Early Detection Research Network

Assessing aneuploidy with repetitive element sequencing.

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.

Bettegowda C, Cohen JD, Dobbyn L, Douville C, Gibbs P, Goggins M, Hruban RH, Karchin R, Kinzler KW, Lennon AM, Papadopoulos N, Popoli M, Ptak J, Schaefer J, Schoen RE, Shih IM, Silliman N, Tie J, Tomasetti C, Vogelstein B, Wang TL, Wolfgang CL


Proc. Natl. Acad. Sci. U.S.A., 2020, 117 (9)

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