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Figure 1.

An inversion resulting from non-allelic homologous recombination (NAHR) between two nearly identical segmental duplications (blue boxes) with opposite orientations (arrows).

The inversion flips the orientation of the subsequence, or block, in one genome relative to the other genome.

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Figure 2.

Two major approaches to detect structural variants in an individual genome from next-generation sequencing data are de novo assembly and resequencing.

In de novo assembly, the individual genome sequence is constructed by examining overlaps between reads. In resequencing approaches, reads from the individual genome are aligned to a closely related reference genome. Examination of the resulting alignments reveals differences between the individual genome and the reference genome.

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Figure 3.

A strobe with 3 subreads.

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Figure 4.

Identification of a deletion in an individual genome by split read analysis (middle), and by depth of coverage analysis (bottom).

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Figure 5.

Paired end mapping (PEM).

Fragments from an individual genome are sequenced from both ends and the resulting paired reads are aligned to a reference genome. Most paired reads correspond to concordant pairs, where the distance between the alignment of each read agrees with the distribution of fragment lengths (right). The remaining discordant pairs suggest structural variants (here a deletion) that distinguish the individual and reference genomes.

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Figure 6.

(Top) A discordant pair (arc) indicates a deletion with unknown breakpoints and located in orange blocks. Positions , and the minimum and maximum length of end-sequenced fragments constrain breakpoints to lie within the indicated orange blocks, and are governed by the indicated linear inequalities. (Bottom) A polygon in 2D genome space expresses the linear dependency between breakpoints and and records the uncertainty in the location of the breakpoints.

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Figure 7.

Mutation, selection, and clonal expansion in tumor development leads to genomic heterogeneity between cells in a tumor.

Current DNA sequencing approaches sequence DNA from many cells and thus result in a heterogenous mixture of mutations, with varying numbers of both passenger mutations (black) and driver mutations (red).

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