Plasma DNA-based molecular diagnosis, prognostication, and monitoring of patientswith EWSR1 fusion-positive sarcomas

Neerav N. Shukla, Juber A. Patel, Heather Magnan, Ahmet Zehir, Daoqi You, Jiabin Tang, Fanli Meng, Aliaksandra Samoila, Emily K. Slotkin, Srikanth R. Ambati, Alexander J. Chou, Leonard H. Wexler, Paul A. Meyers, Ellinor I. Peerschke, Agnes Viale, Michael F. Berger, Marc Ladanyi

Research output: Contribution to journalArticle

Abstract

Purpose Ewing sarcoma (ES) and desmoplastic small round cell tumors (DSRCTs) are aggressive sarcomas molecularly characterized by EWSR1 gene fusions. As pathognomonic genomic events in these respective tumor types, EWSR1 fusions represent robust potential biomarkers for disease monitoring. Methods To investigate the feasibility of identifying EWSR1 fusions in plasma-derived cell-free DNA(cfDNA) from patients withESandDSRCT,weevaluated two complementary approaches in samples from 17 patients with radiographic evidence of disease. The first approach involved identification of patient-specific genomicEWSR1fusion breakpoints in formalin-fixed, paraffinembedded tumorDNAusing a broad, hybridization capture-based next-generation sequencing (NGS) panel, followed by design of patient-specific droplet digital polymerase chain reaction (ddPCR) assays for plasma cfDNA interrogation. The second approach used a disease-tailored targeted hybridization capture-based NGS panel applied directly to cfDNA, which included EWSR1 as well as several other genes with potential prognostic use. Results EWSR1 fusions were identified in 11 of 11 (100%) ES and five of six (83%) DSRCT cfDNA samples by ddPCR, whereas 10 of 11 (91%) and four of six (67%) were identified byNGS. The ddPCR approach had higher sensitivity, ranging between 0.009% and 0.018%. However, the hybrid capture-based NGS assay identified the precise fusion breakpoints in the majority of cfDNA samples, as well as mutations in TP53 and STAG2, two other recurrent, clinically significant alterations in ES, all without prior knowledge of the tumor genotype. Conclusion These results provide a compelling rationale for an integrated approach using both NGS and ddPCR for plasma cfDNA-based biomarker evaluations in prospective cooperative group studies.

Original languageEnglish (US)
Pages (from-to)1-11
Number of pages11
JournalJCO Precision Oncology
Volume2017
Issue number1
DOIs
StatePublished - Jan 1 2017

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Sarcoma
Ewing's Sarcoma
DNA
Desmoplastic Small Round Cell Tumor
Plasma Cells
Polymerase Chain Reaction
Biomarkers
Gene Fusion
Formaldehyde
Neoplasms
Genotype
Mutation
Genes

ASJC Scopus subject areas

  • Cancer Research
  • Oncology

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Plasma DNA-based molecular diagnosis, prognostication, and monitoring of patientswith EWSR1 fusion-positive sarcomas. / Shukla, Neerav N.; Patel, Juber A.; Magnan, Heather; Zehir, Ahmet; You, Daoqi; Tang, Jiabin; Meng, Fanli; Samoila, Aliaksandra; Slotkin, Emily K.; Ambati, Srikanth R.; Chou, Alexander J.; Wexler, Leonard H.; Meyers, Paul A.; Peerschke, Ellinor I.; Viale, Agnes; Berger, Michael F.; Ladanyi, Marc.

In: JCO Precision Oncology, Vol. 2017, No. 1, 01.01.2017, p. 1-11.

Research output: Contribution to journalArticle

Shukla, NN, Patel, JA, Magnan, H, Zehir, A, You, D, Tang, J, Meng, F, Samoila, A, Slotkin, EK, Ambati, SR, Chou, AJ, Wexler, LH, Meyers, PA, Peerschke, EI, Viale, A, Berger, MF & Ladanyi, M 2017, 'Plasma DNA-based molecular diagnosis, prognostication, and monitoring of patientswith EWSR1 fusion-positive sarcomas', JCO Precision Oncology, vol. 2017, no. 1, pp. 1-11. https://doi.org/10.1200/PO.16.00028
Shukla, Neerav N. ; Patel, Juber A. ; Magnan, Heather ; Zehir, Ahmet ; You, Daoqi ; Tang, Jiabin ; Meng, Fanli ; Samoila, Aliaksandra ; Slotkin, Emily K. ; Ambati, Srikanth R. ; Chou, Alexander J. ; Wexler, Leonard H. ; Meyers, Paul A. ; Peerschke, Ellinor I. ; Viale, Agnes ; Berger, Michael F. ; Ladanyi, Marc. / Plasma DNA-based molecular diagnosis, prognostication, and monitoring of patientswith EWSR1 fusion-positive sarcomas. In: JCO Precision Oncology. 2017 ; Vol. 2017, No. 1. pp. 1-11.
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abstract = "Purpose Ewing sarcoma (ES) and desmoplastic small round cell tumors (DSRCTs) are aggressive sarcomas molecularly characterized by EWSR1 gene fusions. As pathognomonic genomic events in these respective tumor types, EWSR1 fusions represent robust potential biomarkers for disease monitoring. Methods To investigate the feasibility of identifying EWSR1 fusions in plasma-derived cell-free DNA(cfDNA) from patients withESandDSRCT,weevaluated two complementary approaches in samples from 17 patients with radiographic evidence of disease. The first approach involved identification of patient-specific genomicEWSR1fusion breakpoints in formalin-fixed, paraffinembedded tumorDNAusing a broad, hybridization capture-based next-generation sequencing (NGS) panel, followed by design of patient-specific droplet digital polymerase chain reaction (ddPCR) assays for plasma cfDNA interrogation. The second approach used a disease-tailored targeted hybridization capture-based NGS panel applied directly to cfDNA, which included EWSR1 as well as several other genes with potential prognostic use. Results EWSR1 fusions were identified in 11 of 11 (100{\%}) ES and five of six (83{\%}) DSRCT cfDNA samples by ddPCR, whereas 10 of 11 (91{\%}) and four of six (67{\%}) were identified byNGS. The ddPCR approach had higher sensitivity, ranging between 0.009{\%} and 0.018{\%}. However, the hybrid capture-based NGS assay identified the precise fusion breakpoints in the majority of cfDNA samples, as well as mutations in TP53 and STAG2, two other recurrent, clinically significant alterations in ES, all without prior knowledge of the tumor genotype. Conclusion These results provide a compelling rationale for an integrated approach using both NGS and ddPCR for plasma cfDNA-based biomarker evaluations in prospective cooperative group studies.",
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T1 - Plasma DNA-based molecular diagnosis, prognostication, and monitoring of patientswith EWSR1 fusion-positive sarcomas

AU - Shukla, Neerav N.

AU - Patel, Juber A.

AU - Magnan, Heather

AU - Zehir, Ahmet

AU - You, Daoqi

AU - Tang, Jiabin

AU - Meng, Fanli

AU - Samoila, Aliaksandra

AU - Slotkin, Emily K.

AU - Ambati, Srikanth R.

AU - Chou, Alexander J.

AU - Wexler, Leonard H.

AU - Meyers, Paul A.

AU - Peerschke, Ellinor I.

AU - Viale, Agnes

AU - Berger, Michael F.

AU - Ladanyi, Marc

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N2 - Purpose Ewing sarcoma (ES) and desmoplastic small round cell tumors (DSRCTs) are aggressive sarcomas molecularly characterized by EWSR1 gene fusions. As pathognomonic genomic events in these respective tumor types, EWSR1 fusions represent robust potential biomarkers for disease monitoring. Methods To investigate the feasibility of identifying EWSR1 fusions in plasma-derived cell-free DNA(cfDNA) from patients withESandDSRCT,weevaluated two complementary approaches in samples from 17 patients with radiographic evidence of disease. The first approach involved identification of patient-specific genomicEWSR1fusion breakpoints in formalin-fixed, paraffinembedded tumorDNAusing a broad, hybridization capture-based next-generation sequencing (NGS) panel, followed by design of patient-specific droplet digital polymerase chain reaction (ddPCR) assays for plasma cfDNA interrogation. The second approach used a disease-tailored targeted hybridization capture-based NGS panel applied directly to cfDNA, which included EWSR1 as well as several other genes with potential prognostic use. Results EWSR1 fusions were identified in 11 of 11 (100%) ES and five of six (83%) DSRCT cfDNA samples by ddPCR, whereas 10 of 11 (91%) and four of six (67%) were identified byNGS. The ddPCR approach had higher sensitivity, ranging between 0.009% and 0.018%. However, the hybrid capture-based NGS assay identified the precise fusion breakpoints in the majority of cfDNA samples, as well as mutations in TP53 and STAG2, two other recurrent, clinically significant alterations in ES, all without prior knowledge of the tumor genotype. Conclusion These results provide a compelling rationale for an integrated approach using both NGS and ddPCR for plasma cfDNA-based biomarker evaluations in prospective cooperative group studies.

AB - Purpose Ewing sarcoma (ES) and desmoplastic small round cell tumors (DSRCTs) are aggressive sarcomas molecularly characterized by EWSR1 gene fusions. As pathognomonic genomic events in these respective tumor types, EWSR1 fusions represent robust potential biomarkers for disease monitoring. Methods To investigate the feasibility of identifying EWSR1 fusions in plasma-derived cell-free DNA(cfDNA) from patients withESandDSRCT,weevaluated two complementary approaches in samples from 17 patients with radiographic evidence of disease. The first approach involved identification of patient-specific genomicEWSR1fusion breakpoints in formalin-fixed, paraffinembedded tumorDNAusing a broad, hybridization capture-based next-generation sequencing (NGS) panel, followed by design of patient-specific droplet digital polymerase chain reaction (ddPCR) assays for plasma cfDNA interrogation. The second approach used a disease-tailored targeted hybridization capture-based NGS panel applied directly to cfDNA, which included EWSR1 as well as several other genes with potential prognostic use. Results EWSR1 fusions were identified in 11 of 11 (100%) ES and five of six (83%) DSRCT cfDNA samples by ddPCR, whereas 10 of 11 (91%) and four of six (67%) were identified byNGS. The ddPCR approach had higher sensitivity, ranging between 0.009% and 0.018%. However, the hybrid capture-based NGS assay identified the precise fusion breakpoints in the majority of cfDNA samples, as well as mutations in TP53 and STAG2, two other recurrent, clinically significant alterations in ES, all without prior knowledge of the tumor genotype. Conclusion These results provide a compelling rationale for an integrated approach using both NGS and ddPCR for plasma cfDNA-based biomarker evaluations in prospective cooperative group studies.

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