Validation of Copy Number Changes Identified by aCGH

<div><p>(A) Log₂ ratio plot demonstrates a 109.2-kb segment of copy number loss on Chromosome 6 in C57L/J, compared to C57BL/6J.</p><p>(B) qPCR using a primer/probe set in the altered region demonstrates normal copy number (normalized to a relative copy number of one in C57BL/6J) in unaffected strains and significantly reduced copy number in four affected strains (inset, zoom-in view of <i>y</i>-axis).</p><p>(C) qPCR fails to generate an amplicon of expected size in the altered region from affected strains. B6, C57BL/6J reference strain.</p><p>(D) Log₂ ratio plot demonstrates a 473.7-kb segment of copy number gain on Chromosome 17 in BALB/cByJ compared to C57BL/6J.</p><p>(E) qPCR demonstrates heterogeneity of copy number (normalized to a relative copy number of one in C57BL/6J) in this region among 20 strains.</p><p>(F) Copy number estimates from aCGH and qPCR are highly concordant (<i>p</i> < 0.0001).</p></div

Relationship between Genomic Distance and Overlap between Segmental Duplications and CNVs

<p>The number of CNVs that overlap at least one segmental duplication was calculated for a range of margin sizes. At a margin size of zero (complete overlap with CNV), 38 of 80 observed CNVs overlap segmental duplications. The extent of overlap between CNVs and segmental duplications (black solid line) increases with margin size. The red dotted line (expected CNVs) indicates the colocalization of segmental duplications with randomly permuted genomic regions of lengths equal to the observed CNVs. Each point of the permuted data was calculated by determining the 95th percentile of the overlap counts. The association between CNVs and segmental duplications remains significant to the 2-Mb window size (<i>p</i> < 0.01) and is highlighted in the yellow rectangle.</p

Representative Germline CNVs in Mice Identified by High-Resolution aCGH

<div><p>The log₂ ratios of signal intensity for C57BL/6J (reference) versus 20 test strains are shown. Inset, an expanded view of the CNVs in NOD/LtJ and A/J from (A) and (B). Scale, 500 kb.</p><p>(A) A 135.6-kb segment of reduced copy number (mean log₂ = −1.02) on Chromosome 14 is present in most strains.</p><p>(B) A 61.7-kb amplified segment (mean log₂ = +1.01) on Chromosome 1 is present in most strains.</p></div

Heatmap Representation of Copy Number Changes in Mice

<p>Unsupervised clustering of segmental gains (green) and losses (red) yields a dendrogram that recapitulates features of the known genealogy of these strains. Clustering in the vertical axis demonstrates three clusters: segments amplified in most strains, segments reduced in most strains, and a third cluster containing either singleton CNVs or mixtures of amplifications and deletions.</p

Genome-wide Distribution of CNVs

<p>The ideograms depict chromosomal locations of copy number gains (green arrows), losses (red arrows), and gains or losses (blue arrows) relative to C57BL/6J in autosomes from 20 inbred strains.</p