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December 8, 2025Blood

Comprehensive and rapid detection of genomic alterations in pediatric leukemias using whole-genome sequencing with adaptive sampling

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Authors

ASAdam ShlienDSDaniel SinnettVLVincent‐Philippe Lavallée

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Overview

Optimized AS-WGS improves risk stratification and therapeutic decisions in pediatric leukemias, indicating its clinical utility.

Key Points

  • This research aims to enhance detection of genomic alterations in pediatric leukemias using whole-genome sequencing with adaptive sampling.
  • Applied optimized AS-WGS to 31 samples from 30 pediatric patients, including 20 leukemia cases and 11 controls.
  • Sequenced genomic DNA using Oxford Nanopore Technologies and performed adaptive sampling on a custom list of genes.
  • Developed an open-source analysis pipeline, Oncoseq, to streamline data processing.
  • Achieved a mean on-target coverage of 160X across 31 samples, and detected all clinical somatic mutations in leukemias.
  • Identified all copy-number variants in 11 of 12 samples, including significant alterations like hyperdiploidy.
  • Methylation calling was possible from AS-WGS signal, aiding in molecular classification of B-ALL samples.

Cite This Study

Shlien et al. (2025) studied this question.

synapsesocial.com/papers/69362f484fa91c937236d66chttps://doi.org/10.1182/blood-2025-4337
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