Figure 1

Genomic waves appearing in parents and offspring induce false positive de novo deletions. Panels in (a) and (b) plot log R ratios and B allele frequencies, respectively, for father (top), mother (middle), and offspring (bottom). Overlaying the log R ratio plots is a lowess curve with a span of 1/10. The calls from the joint HMM are indicated in the offspring panel of Figures (a) and (b). The state codes 232, 322, and 332 correspond to a paternally inherited deletion, a maternally inherited deletion, and de novo deletion, respectively. (c) The minimum distance calculated from the log R ratios in (a). Overlaying the minimum distance is a lowess curve with the same span as in (a) and (b). The blue rectangle demarcates the de novo hemizygous deletion called by PennCNV.