Genetic variants detected using cell-free DNA from blood and tumor samples in patients with inflammatory breast cancer

Jennifer S. Winn, Zachary Hasse, Michael Slifker, Jianming Pei, Sebastian M. Arisi-Fernandez, Jacqueline N. Talarchek, Elias Obeid, Donald A. Baldwin, Yulan Gong, Eric Ross, Massimo Cristofanilli, R. Katherine Alpaugh, Sandra V. Fernandez*

*Corresponding author for this work

Research output: Contribution to journalArticle

Abstract

We studied genomic alterations in 19 inflammatory breast cancer (IBC) patients with advanced disease using samples of tissue and paired blood serum or plasma (cell-free DNA, cfDNA) by targeted next generation sequencing (NGS). At diagnosis, the disease was triple negative (TN) in eleven patients (57.8%), ER+ Her2-IBC in six patients (31.6%), ER+ Her2+ IBC in one patient (5.3%), and ER-Her2+ IBC in one other patient (5.3%). Pathogenic or likely pathogenic variants were frequently detected in TP53 (47.3%), PMS2 (26.3%), MRE11 (26.3%), RB1 (10.5%), BRCA1 (10.5%), PTEN (10.5%) and AR (10.5%); other affected genes included PMS1, KMT2C, BRCA2, PALB2, MUTYH, MEN1, MSH2, CHEK2, NCOR1, PIK3CA, ESR1 and MAP2K4. In 15 of the 19 patients in which tissue and paired blood were collected at the same time point, 80% of the variants detected in tissue were also detected in the paired cfDNA. Higher concordance between tissue and cfDNA was found for variants with higher allele fraction in tissue (AFtissue ≥ 5%). Furthermore, 86% of the variants detected in cfDNA were also detected in paired tissue. Our study suggests that the genetic profile measured in blood cfDNA is complementary to that of tumor tissue in IBC patients.

Original languageEnglish (US)
Article number1290
JournalInternational journal of molecular sciences
Volume21
Issue number4
DOIs
StatePublished - Feb 2 2020

Keywords

  • Cell-free DNA (cfDNA)
  • Inflammatory breast cancer (IBC)
  • Next generation sequencing (NGS)

ASJC Scopus subject areas

  • Catalysis
  • Molecular Biology
  • Spectroscopy
  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Organic Chemistry
  • Inorganic Chemistry

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  • Cite this

    Winn, J. S., Hasse, Z., Slifker, M., Pei, J., Arisi-Fernandez, S. M., Talarchek, J. N., Obeid, E., Baldwin, D. A., Gong, Y., Ross, E., Cristofanilli, M., Alpaugh, R. K., & Fernandez, S. V. (2020). Genetic variants detected using cell-free DNA from blood and tumor samples in patients with inflammatory breast cancer. International journal of molecular sciences, 21(4), [1290]. https://doi.org/10.3390/ijms21041290