The proposed aims of this project center on constructing whole genome maps from 30 different oligodendroglioma tumor samples - a solid tumor that has confounded conventional genome analysis approaches to associate loss of heterozygosity (LOH) with a distinct set of gene(s). The research proposed reflects a multi-disciplinary collaborative effort to use a robust single molecule platform (Optical Mapping) to construct high-resolution restriction maps from a selected group of characterized tumors bearing a heterogeneous genome population. Chromosomal aberrations will be scored and classified on a whole genome basis in the absence of any hypothesis, outside of the established link between 1p/19q LOH and diagnostic purposes. Genomic aberrations in the tumor samples - deletions, insertions, translocations, tandem amplifications, and gross rearrangements - will be precisely located and characterized. Map coverage of 20-50x will ensure discernment of separate populations of chromosomal aberrations within each sample at 50 kb-500 kb genome intervals. New algorithms will be developed, based on Optical Mapping data, to identify breakpoints within a heterogeneous population of aberrant genomes based on the local alignment of single molecule barcodes, or Optical Maps, with the latest build of the human genome sequence. Aberrations will be statistically assessed to discern the percent of the tumor cell population bearing a given genomic lesion. To synergize this, a new generation of microfluidic device to incorporate cell lysis and DNA loading within the same disposable silicone fabrication will be perfected. These first-ever whole genome maps of oligodendroglioma tumor genomes and comprehensive determinations of aberrations will be entered into a customized Santa Cruz Genome Browser as additional annotation tracks. This technology provides a unique platform to decipher the complex molecular anatomy of cancer cells, on a whole genome basis, at high resolution.
| Li, Yang; Zhou, Shiguo; Schwartz, David C et al. (2016) Allele-Specific Quantification of Structural Variations in Cancer Genomes. Cell Syst 3:21-34 |
| Lee, Seonghyun; Oh, Yeeun; Lee, Jungyoon et al. (2016) DNA binding fluorescent proteins for the direct visualization of large DNA molecules. Nucleic Acids Res 44:e6 |
| Gupta, Aditya; Place, Michael; Goldstein, Steven et al. (2015) Single-molecule analysis reveals widespread structural variation in multiple myeloma. Proc Natl Acad Sci U S A 112:7689-94 |
| Ray, Mohana; Goldstein, Steve; Zhou, Shiguo et al. (2013) Discovery of structural alterations in solid tumor oligodendroglioma by single molecule analysis. BMC Genomics 14:505 |
| Teague, Brian; Waterman, Michael S; Goldstein, Steven et al. (2010) High-resolution human genome structure by single-molecule analysis. Proc Natl Acad Sci U S A 107:10848-53 |
| Li, Haifeng; Valouev, Anton; Schwartz, David C et al. (2007) A quantile method for sizing optical maps. J Comput Biol 14:255-66 |
