Assessing aneuploidy with repetitive element sequencing.

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.; Kinzler, K. W.; Papadopoulos, N.; Vogelstein, B.

doi:10.1101/660258

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bioRxiv · 10.1101/660258

Assessing aneuploidy with repetitive element sequencing.

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Abstract

We report a sensitive PCR-based assay that can detect aneuploidy in samples containing as little as 3 picograms of DNA. Using a single primer pair, we amplified [~]750,000 amplicons distributed throughout the genome Aneuploidy was detected in 49% of liquid biopsies from a total of 883 non-metastatic cancers of eight different types. Combining aneuploidy with somatic mutation detection and eight standard protein biomarkers yielded a median sensitivity of 80% at 99% specificity.

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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., Kinzler, K. W., Papadopoulos, N., Vogelstein, B.. 2019-06-05. Assessing aneuploidy with repetitive element sequencing.. https://doi.org/10.1101/660258

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