Identification of Recurring Tumor-Specific Somatic Mutations In Acute Myeloid Leukemia by Transcriptome Sequencing

Abstract 1059 Aims: Genetic lesions are crucial for cancer initiation. Recently, whole genome sequencing using next generation technology was used as a systematic approach to identify mutations in genomes of various types of tumors including melanoma, lung and breast cancer as well as cytognetically normal acute myeloid leukaemia (CN-AML). Despite its technical feasibility, whole genome sequencing is still time consuming and cost intensive. As an alternative approach, here we identify tumor-specific somatic mutations by sequencing transcriptionally active genes. Methods: Mutations were detected by comparing the transcriptome sequence of a CN-AML with the corresponding remission sample. In a single Genome Analyzer II run, we generated 4.35 Gbp of CN-AML and 5.54 of remission transcriptome sequence from the same patient. 63% of AML reads and 74% of remission reads mapped to exon regions. 10,152 genes had an average read depth of at least 7-fold and 6,989 genes an average read depth of 20 or greater in both samples. By comparing the 8,978 coding Single Nucleotide Variants (SNVs) discovered in the CN-AML sample with the remission sample, we identified 5 non-synonymous mutations specific to the tumor sample. Results: We found 5 tumor-specific somatic mutations. Among them is a nonsense mutation affecting the RUNX1 gene, which is a frequent mutational target in AML, and a missense mutation in the putative tumor suppressor gene TLE4, which encodes a RUNX1 interacting protein. A second missense mutation was identified in SHKBP1, which acts downstream of FLT3, a receptor tyrosine kinase mutated in about 30% of AML cases. The frequency of mutations in TLE4 and SHKBP1 in a cohort of 95 CN-AML patients was 2%. Conclusion: Our study demonstrates that whole transcriptome sequencing leads to the rapid detection of recurring point mutations in the coding regions of genes relevant to malignant transformation. Disclosures: No relevant conflicts of interest to declare.