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

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  • Mattias Pilheden
  • Louise Ahlgren
  • Axel Hyrenius-Wittsten
  • Veronica Gonzalez-Pena
  • Helena Sturesson
  • 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

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 FLT3D835Hor NRASG13D/G12Smutations 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.

Udgave nummer10
StatusUdgivet - 2022

Bibliografisk note

Funding Information:
This work was supported by The Swedish Childhood Cancer Fund, The Swedish Cancer Society, The Swedish Research Council, The Knut and Alice Wallenberg Foundation, The Crafoord Foundation, The Per-Eric and Ulla Schyberg Foundation, The Nilsson-Ehle Donations, Governmental Funding of Clinical Research within the National Health Service.

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