Quantification of Somatic Chromosomal Rearrangements in Circulating Cell-Free DNA from Ovarian Cancers

Faye R. Harris, Irina V Kovtun, James Smadbeck, Francesco Multinu, Aminah Jatoi, Farhad Kosari, Kimberly R. Kalli, Stephen J. Murphy, Geoffrey C. Halling, Sarah H. Johnson, Minetta C Liu, Andrea Mariani, George Vasmatzis

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Abstract

Recently, the use of a liquid biopsy has shown promise in monitoring tumor burden. While point mutations have been extensively studied, chromosomal rearrangements have demonstrated greater tumor specificity. Such rearrangements can be identified in the tumor and subsequently detected in the plasma of patients using quantitative PCR (qPCR). In this study we used a whole-genome mate-pair protocol to characterize a landscape of genomic rearrangements in the primary tumors of ten ovarian cancer patients. Individualized tumor-specific primer panels of aberrant chromosomal junctions were identified for each case and detected by qPCR within the cell-free DNA. Selected chromosomal junctions were detected in pre-surgically drawn blood in eight of the ten patients. Of these eight, three demonstrated the continued presence of circulating tumor DNA (ctDNA) post-surgery, consistent with their documented presence of disease, and in five ctDNA was undetectable in the post-surgical blood collection, consistent with their lack of detectable disease. The ctDNA fraction was calculated using a novel algorithm designed for the unique challenges of quantifying ctDNA using qPCR to allow observations of real-time tumor dynamics. In summary, a panel of individualized junctions derived from tumor DNA could be an effective way to monitor cancer patients for relapse and therapeutic efficacy using cfDNA.

Original languageEnglish (US)
Article number29831
JournalScientific Reports
Volume6
DOIs
StatePublished - Jul 20 2016

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Ovarian Neoplasms
DNA
Neoplasms
Polymerase Chain Reaction
Tumor Burden
Point Mutation
Genome
Biopsy
Recurrence

ASJC Scopus subject areas

  • General

Cite this

Quantification of Somatic Chromosomal Rearrangements in Circulating Cell-Free DNA from Ovarian Cancers. / Harris, Faye R.; Kovtun, Irina V; Smadbeck, James; Multinu, Francesco; Jatoi, Aminah; Kosari, Farhad; Kalli, Kimberly R.; Murphy, Stephen J.; Halling, Geoffrey C.; Johnson, Sarah H.; Liu, Minetta C; Mariani, Andrea; Vasmatzis, George.

In: Scientific Reports, Vol. 6, 29831, 20.07.2016.

Research output: Contribution to journalArticle

Harris, Faye R. ; Kovtun, Irina V ; Smadbeck, James ; Multinu, Francesco ; Jatoi, Aminah ; Kosari, Farhad ; Kalli, Kimberly R. ; Murphy, Stephen J. ; Halling, Geoffrey C. ; Johnson, Sarah H. ; Liu, Minetta C ; Mariani, Andrea ; Vasmatzis, George. / Quantification of Somatic Chromosomal Rearrangements in Circulating Cell-Free DNA from Ovarian Cancers. In: Scientific Reports. 2016 ; Vol. 6.
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