Figure 2: DDX41 gene structure and clonal architecture in DDX41 mutants.

(A) DDX41 is located at the distal end of chromosome 5q, 5q35.3, and encodes a protein that contains three known domains and ATP binding sites, as illustrated. The pink bars visualize deletions of chromosome 5q in our MDS cohort that include the DDX41 locus. The red triangles indicate DDX41 mutations in patients with hematological malignancies from our cohort and TCGA. Red circles indicate the identified germline mutations of DDX41 (p.Q52fs, p.D140fs, p.M155I and p.I396T). The p.R525H mutation was detected in 13 out of 1,045 cases. Purple triangles show DDX41 mutations in non-hematological malignancies. Sanger sequencing confirming recurrent germline mutation (p.D140fs; left) and somatic mutation (p.R525H; right) of DDX41 are shown.

(B) DDX41 mRNA expression was analyzed by real-time RT-PCR in cases with deleted DDX41 locus compared with cases without deletion. Boxes represent 25–75 percentiles. A line inside a box represents median. Whiskers indicate maximum and minimum values.

(C) For cases with DDX41 mutations, variant allelic frequencies (VAFs) of DDX41 mutations (germline and somatic) and concomitant mutations of other genes (somatic) are shown. Mean values of VAFs were compared between somatic DDX41 and concomitant mutations (Mean±SD: 25±10% and 29±14%, respectively; p>.05).

(D) For cases in the whole examined cohort, VAFs of DDX41 mutations (Mean±SD: 25±10%) were compared to those of other genes affected by somatic mutations in myeloid neoplasms, including patients with DDX41 mutations. VAF is indicated as mean±SD. * indicates a p value of p=.004.

(E) Clonal architecture of 8 cases with DDX41 mutations. The percentages represent allelic frequencies with 50% set as the largest circle; case 1: 50% of DDX41-D140fs (germline mutation), 25% of SMAD1-T4I and 21% of DDX41-R525H; case 3: 50% of DDX41-D140fs (germline mutation) and 12% of DDX41-R525H; case4: 50% of DDX41-I396T (germline mutation), 42% of DDX41-R525H, 15% of PHF6-C20fs and 14% of DNMT3A-C394R; case5: 50% of DDX41-I396T (germline mutation), 46% of JAK2-V617F and 37% of DDX41-R525H; case 6: 50% of DDX41-D140fs (germline mutation), 37% of CDH26-P304S, 22% of TP53-S94X and 20% of DDX41-R525H; case 9: 50% of DDX41-D140fs (germline mutation), 30% of RUNX1-P68R and 25% of DDX41-R525H; case 12: 50% of DDX41-D140fs (germline mutation) and 11% of DDX41-R525H; case 23: 36% of DDX41-R525H, 34.8% of TP53-D149G and 11.1% of RUNX1-G108D. (Case number is annotated according to Table1)

See also Figure S3