Assessing aneuploidy with repetitive element sequencing

Proc Natl Acad Sci U S A. 2020 Mar 3;117(9):4858-4863. doi: 10.1073/pnas.1910041117. Epub 2020 Feb 19.


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.

Keywords: aneuploidy; circulating tumor DNA; early cancer detection; liquid biopsy.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aneuploidy*
  • Biomarkers, Tumor
  • Circulating Tumor DNA
  • DNA / genetics
  • Esophagus
  • Humans
  • Liquid Biopsy
  • Mutation
  • Neoplasms* / diagnosis
  • Neoplasms* / genetics
  • Repetitive Sequences, Nucleic Acid* / genetics
  • Whole Genome Sequencing


  • Biomarkers, Tumor
  • Circulating Tumor DNA
  • DNA