This proposal brings together two research teams with expertise in single cell manipulation, amplification strategies, sequencing, and translational cancer research to advance technologies to tackle important questions in cancer biology. It responds to RFA-CA-12-003, and proposes to create and validate a platform for robust single cell sequencing of human samples based on our most recent advance in single cell whole genome amplification. The immediate goal is to combine different technical approaches and then use them to determine how individual cancer cells differ in populations. Our focus will be on sequencing single cancer cells in peripheral blood, as well as from primary and metastatic cancer tissues by fine needle aspiration.
Aim 1 will develop and validate integrated approaches so that immunocytochemical analyses can inform decisions on which cells to sequence.
Aim 2 will focus on applying the single cell amplification and sequencing technology to primary human samples with phenotypic identification achieved in Aim 1. Overall, our goal is to adapt and further develop a suite of recently developed and highly promising single cell analytical technologies to gain an understanding of genomic variations in primary and shed cancer cells. Success of the project will result in an integrated platform that will serve to overcome prevailing impediments in cancer research. The research is expected to have a broad impact on basic research, clinical practice, and the development of emerging anti- cancer drugs.
We will validate single cell whole genome amplification (MALBAC) and sequencing on small individual clinical cancer cells. We will assess the potential of single cell genome sequencing for profiling cancer mutations, as well as the prospects for diagnosis and therapeutic response.
| Blanshard, Robert C; Chen, Chongyi; Xie, Xiaoliang Sunney et al. (2018) Single cell genomics to study DNA and chromosome changes in human gametes and embryos. Methods Cell Biol 144:441-457 |
| Chen, Chongyi; Xing, Dong; Tan, Longzhi et al. (2017) Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion (LIANTI). Science 356:189-194 |
| Chapman, Alec R; He, Zi; Lu, Sijia et al. (2015) Single cell transcriptome amplification with MALBAC. PLoS One 10:e0120889 |
| Huang, Lei; Ma, Fei; Chapman, Alec et al. (2015) Single-Cell Whole-Genome Amplification and Sequencing: Methodology and Applications. Annu Rev Genomics Hum Genet 16:79-102 |
