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Deger T, Mendelaar PAJ, Kraan J, et al. A pipeline for copy number profiling of single circulating tumor cells to assess intra-patient tumor heterogeneity. Mol Oncol. 2021;doi: 10.1002/1878-0261.13174.
Deger, T., Mendelaar, P. A. J., Kraan, J., Prager-van der Smissen, W. J. C., van der Vlugt-Daane, M., Bindels, E. M. J., Sieuwerts, A. M., Sleijfer, S., Wilting, S. M., Hollestelle, A., & Martens, J. W. M. (2021). A pipeline for copy number profiling of single circulating tumor cells to assess intra-patient tumor heterogeneity. Molecular oncology, . https://doi.org/10.1002/1878-0261.13174
Deger, Teoman, et al. "A pipeline for copy number profiling of single circulating tumor cells to assess intra-patient tumor heterogeneity." Molecular oncology vol. (2021). doi: https://doi.org/10.1002/1878-0261.13174
Deger T, Mendelaar PAJ, Kraan J, Prager-van der Smissen WJC, van der Vlugt-Daane M, Bindels EMJ, Sieuwerts AM, Sleijfer S, Wilting SM, Hollestelle A, Martens JWM. A pipeline for copy number profiling of single circulating tumor cells to assess intra-patient tumor heterogeneity. Mol Oncol. 2021 Dec 29; doi: 10.1002/1878-0261.13174. Epub 2021 Dec 29. PMID: 34964258.
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Mol Oncol. 2021 Dec 29; doi: 10.1002/1878-0261.13174. Epub 2021 Dec 29.

A pipeline for copy number profiling of single circulating tumor cells to assess intra-patient tumor heterogeneity.

Molecular oncology

Teoman Deger, Pauline A J Mendelaar, Jaco Kraan, Wendy J C Prager-van der Smissen, Michelle van der Vlugt-Daane, Eric M J Bindels, Anieta M Sieuwerts, Stefan Sleijfer, Saskia M Wilting, Antoinette Hollestelle, John W M Martens

Affiliations

  1. Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
  2. Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.

PMID: 34964258 DOI: 10.1002/1878-0261.13174

Abstract

Intra-patient tumor heterogeneity is likely a major determinant of clinical outcome in cancer patients. To assess heterogeneity in a minimally invasive manner, methods to perform single circulating tumor cell (CTC) genomics at high resolution are necessary. However, due to the rarity of CTCs, development of such methods is challenging. Here, we developed a modular single-CTC analysis pipeline to assess intra-patient heterogeneity by copy number (CN) profiling. To optimize this pipeline, spike-in experiments using MCF-7 breast cancer cells were performed. The VyCAP puncher system was used to isolate single cells. The quality of whole genome amplification (WGA) products generated by REPLI-g and Ampli1™ methods, as well as the results from the Illumina Truseq and the Ampli1™ LowPass library preparation techniques, were compared. Moreover, a bioinformatics pipeline was designed to generate CN profiles from single CTCs. The optimal combination of Ampli1™ WGA and Illumina Truseq library preparation was successfully validated on patient-derived CTCs. In conclusion, we developed a novel modular pipeline to isolate single CTCs and subsequently generate detailed patient-derived CN profiles that allow assessment of intra-patient heterogeneity in future studies.

This article is protected by copyright. All rights reserved.

Keywords: bioinformatics pipeline, breast cancer, prostate cancer; circulating tumor cells; next-generation sequencing; single cell genomics; whole genome amplification

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