HemaSphere (Oct 2022)

Duplex Sequencing Uncovers Recurrent Low-frequency Cancer-associated Mutations in Infant and Childhood KMT2A-rearranged Acute Leukemia

  • Mattias Pilheden,
  • Louise Ahlgren,
  • Axel Hyrenius-Wittsten,
  • Veronica Gonzalez-Pena,
  • Helena Sturesson,
  • Hanne Vibeke Hansen Marquart,
  • Birgitte Lausen,
  • Anders Castor,
  • Cornelis Jan Pronk,
  • Gisela Barbany,
  • Katja Pokrovskaja Tamm,
  • Linda Fogelstrand,
  • Olli Lohi,
  • Ulrika Norén-Nyström,
  • Johanna Asklin,
  • Yilun Chen,
  • Guangchun Song,
  • Michael Walsh,
  • Jing Ma,
  • Jinghui Zhang,
  • Lao H. Saal,
  • Charles Gawad,
  • Anna K. Hagström-Andersson

DOI
https://doi.org/10.1097/HS9.0000000000000785
Journal volume & issue
Vol. 6, no. 10
p. e785

Abstract

Read online

Infant acute lymphoblastic leukemia (ALL) with KMT2A-gene rearrangements (KMT2A-r) have few mutations and a poor prognosis. To uncover mutations that are below the detection of standard next-generation sequencing (NGS), a combination of targeted duplex sequencing and NGS was applied on 20 infants and 7 children with KMT2A-r ALL, 5 longitudinal and 6 paired relapse samples. Of identified nonsynonymous mutations, 87 had been previously implicated in cancer and targeted genes recurrently altered in KMT2A-r leukemia and included mutations in KRAS, NRAS, FLT3, TP53, PIK3CA, PAX5, PIK3R1, and PTPN11, with infants having fewer such mutations. Of identified cancer-associated mutations, 62% were below the resolution of standard NGS. Only 33 of 87 mutations exceeded 2% of cellular prevalence and most-targeted PI3K/RAS genes (31/33) and typically KRAS/NRAS. Five patients only had low-frequency PI3K/RAS mutations without a higher-frequency signaling mutation. Further, drug-resistant clones with FLT3D835H or NRASG13D/G12S mutations that comprised only 0.06% to 0.34% of diagnostic cells, expanded at relapse. Finally, in longitudinal samples, the relapse clone persisted as a minor subclone from diagnosis and through treatment before expanding during the last month of disease. Together, we demonstrate that infant and childhood KMT2A-r ALL harbor low-frequency cancer-associated mutations, implying a vast subclonal genetic landscape.