Undifferentiated sarcomas in children harbor clinically relevant oncogenic fusions and gene copy-number alterations: A report from the children's oncology group

Theodore W. Laetsch, Angshumoy Roy, Lin Xu, Jennifer O. Black, Cheryl M. Coffin, Yueh Yun Chi, Jing Tian, Sheri L. Spunt, Douglas S. Hawkins, Julia A. Bridge, D. Williams Parsons, Stephen X. Skapek

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Abstract

Purpose: A comprehensive analysis of the genomics of undifferentiated sarcomas (UDS) is lacking. We analyzed copy-number alterations and fusion status in patients with UDS prospectively treated on Children's Oncology Group protocol ARST0332. Experimental Design: Copy-number alterations were assessed by OncoScan FFPE Express on 32 UDS. Whole-exome and transcriptome libraries from eight tumors with sufficient archived material were sequenced on HiSeq (2 100 bp). Targeted RNA-sequencing using Archer chemistry was performed on two additional cases. Results: Five-year overall survival for patients with UDS was 83% (95% CI, 69%–97%) with risk-adapted therapy (surgery, chemotherapy, and radiotherapy). Both focal and arm-level copy-number alterations were common including gain of 1q (8/32, 25%) and loss of 1p (7/32, 22%), both of which occurred more often in clinically defined high-risk tumors. Tumors with both loss of 1p and gain of 1q carried an especially poor prognosis with a 5-year event-free survival of 20%. GISTIC analysis identified recurrent amplification of FGF1 on 5q31.3 (q ¼ 0.03) and loss of CDKN2A and CDKN2B on 9p21.3 (q ¼ 0.07). Known oncogenic fusions were identified in eight of 10 cases analyzed by next-generation sequencing. Conclusions: Pediatric UDS generally has a good outcome with risk-adapted therapy. A high-risk subset of patients whose tumors have copy-number loss of 1p and gain of 1q was identified with only 20% survival. Oncogenic fusions are common in UDS, and next-generation sequencing should be considered for children with UDS to refine the diagnosis and identify potentially targetable drivers.

Original languageEnglish (US)
Pages (from-to)3888-3897
Number of pages10
JournalClinical Cancer Research
Volume24
Issue number16
DOIs
StatePublished - Aug 15 2018

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Gene Dosage
Sarcoma
Neoplasms
Exome
RNA Sequence Analysis
Fibroblast Growth Factor 1
Survival
Genomics
Transcriptome
Disease-Free Survival
Research Design
Radiotherapy
Pediatrics
Drug Therapy
Therapeutics

ASJC Scopus subject areas

  • Oncology
  • Cancer Research

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Undifferentiated sarcomas in children harbor clinically relevant oncogenic fusions and gene copy-number alterations : A report from the children's oncology group. / Laetsch, Theodore W.; Roy, Angshumoy; Xu, Lin; Black, Jennifer O.; Coffin, Cheryl M.; Chi, Yueh Yun; Tian, Jing; Spunt, Sheri L.; Hawkins, Douglas S.; Bridge, Julia A.; Williams Parsons, D.; Skapek, Stephen X.

In: Clinical Cancer Research, Vol. 24, No. 16, 15.08.2018, p. 3888-3897.

Research output: Contribution to journalArticle

Laetsch, Theodore W. ; Roy, Angshumoy ; Xu, Lin ; Black, Jennifer O. ; Coffin, Cheryl M. ; Chi, Yueh Yun ; Tian, Jing ; Spunt, Sheri L. ; Hawkins, Douglas S. ; Bridge, Julia A. ; Williams Parsons, D. ; Skapek, Stephen X. / Undifferentiated sarcomas in children harbor clinically relevant oncogenic fusions and gene copy-number alterations : A report from the children's oncology group. In: Clinical Cancer Research. 2018 ; Vol. 24, No. 16. pp. 3888-3897.
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title = "Undifferentiated sarcomas in children harbor clinically relevant oncogenic fusions and gene copy-number alterations: A report from the children's oncology group",
abstract = "Purpose: A comprehensive analysis of the genomics of undifferentiated sarcomas (UDS) is lacking. We analyzed copy-number alterations and fusion status in patients with UDS prospectively treated on Children's Oncology Group protocol ARST0332. Experimental Design: Copy-number alterations were assessed by OncoScan FFPE Express on 32 UDS. Whole-exome and transcriptome libraries from eight tumors with sufficient archived material were sequenced on HiSeq (2 100 bp). Targeted RNA-sequencing using Archer chemistry was performed on two additional cases. Results: Five-year overall survival for patients with UDS was 83{\%} (95{\%} CI, 69{\%}–97{\%}) with risk-adapted therapy (surgery, chemotherapy, and radiotherapy). Both focal and arm-level copy-number alterations were common including gain of 1q (8/32, 25{\%}) and loss of 1p (7/32, 22{\%}), both of which occurred more often in clinically defined high-risk tumors. Tumors with both loss of 1p and gain of 1q carried an especially poor prognosis with a 5-year event-free survival of 20{\%}. GISTIC analysis identified recurrent amplification of FGF1 on 5q31.3 (q ¼ 0.03) and loss of CDKN2A and CDKN2B on 9p21.3 (q ¼ 0.07). Known oncogenic fusions were identified in eight of 10 cases analyzed by next-generation sequencing. Conclusions: Pediatric UDS generally has a good outcome with risk-adapted therapy. A high-risk subset of patients whose tumors have copy-number loss of 1p and gain of 1q was identified with only 20{\%} survival. Oncogenic fusions are common in UDS, and next-generation sequencing should be considered for children with UDS to refine the diagnosis and identify potentially targetable drivers.",
author = "Laetsch, {Theodore W.} and Angshumoy Roy and Lin Xu and Black, {Jennifer O.} and Coffin, {Cheryl M.} and Chi, {Yueh Yun} and Jing Tian and Spunt, {Sheri L.} and Hawkins, {Douglas S.} and Bridge, {Julia A.} and {Williams Parsons}, D. and Skapek, {Stephen X.}",
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T1 - Undifferentiated sarcomas in children harbor clinically relevant oncogenic fusions and gene copy-number alterations

T2 - A report from the children's oncology group

AU - Laetsch, Theodore W.

AU - Roy, Angshumoy

AU - Xu, Lin

AU - Black, Jennifer O.

AU - Coffin, Cheryl M.

AU - Chi, Yueh Yun

AU - Tian, Jing

AU - Spunt, Sheri L.

AU - Hawkins, Douglas S.

AU - Bridge, Julia A.

AU - Williams Parsons, D.

AU - Skapek, Stephen X.

PY - 2018/8/15

Y1 - 2018/8/15

N2 - Purpose: A comprehensive analysis of the genomics of undifferentiated sarcomas (UDS) is lacking. We analyzed copy-number alterations and fusion status in patients with UDS prospectively treated on Children's Oncology Group protocol ARST0332. Experimental Design: Copy-number alterations were assessed by OncoScan FFPE Express on 32 UDS. Whole-exome and transcriptome libraries from eight tumors with sufficient archived material were sequenced on HiSeq (2 100 bp). Targeted RNA-sequencing using Archer chemistry was performed on two additional cases. Results: Five-year overall survival for patients with UDS was 83% (95% CI, 69%–97%) with risk-adapted therapy (surgery, chemotherapy, and radiotherapy). Both focal and arm-level copy-number alterations were common including gain of 1q (8/32, 25%) and loss of 1p (7/32, 22%), both of which occurred more often in clinically defined high-risk tumors. Tumors with both loss of 1p and gain of 1q carried an especially poor prognosis with a 5-year event-free survival of 20%. GISTIC analysis identified recurrent amplification of FGF1 on 5q31.3 (q ¼ 0.03) and loss of CDKN2A and CDKN2B on 9p21.3 (q ¼ 0.07). Known oncogenic fusions were identified in eight of 10 cases analyzed by next-generation sequencing. Conclusions: Pediatric UDS generally has a good outcome with risk-adapted therapy. A high-risk subset of patients whose tumors have copy-number loss of 1p and gain of 1q was identified with only 20% survival. Oncogenic fusions are common in UDS, and next-generation sequencing should be considered for children with UDS to refine the diagnosis and identify potentially targetable drivers.

AB - Purpose: A comprehensive analysis of the genomics of undifferentiated sarcomas (UDS) is lacking. We analyzed copy-number alterations and fusion status in patients with UDS prospectively treated on Children's Oncology Group protocol ARST0332. Experimental Design: Copy-number alterations were assessed by OncoScan FFPE Express on 32 UDS. Whole-exome and transcriptome libraries from eight tumors with sufficient archived material were sequenced on HiSeq (2 100 bp). Targeted RNA-sequencing using Archer chemistry was performed on two additional cases. Results: Five-year overall survival for patients with UDS was 83% (95% CI, 69%–97%) with risk-adapted therapy (surgery, chemotherapy, and radiotherapy). Both focal and arm-level copy-number alterations were common including gain of 1q (8/32, 25%) and loss of 1p (7/32, 22%), both of which occurred more often in clinically defined high-risk tumors. Tumors with both loss of 1p and gain of 1q carried an especially poor prognosis with a 5-year event-free survival of 20%. GISTIC analysis identified recurrent amplification of FGF1 on 5q31.3 (q ¼ 0.03) and loss of CDKN2A and CDKN2B on 9p21.3 (q ¼ 0.07). Known oncogenic fusions were identified in eight of 10 cases analyzed by next-generation sequencing. Conclusions: Pediatric UDS generally has a good outcome with risk-adapted therapy. A high-risk subset of patients whose tumors have copy-number loss of 1p and gain of 1q was identified with only 20% survival. Oncogenic fusions are common in UDS, and next-generation sequencing should be considered for children with UDS to refine the diagnosis and identify potentially targetable drivers.

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