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The elusive evidence for chromothripsis.

Kinsella M, Patel A, Bafna V - Nucleic Acids Res. (2014)

Bottom Line: Lastly, we provide an algorithm to find a sequence of progressive rearrangements that explains all observed breakpoints from a proposed chromothripsis chromosome.Thus, the proposed signature cannot be considered a sufficient proof for this extraordinary hypothesis.Great caution should be exercised when labeling complex rearrangements as chromothripsis from genome hybridization and sequencing experiments.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics and Systems Biology Program, University of California, San Diego, CA, USA.

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Counts of breakpoints and copy number states from a simulation based on the breakpoints from simulated chromosome in Supplementary Figure S1. The breakpoints and copy number states of the simulated chromosome are indicated on the chart.
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Figure 5: Counts of breakpoints and copy number states from a simulation based on the breakpoints from simulated chromosome in Supplementary Figure S1. The breakpoints and copy number states of the simulated chromosome are indicated on the chart.

Mentions: We then applied the simulation method to the breakpoints of this chromosome and recorded the results as we did in Figure 3b. The resulting distribution of breakpoints and copy number states in Figure 5 is not different from Figure 3b even though we know the chromosome was rearranged progressively. This result casts doubt on the usefulness of the simulation method to detect chromothripsis. Rather than distinguishing between chromosomes that shattered and chromosomes that were rearranged progressively, it always reports that chromosomes with many complex rearrangements and few copy number states are the product of chromothripsis even when they are not.


The elusive evidence for chromothripsis.

Kinsella M, Patel A, Bafna V - Nucleic Acids Res. (2014)

Counts of breakpoints and copy number states from a simulation based on the breakpoints from simulated chromosome in Supplementary Figure S1. The breakpoints and copy number states of the simulated chromosome are indicated on the chart.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4117757&req=5

Figure 5: Counts of breakpoints and copy number states from a simulation based on the breakpoints from simulated chromosome in Supplementary Figure S1. The breakpoints and copy number states of the simulated chromosome are indicated on the chart.
Mentions: We then applied the simulation method to the breakpoints of this chromosome and recorded the results as we did in Figure 3b. The resulting distribution of breakpoints and copy number states in Figure 5 is not different from Figure 3b even though we know the chromosome was rearranged progressively. This result casts doubt on the usefulness of the simulation method to detect chromothripsis. Rather than distinguishing between chromosomes that shattered and chromosomes that were rearranged progressively, it always reports that chromosomes with many complex rearrangements and few copy number states are the product of chromothripsis even when they are not.

Bottom Line: Lastly, we provide an algorithm to find a sequence of progressive rearrangements that explains all observed breakpoints from a proposed chromothripsis chromosome.Thus, the proposed signature cannot be considered a sufficient proof for this extraordinary hypothesis.Great caution should be exercised when labeling complex rearrangements as chromothripsis from genome hybridization and sequencing experiments.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics and Systems Biology Program, University of California, San Diego, CA, USA.

Show MeSH
Related in: MedlinePlus