AmplificationTimeR

AmplificationTimeR times sequential amplification events in genomic regions, enabling inference of amplification order and providing insight into tumor evolution.

Key Features:

• Extended copy number state timing: AmplificationTimeR times higher level copy number gains beyond the scope of existing methods.
• Event order inference: The method infers the most parsimonious order of events for regions that have undergone both single gains and whole genome duplication.
• Established approach extension: The package builds upon and extends established approaches for timing genomic gains.
• Comparable accuracy: In copy number states covered by other methods, results are comparable to previously published methods.

Scientific Applications:

• Tumor evolution studies: AmplificationTimeR provides insight into tumor evolution through timing of sequential amplification events.
• Focal amplification analysis: The method enables timing of individual amplification events in regions of focal amplification.
• Whole genome duplication contexts: AmplificationTimeR addresses regions with combined single gains and whole genome duplication events.

Methodology:

AmplificationTimeR extends established approaches for timing genomic gains to enable timing of higher level copy number states and inference of the most parsimonious order of amplification events.