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. 2018 Aug 2;35(4):571–578. doi: 10.1093/bioinformatics/bty677

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© The Author(s) 2018. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Fig. 4. — Examples of Mendelian events with a heterozygous deletion in the proband. [Left Column] A rare Mendelian inheritance event observed on chromosome 8 in family DS11025. (A) The average of the M scores for the proband (−0.88, black arrow) and the parents (−4.3 and −0.01, green and pink arrows, respectively), and all other subjects (gray histogram) between loci 130 113 612 and 130 132 753 on chr8. This is consistent with a heterozygous deletion for the proband, inheriting one copy of the allele from the copy-neutral parent 2, and the deletion from parent 1 showing a homozygous deletion. (B–D) Read-pairs observed among the members of family DS11025 near the region with the inferred Mendelian inheritance event, using the same plotting approach as described in the Figure 3 legend. The Z-shaped signature of a substantial number of read pairs flanked by aberrantly spaced reads seen for the proband again is evidence for a 1-copy (heterozygous) deletion. The Z-shaped signature sandwiching very few (presumably incorrectly mapped) reads for parent 1 is evidence for a 2-copy (homozygous) deletion. The read pairs for parent 2 show a copy-neutral state. The gray region in these panels indicate the inferred 18 956 bp inherited deletion region. The number at the bottom of the grey regions in each panel indicates the total number of reads mapped to the inferred de novo deletion. [Right Column] A Mendelian inheritance event observed at a copy number polymorphic region on chromosome 1 in family DS11230. (E) The average of the M scores for the proband (0.084, black arrow) and the parents (−5.58 and 1.06, green and pink arrows, respectively), and all other subjects (gray histogram) between loci 210 078 417 and 210 085 527 on chr1. This again is consistent with a heterozygous deletion for the proband, inheriting one copy of the allele from the copy-neutral parent 2, and the deletion from parent 1 showing a homozygous deletion. Due to the polymorphic nature of this region, the initial median normalization failed to correctly center the copy neutral state at zero, which was subsequently inferred by the post-segmentation filter. (F–H) Read-pairs observed among the members of family DS11230 near the region with the inferred Mendelian inheritance event, supporting the inferred 7111 bp heterozygous (homozygous) deletion in the proband (parent 1) (Color version of this figure is available at Bioinformatics online.)