Fig. 3
From: Paternal exposure to benzo(a)pyrene induces genome-wide mutations in mouse offspring
Identification and characterization of de novo CNVs. a Example of a 533-kb duplication. Red diamonds show the DNA probes with higher offspring signal (elevated Cy5 at CNV locus) and the yellow diamonds show the DNA probes where offspring DNA is the same quantity as the parental DNA. The red glowing line shows the average log2 ratio (0.61) for the mouse with a CNV while the yellow glowing lines show the average log2 ratio for the six litter mates. The log2 ratio of zero indicates no change in copy number. b The copy number measured by qPCR revealed that the putative CNV was a true de novo event because it was present in multiple tissues with a copy number of three, and the CNV was not present in the parents or sibling. c Mate-pair sequencing revealed that the CNV came from the sire because the paternal SNPs were present at a higher allele fraction within the CNV locus. d Mate-pair sequencing identified the breakpoint locations by mapping discordant mate-pairs against the genome (mapping at chromosome 10 in orange and 4 in pink). Split reads mapping to both chromosome locations simultaneously allowed for the breakpoint sequence to be determined. In this example, the CNV was facilitated by microhomology of two base pairs (CT)
