Assessing Aneuploidy with Repetitive Element Sequencing

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 2020 Feb 21

PMID 32075918

Citations 31

Authors

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

Affiliations

Soon will be listed here.

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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