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<p>Gene fusions are common primary drivers of pediatric leukemias and are the result of underlying structural variants (SVs). Current clinical workflows to detect such alterations rely on a multimodal approach, which often increases analysis time and overall cost of testing. In this study, we used long-read sequencing (lrSeq) as a proof-of-concept to determine whether clinically relevant (cr) SVs could be detected within a small (<i>n</i> = 17) pediatric leukemia cohort. We show that this methodology successfully determined all known crSVs (<i>n</i> = 5/5) detected through routine clinical testing. This approach also identified crSVs that resulted in the classification of a leukemia genetic subtype for four additional patients (<i>n</i> = 4/12), such as an ins(11;10)(q23.3;p12p12) forming a <i>KMT2A</i>::<i>MLLT10</i> fusion, that were missed by routine clinical approaches. This study demonstrates the diagnostic potential of lrSeq as an assay for SV detection in pediatric leukemia and supports lrSeq as a valuable tool for the accurate detection of crSVs.</p>

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Proof-of-concept study for the detection of somatic structural variant driver alterations using HiFi long-read sequencing in a pediatric leukemia cohort

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年4月9日

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  • Lisa A. Lansdon,
  • Byunggil Yoo,
  • Ayse Keskus,
  • Irina Pushel,
  • Chengpeng Bi,
  • Tanveer Ahmad,
  • Asher Bryant,
  • Adam Walter,
  • Margaret Gibson,
  • Mary Rindler,
  • Weijie Li,
  • Sultan M. Habeebu,
  • Linda D. Cooley,
  • John Herriges,
  • Elena Repnikova,
  • Lei Zhang,
  • Keith J. August,
  • Terrie G. Flatt,
  • Alan S. Gamis,
  • Erin M. Guest,
  • J. Allyson Hays,
  • Maxine Hetherington,
  • Karen Lewing,
  • Tomi Pastinen,
  • Mikhail Kolmogorov,
  • Midhat S. Farooqi

摘要

Gene fusions are common primary drivers of pediatric leukemias and are the result of underlying structural variants (SVs). Current clinical workflows to detect such alterations rely on a multimodal approach, which often increases analysis time and overall cost of testing. In this study, we used long-read sequencing (lrSeq) as a proof-of-concept to determine whether clinically relevant (cr) SVs could be detected within a small (n = 17) pediatric leukemia cohort. We show that this methodology successfully determined all known crSVs (n = 5/5) detected through routine clinical testing. This approach also identified crSVs that resulted in the classification of a leukemia genetic subtype for four additional patients (n = 4/12), such as an ins(11;10)(q23.3;p12p12) forming a KMT2A::MLLT10 fusion, that were missed by routine clinical approaches. This study demonstrates the diagnostic potential of lrSeq as an assay for SV detection in pediatric leukemia and supports lrSeq as a valuable tool for the accurate detection of crSVs.