Duplex Sequencing Uncovers Recurrent Low-frequency Cancer-associated Mutations in Infant and Childhood KMT2A-rearranged Acute Leukemia
Pilheden, Mattias; Ahlgren, Louise; Hyrenius-Wittsten, Axel; Gonzalez-Pena, Veronica; Sturesson, Helena; Hansen Marquart, Hanne Vibeke; Lausen, Birgitte; Castor, Anders; Pronk, Cornelis Jan; Barbany, Gisela; Pokrovskaja Tamm, Katja; Fogelstrand, Linda; Lohi, Olli; Norén-Nyström, Ulrika; Asklin, Johanna; Chen, Yilun; Song, Guangchun; Walsh, Michael; Ma, Jing; Zhang, Jinghui; Saal, Lao H; Gawad, Charles; Hagström-Andersson, Anna K (2022-10)
Pilheden, Mattias
Ahlgren, Louise
Hyrenius-Wittsten, Axel
Gonzalez-Pena, Veronica
Sturesson, Helena
Hansen Marquart, Hanne Vibeke
Lausen, Birgitte
Castor, Anders
Pronk, Cornelis Jan
Barbany, Gisela
Pokrovskaja Tamm, Katja
Fogelstrand, Linda
Lohi, Olli
Norén-Nyström, Ulrika
Asklin, Johanna
Chen, Yilun
Song, Guangchun
Walsh, Michael
Ma, Jing
Zhang, Jinghui
Saal, Lao H
Gawad, Charles
Hagström-Andersson, Anna K
10 / 2022
e785
Julkaisun pysyvä osoite on
https://urn.fi/URN:NBN:fi:tuni-202301251722
https://urn.fi/URN:NBN:fi:tuni-202301251722
Kuvaus
Peer reviewed
Tiivistelmä
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 FLT3 D835H or NRAS G13D/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.
Kokoelmat
- TUNICRIS-julkaisut [19236]