Genomes evolve and diversify through di?erent mechanisms, including small point mutations, but also larger, structural variations (SV). SVs can be mediated by simple repeats and microhomology based recombination (termed 'progressive SVs' in this proposal). However, progressive SV mechanisms cannot explain all forms of large genomic variation; sometimes, more 'complex mechanisms' are needed; examples include Breakage Fusion Bridge, and Chromothripsis. Moreover, there is little understanding of the genetic mechanisms of genome instability that lead to complex SV formation. It is suspected that random viral genome insertions into the genome can on occasion disrupt key genes, causing genome instability and hyper-variability. To address these problems, the proposal will design and implement computational methods to (a) reconstruct and validate episomal structures of viral genome insertions; (b) determine if genomic sequence sampled from tumor genomes has a signature of complex variation; and, (b) phase and sub-type regions with complex SV including KIR and HLA; As clinical/translational applications of genomics come to the forefront, the impact of complex SVs on the phenotype of an individual become increasingly important. Understanding the computational signatures of BFB and Chromothripsis will help sub-type and characterize cancers. The knowledge of KIR/HLA sub-type will be correlated with immune related phenotypes, and the reconstruction of viral episomes will help clarify the etiology of virus mediated cancers. Thus, the proposed set of computational tools will directly impact the translational/medical aspect of genomics.
The proposed computational tools will be used to detect complex structural variations in human genomes, and will provide a starting point for understanding their role in disease. The development of computational signatures of BFB and Chromothripsis will help sub-type and characterize cancers; similarly, the knowledge of KIR/HLA sub- type could be correlated with immune related phenotypes, and the reconstruction of viral episomes will help clarify the etiology of virus mediated cancers. Thus, the proposed set of computational tools will have an immediate and long term impact on human health.
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| Turner, Kristen M; Deshpande, Viraj; Beyter, Doruk et al. (2017) Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity. Nature 543:122-125 |
| Iranmehr, Arya; Akbari, Ali; Schlötterer, Christian et al. (2017) Clear: Composition of Likelihoods for Evolve and Resequence Experiments. Genetics 206:1011-1023 |
| Azad, Priti; Stobdan, Tsering; Zhou, Dan et al. (2017) High-altitude adaptation in humans: from genomics to integrative physiology. J Mol Med (Berl) 95:1269-1282 |
| Chu, Wai Keung; Edge, Peter; Lee, Ho Suk et al. (2017) Ultraaccurate genome sequencing and haplotyping of single human cells. Proc Natl Acad Sci U S A 114:12512-12517 |
| Stobdan, Tsering; Akbari, Ali; Azad, Priti et al. (2017) New Insights into the Genetic Basis of Monge's Disease and Adaptation to High-Altitude. Mol Biol Evol 34:3154-3168 |
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