.

Comparison of CNVs >100 kb in Affected versus Unaffected Individuals at Four Selected Loci Scoring Highly for Potential Pathogenicity
Duplications, deletions, and homozygous deletions are plotted blue, red, and black, respectively, in human reference assembly coordinates (x axis in each plot). Tick marks are spaced 10 Mb apart, centromeres are indicated in gray, and hotspots are shown as two green vertical lines connected by a green diagonal. Scale in bottom right indicates 1 Mb. Rearrangement hotspots that have been associated with disease are highlighted in purple. Plotting is cropped after 30 overlapping CNVs at a given locus.
(A and B) Known disease loci.
(A) 22q11-12. Disease hotspots (left to right): VCFS, critical region; VCFS, distal region, Distal 22q11 deletion syndrome (MIM 611867). 55
(B) 15q11-q14. Disease hotspots: Prader-Willi/Angelman Syndrome BP1-BP3 (MIM 176270, 105830), and 15q13.3 (MIM 612001). 20
(C and D) Candidate disease loci.
(C) 16p11-13. An inversion-containing region found in 7/8 analyzed HapMap samples 42 has been colored orange along the x axis. Disease hotspots from left to right: 16p13 deletion syndrome distal and proximal regions, 56 16p11.2-p12.2 deletion syndrome, 15 and 16p11 region associated with autism. 19,49
(D) 15q22-25. Disease hotspots from left to right: 15q24 deletion syndrome BP0-BP1, BP1-BP2, and BP2-BP3. 17

Andy Itsara, et al. Am J Hum Genet. 2009 February 13;84(2):148-161.

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