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Significance The detection of aneuploidy in clinical samples can be critical for various diagnostic applications in cancer and can also inform cancer genetics. Next-generation sequencing protocols such as whole-genome and exome sequencing are typically used to detect aneuploidy in cancer samples, but amplicon-based protocols achieve high coverage depth at relatively low cost and can be used when only tiny amounts of DNA are available. In this paper, we describe new bioinformatic tools to detect aneuploidy using data generated from amplification with a single primer pair. This approach can be applied to samples containing only a few nanograms of DNA and as little as 1% neoplastic content and has a variety of applications in cancer diagnostics and forensic science.

Detection of aneuploidy in patients with cancer through amplification of long interspersed nucleotide elements (LINEs)