Family with a complex germline mutational landscape
In Family4, both siblings carried three heterozygous germline mutations annotated as VUS: p.S858R in FANCA , p.G571S in JAK2 and p.E1280Q in ERBB4 (Table 2). These patients also shared the presence in their AML samples of the most common somatic pathogenic variant in SF3B1 : p.K700E, with a VAF of 34.2% and 31.7% in patient ID7 and ID8, respectively (Table 3). Using Sanger sequencing, we confirmed this is an acquired somatic mutation in a hematopoietic clone with high VAF; indeed, the variant was not detected in buccal DNA collected from either siblings (Supplementary Figure 2). Patient ID7 harbored also two likely pathogenic somatic variants (TET2p.E566* and ETV6 p.V158Pfs*10) and 3 VUS with VAF>5% (GATA2 p.H323P, FGFR3 p.A634T andBRCA2 p.L1545P; Table 3). Patient ID8 harbored two subclonal pathogenic mutations in both IDH2 (p.R140Q; VAF=11.64%) andIDH1 (p.R132H; VAF=2.38%).
As for patient ID5, we were able to reconstruct the genomic evolution of AML in patient ID7, based on NGS analysis performed for clinical monitoring. Following induction chemotherapy, the patient showed persistence of the hematopoietic clone harboring the SF3B1p.K700E mutation, which maintained almost constant VAF (30-40%), showing complete resistance along the entire course of the disease. After induction, the blasts acquired two new variants: TET2p.T1093Kfs*12 and GATA2 p.N317S. Therefore, the patient underwent re-induction chemotherapy, that affected the primary responsive clone, but again showed no efficacy on the clone with SF3B1 p.K700E variant or clones with the two mutations acquired post-induction. This patient succumbed to the disease within three months post-relapse, with reappearance of all mutations identified both pre- and post-induction therapy (Figure 1B).