Jason PITT

Special Fellow, Cancer Science Institute of Singapore, NUS

jason.j.pitt[at]nus.edu.sg


My laboratory focuses on scalable genomic data science. As such, we emphasize two complementary research areas: 1) the development of platforms that enable efficient processing and querying of large cancer genomics datasets; and 2) applying these platforms to better understand cancer etiology — namely as it relates to genomic instability.

Research

The world is an ecosystem flooded with data. Tech giants have capitalized on this by transforming torrential data streams into actionable intelligence. Advances in biotechnology have fostered a similar data niche in cancer genomics, which offers considerable scientific returns to those who exploit it. Our laboratory builds scalable NGS workflows (SwiftSeq & Swag), machine learning software (ParaOpt & VariOpt), and artificial intelligence platforms (Melvin) to harmonize and interrogate large cancer genomics datasets. Scientifically, we utilize these tools to investigate cancer etiology, often through the lens of genomic instability (GI). GI — a hallmark of cancer — is defined as the accumulation of numerous DNA aberrations. Over the past decade, GI patterns have been shown to take many forms and can vary by driver mutation, cell-of-origin, germline susceptibility, race/ethnicity, and mutagenic exposure amongst others. Leveraging large-scale data to understand GI signatures and their sources will help facilitate more effective treatments across all evolutionary stages of cancer.

Lab Members

Selected Publications

  1. Wang, S.*, Pitt, J. J.*, Zheng, Y., Yoshimatsu, T., Gao, G. , Sanni, A., Oluwasola, O., Ajani, M. … Olopade, O. I. Germline variants and somatic mutation signatures of breast cancer across populations of African and European ancestry in the US and Nigeria. In press (International Journal of Cancer).
  2. Baughman, M., Chard, R., Ward, L., Pitt, J. J., Chard, K., & Foster, I. T. (2018). Profiling and Predicting Application Performance on the Cloud. 2018 IEEE/ACM 11th International Conference on Utility and Cloud Computing (UCC), 21–30.
  3. Pitt, J. J.*, Riester, M.*, Zheng, Y., Yoshimatsu, T. F., Sanni, A., Oluwasola, O., … Barretina, J. (2018). Characterization of Nigerian breast cancer reveals prevalent homologous recombination deficiency and aggressive molecular features. Nature Communications, 9(1), 4181.
  4. Pitt, J. J., Zheng, Y., & Olopade, O. I. (2018). Genetic Ancestry May Influence the Evolutionary Trajectory of Cancers. Cancer Cell, 34(4), 529–530.
  5. Pitroda, S. P., Khodarev, N. N., Huang, L., Uppal, A., Wightman, S. C., Ganai, S., Joseph, N., Pitt, J. … Weichselbaum, R. R. (2018). Integrated molecular subtyping defines a curable oligometastatic state in colorectal liver metastasis. Nature Communications, 9(1), 1793.
  6. Cheng, J., Demeulemeester, J., Wedge, D. C., Vollan, H. K. M., Pitt, J. J., Russnes, H. G., … Van Loo, P. (2017). Pan-cancer analysis of homozygous deletions in primary tumours uncovers rare tumour suppressors. Nature Communications, 8(1), 1221.
  7. Huo, D., Hu, H., Rhie, S. K., Gamazon, E. R., Cherniack, A. D., Liu, J., Yoshimatsu, T., Pitt, J.J. … Olopade, O. I. (2017). Comparison of Breast Cancer Molecular Features and Survival by African and European Ancestry in The Cancer Genome Atlas. JAMA Oncol. 3(12), 1654–1662.
  8. Camps, J., Pitt, J. J., Emons, G., Hummon, A. B., Case, C. M., Grade, M., … Ried, T. (2013). Genetic amplification of the NOTCH modulator LNX2 upregulates the WNT/B-catenin pathway in colorectal cancer. Cancer Research73(6), 2003–2013.
  9. Hummon, A. B., Pitt, J. J., Camps, J., Emons, G., Skube, S. B., Huppi, K., … Caplen, N. J. (2012). Systems-wide RNAi analysis of CASP8AP2/FLASH shows transcriptional deregulation of the replication-dependent histone genes and extensive effects on the transcriptome of colorectal cancer cells. Molecular Cancer, 11, 1.
  10. Mackiewicz, M., Huppi, K., Pitt, J. J., Dorsey, T. H., Ambs, S., & Caplen, N. J. (2011). Identification of the receptor tyrosine kinase AXL in breast cancer as a target for the human miR-34a microRNA. Breast Cancer Research and Treatment, 130(2), 663–679.

* Indicates co-first authorship

Honors & Awards

2016 Charles J. Epstein Trainee Award for Excellence in Human Genetics Research – Finalist (American Society of Human Genetics)
2012 Partners in International Research (PIRE) Fellow (National Science Foundation)
2011-2014 Genetics and Regulation Training Grant recipient (University of Chicago)
2009 Rupert Anderson Award for Research (Gustavus Adolphus College)
2008 Presidential Research Grant (Gustavus Adolphus College)
2007-2008 Mayo Clinic Scholars Program