Single cell gene expression for diagnosis, prognosis and identification of drug targets
Methods are provided for diagnosis and prognosis of disease by analyzing expression of a set of genes obtained from single cell analysis. Classification allows optimization of treatment, and determination of whether on whether to proceed with a specific therapy, and how to optimize dose, choice of treatment, and the like. Single cell analysis also provides for the identification and development of therapies which target mutations and/or pathways in disease-state cells.
1. A method of identifying different cell populations in a heterogeneous cell sample, comprising:
randomly partitioning individual cells from said heterogeneous cell sample into discrete locations on a cell capture array with wells just large enough to fit a single cell;
identifying certain individually partitioned cells in the discrete locations on the cell capture array using one or more surface markers;
sorting the certain individually partitioned cells from the discrete locations using a microfluidic device;
performing transcriptome analysis on a plurality of genes of the individually sorted cells from the discrete locations; and
performing clustering analysis to identify different cell populations.
2. The method of claim 1 , wherein said individual cells are not enriched prior to said partitioning.
3. The method of claim 1 , wherein said transcriptome analysis is performed on at least 1000 individual cells in parallel.
4. The method of claim 1 , wherein said transcriptome analysis is performed using nucleic acid analysis.
5. The method of claim 1 , wherein said discrete locations are on a microarray.
6. The method of claim 1 , wherein said transcriptome analysis comprises analyzing expressed RNA, non-expressed RNA, or both.
7. The method of claim 1 , wherein said transcriptome analysis is whole transcriptome analysis.
8. The method of claim 1 , wherein said transcriptome analysis comprises amplifying RNA using a set of at least five primer pairs.
9. The method of claim 8 , wherein said at least five primer pairs are not nested primers.
10. The method of claim 1 , wherein said transcriptome analysis is performed in parallel or substantially in real time on said individually sorted cells.
11. The method of claim 1 , wherein said different cell populations are non-cancerous stem cells, non-cancerous progenitor cells, non-cancerous mature cells, inflammatory cells, cancer cells, cancer stem cells or non-tumorigenic cancer stem cells.