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Combined low-pass whole genome and targeted sequencing in liquid biopsies for pediatric solid tumors.
Christodoulou, Eirini; Yellapantula, Venkata; O'Halloran, Katrina; Xu, Liya; Berry, Jesse L; Cotter, Jennifer A; Zdanowicz, Anya; Mascarenhas, Leo; Amatruda, James F; Ostrow, Dejerianne; Bootwalla, Moiz; Gai, Xiaowu; Navid, Fariba; Biegel, Jaclyn A.
Afiliación
  • Christodoulou E; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA.
  • Yellapantula V; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA.
  • O'Halloran K; Keck School of Medicine at the University of Southern California, Los Angeles, CA, USA.
  • Xu L; Keck School of Medicine at the University of Southern California, Los Angeles, CA, USA.
  • Berry JL; Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA.
  • Cotter JA; Keck School of Medicine at the University of Southern California, Los Angeles, CA, USA.
  • Zdanowicz A; The Vision Center, Children's Hospital Los Angeles, Los Angeles, CA, USA.
  • Mascarenhas L; Keck School of Medicine at the University of Southern California, Los Angeles, CA, USA.
  • Amatruda JF; The Vision Center, Children's Hospital Los Angeles, Los Angeles, CA, USA.
  • Ostrow D; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA.
  • Bootwalla M; Keck School of Medicine at the University of Southern California, Los Angeles, CA, USA.
  • Gai X; Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA.
  • Navid F; Keck School of Medicine at the University of Southern California, Los Angeles, CA, USA.
  • Biegel JA; Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA.
NPJ Precis Oncol ; 7(1): 21, 2023 Feb 20.
Article en En | MEDLINE | ID: mdl-36805676
We designed a liquid biopsy (LB) platform employing low-pass whole genome sequencing (LP-WGS) and targeted sequencing of cell-free (cf) DNA from plasma to detect genome-wide copy number alterations (CNAs) and gene fusions in pediatric solid tumors. A total of 143 plasma samples were analyzed from 19 controls and 73 patients, including 44 bone or soft-tissue sarcomas and 12 renal, 10 germ cell, five hepatic, and two thyroid tumors. cfDNA was isolated from plasma collected at diagnosis, during and after therapy, and/or at relapse. Twenty-six of 37 (70%) patients enrolled at diagnosis without prior therapy (radiation, surgery, or chemotherapy) had circulating tumor DNA (ctDNA), based on the detection of CNAs from LP-WGS, including 18 of 27 (67%) patients with localized disease and eight of 10 (80%) patients with metastatic disease. None of the controls had detectable somatic CNAs. There was a high concordance of CNAs identified by LP-WGS to CNAs detected by chromosomal microarray analysis in the matching tumors. Mutations identified in tumor samples with our next-generation sequencing (NGS) panel, OncoKids®, were also detected by LP-WGS of ctDNA in 14 of 26 plasma samples. Finally, we developed a hybridization-based capture panel to target EWSR1 and FOXO1 fusions from patients with Ewing sarcoma or alveolar rhabdomyosarcoma (ARMS), respectively. Fusions were detected in the plasma from 10 of 12 patients with Ewing sarcoma and in two of two patients with ARMS. Combined, these data demonstrate the clinical applicability of our LB platform to evaluate pediatric patients with a variety of solid tumors.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: NPJ Precis Oncol Año: 2023 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Reino Unido
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: NPJ Precis Oncol Año: 2023 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Reino Unido