Figure 2.

Structural abnormalities account for most of the inconsistencies in detection of the platinum haplotypes in the founders. (A) A 20-Mb structural abnormality identified by 177 variants in nine clusters that failed the founder haplotype validation test in NA12889. Based on the marked skew in frequency of the SNV alleles within the rearrangement (4:1) compared to the proximal flanking region (1:1), this event is likely a mosaic on the distal end of Chromosome 11, specific to NA12889. Each point represents the allele count at a SNV location expected to be heterozygous in NA12889 based on seeing the nontransmitted allele at least six times. Red points show the allele counts (average n = 11 within the mosaic) of the haplotype transmitted to NA12877, and blue points show the allele counts (average n = 43 in the mosaic) of the nontransmitted haplotype. The black line shows the average total depth in windows of 100 SNVs, highlighting that this mosaic is not associated with a change in copy number. (B) Allele counts for SNV positions in a possible cell-line somatic deletion in NA12891 identified by a cluster of 174 k-mer failures. Points are colored the same as in A. Within this deletion, there are virtually no reads corresponding to the transmitted haplotype, whereas a relatively constant read depth was observed across the region for the nontransmitted haplotype.