Design and Validation of a Custom Next-Generation Sequencing Panel in Pediatric Acute Lymphoblastic Leukemia.

Autores de IIS La Fe

• Jose Vicente Gil Orti

  Autor

• Esperanza Such Taboada

  Autor

• Claudia Sargas Simarro

  Autor

• Javier Simarro Farinos

  Autor

• Inmaculada De Juan Jiménez

  Autor

• Sarai Palanca Suela

  Autor

• Gayane Avetisyan

  Autor

• Marta Santiago Balsera

  Autor

• Samuel Romero Domínguez

  Autor

• Marta Llop García

  Autor

• Eva Barragán González

  Autor

Participantes ajenos a IIS La Fe

• Miralles, Alberto
• Perez, Gema
• Fuentes, Carolina
• Fernandez, Jose Maria
• Vicente, Ana Isabel

Grupos

• Hematología y Hemoterapia

• Investigación Clínica y Traslacional en Cáncer

Abstract

The molecular landscape of acute lymphoblastic leukemia (ALL) is highly heterogeneous, and genetic lesions are clinically relevant for diagnosis, risk stratification, and treatment guidance. Next-generation sequencing (NGS) has become an essential tool for clinical laboratories, where disease-targeted panels are able to capture the most relevant alterations in a cost-effective and fast way. However, comprehensive ALL panels assessing all relevant alterations are scarce. Here, we design and validate an NGS panel including single-nucleotide variants (SNVs), insertion-deletions (indels), copy number variations (CNVs), fusions, and gene expression (ALLseq). ALLseq sequencing metrics were acceptable for clinical use and showed 100% sensitivity and specificity for virtually all types of alterations. The limit of detection was established at a 2% variant allele frequency for SNVs and indels, and at a 0.5 copy number ratio for CNVs. Overall, ALLseq is able to provide clinically relevant information to more than 83% of pediatric patients, making it an attractive tool for the molecular characterization of ALL in clinical settings.

Keywords

• NGS; childhood acute lymphoblastic leukemia; molecular characterization; next-generation sequencing