Germ line predisposition variants occur in myelodysplastic syndrome patients of all ages

Abstract

The frequency of pathogenic/likely pathogenic (P/LP) germ line variants in patients with myelodysplastic syndrome (MDS) diagnosed at age 40 years or less is 15% to 20%. However, there are no comprehensive studies assessing the frequency of such variants across the age spectrum. We performed augmented whole-exome sequencing of peripheral blood samples from 404 patients with MDS and their related donors before allogeneic hematopoietic stem cell transplantation. Single-nucleotide and copy number variants in 233 genes were analyzed and interpreted. Germ line status was established by the presence of a variant in the patient and related donor or for those seen previously only as germ line alleles. We identified P/LP germ line variants in 28 of 404 patients with MDS (7%), present within all age deciles. Patients with P/LP variants were more likely to develop higher-grade MDS than those without (43% vs 25%; P = .04). There was no statistically significant difference in outcome parameters between patients with and without a germ line variant, but the analysis was underpowered. P/LP variants in bone marrow failure syndrome genes were found in 5 patients aged less than 40 years, whereas variants in DDX41 (n = 4), telomere biology disorder genes (n = 2), and general tumor predisposition genes (n = 17) were found in patients aged more than 40 years. If presumed germ line variants were included, the yield of P/LP variants would increase to 11%, and by adding suspicious variants of unknown significance, it would rise further to 12%. The high frequency of P/LP germ line variants in our study supports comprehensive germ line genetic testing for all patients with MDS regardless of their age at diagnosis.

Graphical abstract

Figure 1.

Work flow diagram for the identification of P/LP germ line variants. DNA was extracted from thawed peripheral blood from 404 patients with MDS and was sequenced using an augmented whole-exome sequencing platform. SNVs and CNVs were called in 233 genes, using custom bioinformatic pipelines. A total of 21,661 SNVs and 334 CNVs were manually curated according to the ACMG/AMP and ClinGen SVI-WG guidelines. P/LP germ line variants were validated by Sanger sequencing, subcloning, and/or RT-qPCR. ACMG, American College of Medical Genetics; AMP, Association for Molecular Pathology; ClinGen SVI-WG, Clinical Genome Sequence Variant Interpretation Working Group; CNV, copy number variant; LP, likely pathogenic; MDS, myelodysplastic syndrome; P, pathogenic; RT-qPCR, quantitative real-time PCR; SNV, single-nucleotide variant; WES, whole-exome sequencing.

Figure 2.

Variant subgroups based on donor status. This schematic identifies subgroups of patients with MDS/HSCT recipients based on the presence or absence of a predisposing variant, the manner of inheritance, whether the variant is shared by the donor and would be disease-causing, as well as subgroups chosen for statistical analyses of outcome parameters. ^†Healthy carriers refer to recipients with a P/LP variant who received donor stem cells lacking an AD P/LP variant or cells with a heterozygous P/LP allele with an AR mode of inheritance. AD, autosomal dominant; AR, autosomal recessive; het, heterozygous; HSCT, hematopoietic stem cell transplantation; LP, likely pathogenic; MDS, myelodysplastic syndrome; mut, mutated; P, pathogenic; wt, wild-type.

Figure 3.

Age distribution of pathogenicknownand presumed germ line variants in patients with MDS. The number of patients with MDS (left y-axis, red) with a confirmed germ line variant (red, solid line), a presumed germ line variant (red, dashed line), or wild-type (ie, without a germ line variant; peach, solid line with shading) is plotted per age decile (x-axis). The percentage (right y-axis, blue) of confirmed germ line variants (blue, solid line) and presumed germ line variants∗ (blue, dashed line) is plotted per age decile. ∗Presumed germ line variants based on a multiple-criteria decision analysis.

Figure 4.

Spectrum and distribution of deleterious germ line variants among subgroups and association with age at diagnosis. (A) Bar chart depicting the number of confirmed P/LP germ line variants per gene identified in 28 patients with MDS. Compound heterozygous variants in the AR gene SBDS were counted as 1 variant per patient. Color schematic: purple, DDX41; green, general tumor predisposition genes; blue, telomere biology disorders; red, bone marrow failure genes; gray, others. (B) Nested pie chart showing the distribution of gene subgroups as well as biological functions. (C) Violin plots of the age at diagnosis of the 4 most common groups of predisposition syndromes identified in this study. (D) Association between the affected gene in the germ line and the age at MDS diagnosis. The data are derived from our study (confirmed/presumed germ line, n = 44) and other larger cross-sectional studies on germ line variants in patients with MDS using either panel-based or WES covering most genes of interest., , , , ^,,, Each circle represents a gene, and the circle size corresponds to the frequency of variants within this gene in the total cohort. Genes in the upper left quadrant were associated with an age at diagnosis of less than 40 years, whereas genes in the upper right quadrant were associated with an age at diagnosis greater than 40 years, based on calculated odds ratio. Color schematic: purple, DDX41; green, general tumor predisposition genes; blue, telomere biology disorders; red, bone marrow failure genes; gray, others. DSB, double-strand break repair; MMR, mismatch repair; RM, ribosome maturation.

Figure 5.

Spectrum and distribution of germ line variants, co-occurring somatic variants, and clinical data. (A) Bar chart displaying the top 20 most commonly affected genes for somatic variants (dark blue, wild-type; light blue, confirmed or presumed germ line variant). Percentages are given at the end of each bar. (B) Bar chart showing the top 10 most commonly affected gene groups (by broad gene ontology and biological pathways) (dark red, wild-type; light red, confirmed or presumed germ line variant). Percentages are given at the end of each bar. (C) Mutational grid with all 28 patients with MDS with confirmed germ line P/LP variants (left) and the 16 patients with MDS with presumed germ line variants (right). Patients are grouped by age at diagnosis in both panels. (Top) Clinical data such as age, MDS subtype, cytogenetic analysis, and outcome parameters, including death, relapse and nonrelapse mortality, and primary graft failure/rejection as well as co-occurring somatic variants (grouped by broad gene ontology and biological pathways) are included. (Bottom) The legend indicates the colors used for age deciles, MDS subgroups, cytogenetic analysis, variant status, and missing data. CMML, chronic myelomonocytic leukemia; MDS, myelodysplastic syndrome; RA, refractory anemia; RAEB, refractory anemia with excess blasts; RARS, refractory anemia with ring sideroblasts; RCMD, refractory cytopenia with multilineage dysplasia; RCMD-RS, refractory cytopenia with multilineage dysplasia and ring sideroblasts.