Genomics of inherited bone marrow failure and myelodysplasia

Thesis (Ph.D.)--University of Washington, 2015Bone marrow failure and myelodysplastic syndromes (BMF/MDS) are disorders of impaired blood cell production with increased leukemia risk. BMF/MDS may be acquired or inherited, a distinction critical for treatment selection. Currently, diagnosis of these inherited syndromes is based on clinical history, family history, and laboratory studies, which directs the ordering of genetic tests on a gene-by-gene basis. However, despite extensive clinical workup and serial genetic testing, many cases remain unexplained. We sought to define the genetic etiology and pathophysiology of unclassified bone marrow failure and myelodysplastic syndromes. First, to determine the extent to which patients remained undiagnosed due to atypical or cryptic presentations of known inherited BMF/MDS, we developed a massively-parallel, next-generation DNA sequencing assay to simultaneously screen for mutations in 85 BMF/MDS genes. Querying 71 pediatric and adult patients with unclassified BMF/MDS using this assay revealed 8 (11%) patients with constitutional, pathogenic mutations in GATA2, RUNX1, DKC1, or LIG4. All eight patients lacked classic features or laboratory findings for their syndromes. These data suggest that the current clinical practice of directed testing of individual genes failed to diagnose patients with cryptic disease presentations and inform the integration of broad genetic screening into the diagnostic workup of BMF/MDS. In cases where broad screening of known genes failed to identify an inherited cause, we sought to discover new genes responsible for inherited BMF/MDS. We identified kindreds with unclassified disease presenting in multiple family members and sequenced the complete coding regions of their genomes (exome). In a family with low blood counts and malignancy, we discovered a novel germline heterozygous mutation in the transcription factor ETV6 segregating with the disease phenotype. The mutant protein is defective in transcriptional regulation, inhibits wild-type ETV6 in a dominant negative manner, and impairs hematopoiesis when expressed in human hematopoietic stem cells. Together, our studies provide new methodologies and genetic associations to enhance the diagnosis of inherited BMF/MDS