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Transcriptome Sequencing Allows Comprehensive Genomic Characterization of Pediatric B-Acute Lymphoblastic Leukemia in an Academic Clinical Laboratory.
Hu, Zunsong; Kovach, Alexandra E; Yellapantula, Venkata; Ostrow, Dejerianne; Doan, Andrew; Ji, Jianling; Schmidt, Ryan J; Gu, Zhaohui; Bhojwani, Deepa; Raca, Gordana.
Afiliación
  • Hu Z; Department of Computational and Quantitative Medicine and Systems Biology, Beckman Research Institute of City of Hope, Duarte, California.
  • Kovach AE; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California.
  • Yellapantula V; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California.
  • Ostrow D; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California.
  • Doan A; Children's Center for Cancer and Blood Diseases, Children's Hospital Los Angeles, Los Angeles, California.
  • Ji J; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California.
  • Schmidt RJ; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California.
  • Gu Z; Department of Computational and Quantitative Medicine and Systems Biology, Beckman Research Institute of City of Hope, Duarte, California. Electronic address: zgu@coh.org.
  • Bhojwani D; Children's Center for Cancer and Blood Diseases, Children's Hospital Los Angeles, Los Angeles, California.
  • Raca G; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California. Electronic address: graca@chla.usc.edu.
J Mol Diagn ; 26(1): 49-60, 2024 Jan.
Article en En | MEDLINE | ID: mdl-37981088
Studies have shown the power of transcriptome sequencing [RNA sequencing (RNA-Seq)] in identifying known and novel oncogenic drivers and molecular subtypes of B-acute lymphoblastic leukemia (B-ALL). The current study investigated whether the clinically validated RNA-Seq assay, coupled with a custom analysis pipeline, could be used for a comprehensive B-ALL classification. Following comprehensive clinical testing, RNA-Seq was performed on 76 retrospective B-ALL cases, 28 of which had known and 48 had undetermined subtype. Subtypes were accurately identified in all 28 known cases, and in 38 of 48 unknown cases (79%). The subtypes of the unknown cases included the following: PAX5alt (n = 12), DUX4-rearranged (n = 6), Philadelphia chromosome-like (n = 5), low hyperdiploid (n = 4), ETV6::RUNX1-like (n = 3), MEF2D-rearranged (n = 2), PAX5 P80R (n = 2), ZEB2/CEBP (n = 1), NUTM1-rearranged (n = 1), ZNF384-rearranged (n = 1), and TCF3::PBX1 (n = 1). In 15 of 38 cases (39%), classification based on expression profile was corroborated by detection of subtype-defining oncogenic drivers missed by clinical testing. RNA-Seq analysis also detected large copy number abnormalities, oncogenic hot-spot sequence variants, and intragenic IKZF1 deletions. This pilot study confirms the feasibility of implementing an RNA-Seq workflow for clinical diagnosis of molecular subtypes in pediatric B-ALL, reinforcing that RNA-Seq represents a promising global genomic assay for this heterogeneous leukemia.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Leucemia-Linfoma Linfoblástico de Células Precursoras / Transcriptoma Límite: Child / Humans Idioma: En Revista: J Mol Diagn Asunto de la revista: BIOLOGIA MOLECULAR Año: 2024 Tipo del documento: Article Pais de publicación: Estados Unidos
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Leucemia-Linfoma Linfoblástico de Células Precursoras / Transcriptoma Límite: Child / Humans Idioma: En Revista: J Mol Diagn Asunto de la revista: BIOLOGIA MOLECULAR Año: 2024 Tipo del documento: Article Pais de publicación: Estados Unidos