The clinical and genomic landscape of patients with DDX41 variants identified during diagnostic sequencing

Abstract

Deleterious germ line variants in DDX41 are a common cause of genetic predisposition to hematologic malignancies, particularly myelodysplastic neoplasms (MDS) and acute myeloid leukemia (AML). Targeted next-generation sequencing was performed in a large cohort of sequentially recruited patients with myeloid malignancy, covering DDX41 as well as 30 other genes frequently mutated in myeloid malignancy. Whole genome transcriptome sequencing data was analyzed on a separate cohort of patients with a range of hematologic malignancies to investigate the spectrum of cancer predisposition. Altogether, 5737 patients with myeloid malignancies were studied, with 152 different DDX41 variants detected. Multiple novel variants were detected, including synonymous variants affecting splicing as demonstrated by RNA-sequencing. The presence of a somatic DDX41 variant was highly associated with DDX41 germ line variants in patients with MDS and AML, and we developed a statistical approach to incorporate the co-occurrence of a somatic DDX41 variant into germ line variant classification at a very strong level (as per the American College of Medical Genetics and Genomics/Association for Molecular Pathology guidelines). Using this approach, the MDS cohort contained 108 of 2865 (3.8%) patients with germ line likely pathogenic/pathogenic (LP/P) variants, and the AML cohort 106 of 2157 (4.9%). DDX41 LP/P variants were markedly enriched in patients with AML and MDS compared with those in patients with myeloproliferative neoplasms, B-cell neoplasm, and T- or B-cell acute lymphoblastic leukemia. In summary, we have developed a framework to enhance DDX41 variant curation as well as highlighted the importance of assessment of all types of genomic variants (including synonymous and multiexon deletions) to fully detect the landscape of possible clinically relevant DDX41 variants.

Graphical abstract

Figure 1.

Distribution of the identified variants along the DDX41 gene in patients with MDS, AML, or MPN. Germ line variants were classified as LP/P or VUS based on our modified criteria (incorporating PP4_very strong and the points-based rule system).

Figure 2.

Genomic alterations in DDX41. (A) RNA-sequencing demonstrated retention of intron 6 with a predicted stop codon after 11 residues in a patient with variant c.571G>A, p.(Ala191Thr). (B) RNA-sequencing showed intron retention in the patient with the synonymous variant c.1230G>A, p.(Gln410Gln). Structural variant calling (GRIDSS) identified 2 patients with novel multiexon deletions: NC_000005.9:g.176937300_176939456del (C) and NC_000005.9:g.176941255_176942766del (D).

Figure 3.

Phase analysis of sequencing from patient MDS-P124 demonstrating the germ line variant c.1585dup/p.(Thr529Asnfs∗13) and the somatic variant c.1574G>A/p.(Arg525His) demonstrating their presence in different reads/alleles. The germ line variant c.1585dup/p.(Thr529Asnfs∗13) is indicated by the purple bar, and the somatic variant c.1574G>A/p.(Arg525His) is indicated by a red T.

Figure 4.

Mutation frequency of MDS- and AML-related genes sorted by descending frequency in patients with DDX41-WT. Mutation frequencies in patients with DDX41-WT MDS are illustrated in red and in patients with MDS with germ line LP/P DDX41 variant in blue (A). Mutation frequencies in patients with DDX41-WT AML are illustrated in red and in patients with AML with germ line LP/P DDX41 variant in blue (B). ∗P < .001 (Fisher exact test).