Research Papers:

Detection of circulating tumor DNA in patients with osteosarcoma

David M. Barris, Shoshana B. Weiner _, Robert A. Dubin, Michael Fremed, Xusheng Zhang, Sajida Piperdi, Wendong Zhang, Shahina Maqbool, Jonathan Gill, Michael Roth, Bang Hoang, David Geller, Richard Gorlick and Daniel A. Weiser

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Oncotarget. 2018; 9:12695-12704. https://doi.org/10.18632/oncotarget.24268

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David M. Barris1,*, Shoshana B. Weiner1,*, Robert A. Dubin2, Michael Fremed1, Xusheng Zhang2, Sajida Piperdi3, Wendong Zhang3, Shahina Maqbool1, Jonathan Gill4, Michael Roth4, Bang Hoang5, David Geller5, Richard Gorlick4 and Daniel A. Weiser6,7

1Department of Genetics and Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA

2Computational Genomics Core, Albert Einstein College of Medicine, Bronx, NY, USA

3Department of Pediatrics, Montefiore Medical Center, Bronx, NY, USA

4Division of Pediatrics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA

5Department of Orthopedic Surgery, Montefiore Medical Center, Bronx, NY, USA

6Division of Hematology/Oncology, Children’s Hospital at Montefiore, Bronx, NY, USA

7Departments of Pediatrics and Genetics, Albert Einstein College of Medicine, Bronx, NY, USA

*These authors contributed equally to this work

Correspondence to:

Shoshana B. Weiner, email: [email protected]

Keywords: circulating tumor DNA; osteosarcoma; targeted sequencing; Next Generation Sequencing; targeted therapy

Received: November 28, 2017     Accepted: January 09, 2018     Published: January 18, 2018


Identification and quantification of somatic alterations in plasma-derived, circulating tumor DNA (ctDNA) is gaining traction as a non-invasive and cost effective method of disease monitoring in cancer patients, particularly to evaluate response to treatment and monitor for disease recurrence. To our knowledge, genetic analysis of ctDNA in osteosarcoma has not yet been studied. To determine whether somatic alterations can be detected in ctDNA and perhaps applied to patient management in this disease, we collected germline, tumor, and serial plasma samples from pediatric, adolescent, and young adult patients with osteosarcoma and used targeted Next Generation Sequencing (NGS) to identify somatic single nucleotide variants (SNV), insertions and deletions (INDELS), and structural variants (SV) in 7 genes commonly mutated in osteosarcoma. We demonstrate that patient-specific somatic alterations identified through comparison of tumor-germline pairs can be detected and quantified in cell-free DNA of osteosarcoma patients.

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