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Updated: Jun 28, 2025

Linear Amplification Mediated PCR – Localization of Genetic Elements and Characterization of Unknown Flanking DNA

Linear Amplification Mediated PCR – Localization of Genetic Elements and Characterization of Unknown Flanking DNA

Published on: June 25, 2014

AmplificationTimeR: an R package for timing sequential amplification events.

G Maria Jakobsdottir^1,2, Stefan C Dentro^3,2, Robert G Bristow^1,4,2

¹Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PL, United Kingdom.

Bioinformatics (Oxford, England)

|April 24, 2024

Summary

This summary is machine-generated.

AmplificationTimeR accurately times higher-level copy number gains and infers the order of genomic events, extending existing methods for timing focal amplifications.

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Area of Science:

Genomics
Computational Biology
Cancer Research

Background:

Limited methods exist for timing individual amplification events in focal genomic regions.
Current techniques are restricted in the copy number states they can analyze.

Purpose of the Study:

To introduce AmplificationTimeR, a novel method for timing higher-level copy number gains.
To infer the most parsimonious order of genomic events, including single gains and whole genome duplication.

Main Methods:

AmplificationTimeR extends established approaches for timing genomic gains.
The method analyzes regions with both single gains and whole genome duplication.

Main Results:

AmplificationTimeR can time a broader range of copy number states.
Results are comparable to existing methods for overlapping copy number states.

Conclusions:

AmplificationTimeR provides a robust tool for analyzing complex genomic amplifications.
The R package is freely available for researchers.