Mutations in Genes Associated with Familial Predisposition to Myeloid Neoplasms: Their Frequency and Associations with Pretreatment Characteristics in Adult Patients (Pts) with Presumably Sporadic De Novo Acute Myeloid Leukemia (AML)
Authors: Eisfeld Ann-Kathrin , Kohlschmidt Jessica , Mrózek Krzysztof , Mims Alice S. , Walker Christopher J. , Nicolet Deedra , Blachly James S. , Genutis Luke K , Carroll Andrew J. , Powell Bayard L. , Kolitz Jonathan E. , Stone Richard M. , de la Chapelle Albert , Byrd John C. , Bloomfield Clara D. 
Published: October 2019

The effects of germline variants in the development of myeloid neoplasms, including AML, were largely neglected for decades. However, several myeloid neoplasms with germline predisposition have been recently recognized as separate entities in the 2016 revision to the World Health Organization (WHO) classification of myeloid neoplasms and acute leukemia. In addition to genes whose mutations are associated with bone marrow failure syndromes, and are long-known contributors to Mendelian disorders that have myelodysplastic syndromes/AML as the main clinical feature (e.g., germline CEBPA, GATA2 and RUNX1 mutations), 3 more genes were included: ANKRD26, DDX41 and SRP72. Mutations in these genes were described in few families, and are thus considered to be very rare. However, it is possible that their frequency might be underestimated, because the associated phenotypes are often vague and family history not routinely considered.

To establish the frequency of ANKRD26, DDX41 and SRP72 mutations, and to characterize molecular and clinical features associated with these mutations, we determined mutational status of 83 cancer- and leukemia-associated genes using 2 targeted sequencing panels in diagnostic samples of 1,021 clinically well-characterized adult pts with de novo AML AML treated on trials conducted by the Alliance for Clinical Trials in Oncology.

Mutations in the 3 familial genes were found in 46 pts (4.5%), specifically, mutations in ANKRD26 in 15, DDX41 in 17 and SRP72 in 19 pts. Three pts had mutations in either 2 or all 3 genes. Mutations occurred at varying variant allele fractions (VAFs, median: 0.47; range: 0.10-0.98), with 76% of mutations observed with VAFs &gt;35%. Mutations were found throughout the genes.

Pts harboring mutations in any of the 3 genes were predominantly younger (median age, 54 years; range, 19-77), 65% of them were male, and 48% belonged to the 2017 European LeukemiaNet (ELN) favorable genetic risk group.

The co-mutation profiles partially differed among the genes. NPM1 mutations were the most frequent co-mutations, occurring in 47%, 41%, and 42% of pts with mutations in ANKRD26, DDX41, and SRP72, respectively. However, ANKRD26-mutated pts frequently harbored FLT3-ITD and mutations in DNMT3A, IDH2 and SRSF2 genes (each detected in 20% of pts). DDX41-mutated pts commonly had mutations in NRAS (18%), SMARCA2 (12%) and TP53 (12%). SRP72-mutated pts often had mutations in TET2 (26%), CEBPA (23%) and IDH1 (21%).

With the exception of a higher complete remission rate in ANKRD26-mutated pts (93% compared with 73% for DDX41- and 81% for SRP72-mutated pts), the clinical outcomes were very similar. Considering all 3 genes combined, the median 3-year disease-free survival rate of 25% and median 3-year overall survival rate of 44% resembled those of pts belonging to the ELN intermediate risk group.

We next tested whether the variants detected in our cohort of pts with presumably sporadic AML were of germline or somatic origin. We performed Sanger sequencing on germline material (buccal swab or remission samples) of 28 pts who had mutations detected at VAF&gt;35% and material available.

Germline origin was determined for the mutations detected in 24 of 28 pts tested (86%; ANKRD26, 9/10 tested pts; SRP72, 9/11 pts; DDX41, 8/10 pts). Of the detected germline changes, 7/9 ANKRD26 mutations, 6/10 DDX41 mutations and 5/9 SRP72 mutations were predicted to have deleterious effects on the respective proteins via Polyphen. The 1 pt with mutations in all 3 genes were found to be somatic mutations.

Additional genes whose germline mutations are known to occur in families, such as GATA2, CEBPA and RUNX1, were sequenced for somatic mutations in our pt cohort, but not yet tested for potential germline origin in our analysis. Thus, it is likely that the frequency of familial AML mutations is even higher in our cohort.

To our knowledge, this is the first study that tested the frequency of 3 leukemia-predisposing gene mutations in a large cohort of adults with presumably sporadic AML. The relatively high number of germline mutations in these 3 genes highlights the importance of testing for germline mutations. Thus, inclusion of those genes in diagnostic sequencing panels should be considered, and critical consideration of obtained family history should be strongly encouraged for providers taking care of pts with myeloid malignancies.

Support: U10CA180821, U10CA180882, U10CA180861, U24CA196171

Disclosures

Mims: Novartis: Consultancy; Abbvie Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees; Agios Pharmaceuticals: Consultancy, Membership on an entity's Board of Directors or advisory committees. Powell:Rafael Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees. Kolitz:Magellan Health: Consultancy, Honoraria.