Figure 3
Identification and validation of pSNMs in the whole-genome sequences from peripheral blood samples of three individuals. (A-C) Pedigree structures of the three participating families. Red arrows point to the three individuals selected for whole-genome sequencing. (D-F) Alternative allele fractions and sequencing depth of the pSNMs identified in the individuals ACC1-II-1 (D), DS1-II-2 (E), and DS2-I-1 (F) using our pipeline. The candidate pSNM sites are shown in red along with the germline sites shown in gray. The sites with extreme depth or allele fraction are not shown. Different shades of red represent mosaic posterior probabilities. (G) Validation by pyrosequencing. The X axis shows the pSNMs identified and validated in the three individuals. pSNM site IDs correspond to Table 2. The Y axis shows the alternative allele fractions of the pSNM sites in the case, unrelated control, and parents, detected by pyrosequencing. The dashed line represents allele fraction of 0.05, which is the detection threshold of pyrosequencing. (H) Copy number abnormalities are ruled out for all but two of the pSNM sites using MLPA. Seventeen sites showed normal copy numbers with normalized signal ratios between 0.7 and 1.3. Two sites with extra DNA copies are marked by asterisks. Error bars represent the SD of three replications of MLPA. (I) Correlation of the minor allele fractions estimated by whole-genome sequencing and pyrosequencing of the validated sites. The sequencing depth is represented by the size of the dots.
