Single cell gene expression for diagnosis, prognosis and identification of drug targets

Patent metadata

Field	Value
Publication number	US-9329170-B2
Application number	US-65745710-A
Country	US
Kind code	B2
Filing date	Jan 20, 2010
Priority date	Jan 20, 2009
Publication date	May 3, 2016
Grant date	May 3, 2016

Abstract

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.

First claim

What is claimed is:

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.

Assignees

• Clarke Michael F
• Quake Stephen R
• Dalerba Piero D
• Liu Huiping
• Leyrat Anne
• Kalisky Tomer
• Diehn Maximilian
• Wang Jianbin
• Univ Leland Stanford Junior

Inventors

• Clarke Michael F
• Quake Stephen R
• Dalerba Piero D
• Liu Huiping
• Leyrat Anne
• Kalisky Tomer
• Diehn Maximilian
• Wang Jianbin

Classifications

• G01N33/5758

  involving compounds serving as markers for tumours, cancers or neoplasias, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides or metabolites · CPC title

• C12Q1/6886 Primary

  for cancer (immunoassay for cancer G01N33/575) · CPC title

• C12Q2600/112

  Disease subtyping, staging or classification · CPC title

• C12Q2600/178

  miRNA, siRNA or ncRNA · CPC title

• C12Q2600/136

  Screening for pharmacological compounds · CPC title