Methods and systems for generating cell lineage tree of multiple cell samples

• US 7,917,306 B2
• Filed: 03/27/2006
• Issued: 03/29/2011
• Est. Priority Date: 03/30/2005
• Status: Active Grant

• Current Assignee: Yeda Research and Development Co. Ltd. (Weizmann Institute of Science)
• Original Assignee: Yeda Research and Development Co. Ltd. (Weizmann Institute of Science)
• Inventors: Wasserstrom, Adam, Frumkin, Dan, Feige, Uriel, Kaplan, Shai, Shapiro, Ehud Y.
• Primary Examiner(s): Raymond; Edward
• Application Number:
  US11/887,551
• Publication Number:
  US 20090292482A1
• Time in Patent Office: 1,828 Days
• Field of Search: 702 20- 24, 702182-185, 702/188, 435/41
• US Class Current: 702/20
• CPC Class Codes: G16B 10/00 ICT specially adapted for evolutionary bioinformatics, e.g. phylogenetic tree construction or analysis
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16B 20/50 Mutagenesis
• CPC Class Codes: G16B 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• CPC Class Codes: G16B 40/10 Signal processing, e.g. from mass spectrometry [MS] or from PCR

Abstract

A method of generating a cell lineage tree of a plurality of cells of an individual is provided. The method comprising: (a) determining at least one genotypic marker for each cell of the plurality of cells; and (b) computationally clustering data representing the at least one genotypic marker to thereby generate the cell lineage tree of the plurality of cells of the individual.

Claims

1. A method of assessing clonality of a neoplasm in an individual, the method comprising:

(a) obtaining a cell sample of the neoplasm of the individual;

(b) determining at least one genotypic marker for each cell of said cell sample of the neoplasm; and

(c) computationally clustering data representing said at least one genotypic marker and additional genotypic markers of a plurality of cells, to thereby assess clonality of the neoplasm in the individual.

2. The method of claim 1, wherein said genotypic marker is a cell division marker.

3. The method of claim 1, wherein said genotypic marker exhibits somatic variability.

4. The method of claim 3, wherein said genotypic marker exhibiting somatic variability is a repetitive sequence element.

5. The method of claim 1, wherein said clustering is effected by a clustering algorithm.

6. The method of claim 1, wherein the neoplasm is of a blood forming tissue.

7. The method of claim 1, wherein the neoplasm is a cancer of unknown primary tumor.