Assessing aneuploidy with repetitive element sequencing

Christopher Douville, Joshua D. Cohen, Janine Ptak, Maria Popoli, Joy Schaefer, Natalie Silliman, Lisa Dobbyn, Robert E. Schoen, Jeanne Tie, Peter Gibbs, Michael Goggins, Christopher L. Wolfgang, Tian Li Wang, Ie Ming Shih, Rachel Karchin, Anne Marie Lennon, Ralph H. Hruban, Cristian Tomasetti, Chetan Bettegowda, Kenneth W. KinzlerNickolas Papadopoulos, Bert Vogelstein

Research output: Contribution to journalArticlepeer-review


We report a sensitive PCR-based assay called Repetitive Element AneupLoidy Sequencing System (RealSeqS) that can detect aneuploidy in samples containing as little as 3 pg of DNA. Using a single primer pair, we amplified ∼350,000 amplicons distributed throughout the genome. Aneuploidy was detected in 49% of liquid biopsies from a total of 883 nonmetastatic, clinically detected cancers of the colorectum, esophagus, liver, lung, ovary, pancreas, breast, or stomach. Combining aneuploidy with somatic mutation detection and eight standard protein biomarkers yielded a median sensitivity of 80% in these eight cancer types, while only 1% of 812 healthy controls scored positive.

Original languageEnglish (US)
Pages (from-to)4858-4863
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number9
StatePublished - Mar 3 2020


  • Aneuploidy
  • Circulating tumor DNA
  • Early cancer detection
  • Liquid biopsy

ASJC Scopus subject areas

  • General

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