Open AccessDuplex Sequencing Uncovers Recurrent Low‐frequency Cancer‐associated Mutations in Infant and Childhood KMT2A ‐rearranged Acute Leukemia
Author(s) -
Pilheden Mattias,
Ahlgren Louise,
HyreniusWittsten Axel,
GonzalezPena Veronica,
Sturesson Helena,
Hansen Marquart Hanne Vibeke,
Lausen Birgitte,
Castor Anders,
Pronk Cornelis Jan,
Barbany Gisela,
Pokrovskaja Tamm Katja,
Fogelstrand Linda,
Lohi Olli,
NorénNyström Ulrika,
Asklin Johanna,
Chen Yilun,
Song Guangchun,
Walsh Michael,
Ma Jing,
Zhang Jinghui,
Saal Lao H.,
Gawad Charles,
HagströmAndersson Anna K.
Publication year - 2022
Publication title -
hemasphere
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.677
H-Index - 11
ISSN - 2572-9241
DOI - 10.1097/hs9.0000000000000785
Subject(s) - neuroblastoma ras viral oncogene homolog , kras , ptpn11 , biology , hras , cancer research , missense mutation , mutation , leukemia , mutation frequency , cancer , genetics , gene
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.