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. Kinzler; Nickolas Papadopoulos; Bert Vogelstein

doi:10.1073/pnas.1910041117

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 journal › Article › peer-review

16 Scopus citations

Abstract

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 language	English (US)
Pages (from-to)	4858-4863
Number of pages	6
Journal	Proceedings of the National Academy of Sciences of the United States of America
Volume	117
Issue number	9
DOIs	https://doi.org/10.1073/pnas.1910041117
State	Published - Mar 3 2020

Keywords

Aneuploidy
Circulating tumor DNA
Early cancer detection
Liquid biopsy

ASJC Scopus subject areas

General

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10.1073/pnas.1910041117

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Douville, C., Cohen, J. D., Ptak, J., Popoli, M., Schaefer, J., Silliman, N., Dobbyn, L., Schoen, R. E., Tie, J., Gibbs, P., Goggins, M., Wolfgang, C. L., Wang, T. L., Shih, I. M., Karchin, R., Lennon, A. M., Hruban, R. H., Tomasetti, C., Bettegowda, C., ... Vogelstein, B. (2020). Assessing aneuploidy with repetitive element sequencing. Proceedings of the National Academy of Sciences of the United States of America, 117(9), 4858-4863. https://doi.org/10.1073/pnas.1910041117

Douville, C, Cohen, JD, Ptak, J, Popoli, M, Schaefer, J, Silliman, N, Dobbyn, L, Schoen, RE, Tie, J, Gibbs, P, Goggins, M, Wolfgang, CL, Wang, TL , Shih, IM , Karchin, R, Lennon, AM, Hruban, RH, Tomasetti, C, Bettegowda, C , Kinzler, KW , Papadopoulos, N & Vogelstein, B 2020, 'Assessing aneuploidy with repetitive element sequencing', Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 9, pp. 4858-4863. https://doi.org/10.1073/pnas.1910041117

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abstract = "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.",

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AU - Silliman, Natalie

AU - Dobbyn, Lisa

AU - Schoen, Robert E.

AU - Tie, Jeanne

AU - Gibbs, Peter

AU - Goggins, Michael

AU - Wolfgang, Christopher L.

AU - Wang, Tian Li

AU - Shih, Ie Ming

AU - Karchin, Rachel

AU - Lennon, Anne Marie

AU - Hruban, Ralph H.

AU - Tomasetti, Cristian

AU - Bettegowda, Chetan

AU - Kinzler, Kenneth W.

AU - Papadopoulos, Nickolas

AU - Vogelstein, Bert

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AB - 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.

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Assessing aneuploidy with repetitive element sequencing

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