Abstract
Background
The mutational landscape in acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) is becoming increasingly apparent. Although some mutations and translocations occur in a substantial fraction of patients, in many, the etiologic mutations are unknown and current cytogenetic testing uninformative. Recent whole genome studies show that the mutational landscape can be very diverse. Genomic studies in families at high risk of developing MDS and AML can be highly informative in identifying potentially oncogenic mutations. We have identified a family with a high incidence of MDS/AML and here report on their unique mutational profile.
Patients and Methods
An index patient presented to our institution with AML with myelodysplasia related changes (AML-MRC) who required allogeneic stem cell transplantation (SCT). Subsequently, 3 other family members developed MDS. DNA from the index case before and after SCT, 3 affected family members, along with 3 healthy family members (controls) was isolated. Whole exome sequencing was performed using the Agilent V4+UTR capture kit. Sequencing of the index case post SCT served as an additional control (100% donor chimerism). Potentially damaging and novel variations in the index case and additional affected patients were detected by comparing their variant files with those of their unaffected relatives. We further excluded variants with an observed MAF greater than 0.01 using annotated populations in HAPMAP, 1k Genomes, Danish-BGI and ESP5400_EU. All variants with a high or moderate effect based on SNPeff were considered.
Results
We sequenced an average of 1 billion base pairs per case, with an at least 30 fold exome coverage. The average number of INDELs was 206/patient (range, 187-214), while the average number of SNV was 142/patient (range, 139 – 153). Sixteen mutations were identified in the patients that were not present in controls and in the post SCT sample. This frequency is similar to that recently reported by the Cancer Genome Atlas Research Network. However, none of the mutations we identified have been reported previously in AML/MDS. We identified a heterozygous mutation in the NAPRT1 gene that led to a premature stop codon (R405*). A mutation in the splice site donor of PODNL1 was also identified, together with non-synonymous mutations in IL36RN, ABCA12, GOLGB1, PLXNA1, ABLIM3 and others. We found no correlation between total SNV and total reads mapped (r=0.48). Given the potential role of NAPRT1in genome repair, we evaluated the frequency of SNV in individuals with and without this mutation. There was no difference in SNV frequency in heterozygotes compared to controls (p=0.45) and the frequency of SNV in patients with the R405* mutation did not increase with age. These observations argue against this mutation as a cause of genomic instability. We found a bimodal distribution of SNV (0.14% versus 0.08%, p=0.00024) that did not correlate with the presence/absence of disease. The mechanism behind this distribution is being evaluated.
Conclusions
The mutational landscape of MDS/AML continues to expand. The functional significance of mutations identified still has to be understood at the molecular level. Although some mutations in AML may be recurrent, it is likely that a substantial number of patients with leukemia have ‘private’ mutations that are oncogenic.
Disclosures:
No relevant conflicts of interest to declare.
Alternative splicing redefines landscape of commonly mutated genes in acute myeloid leukemia
