IDENTIFYING GENETIC VARIATION IN AFFECTED TISSUES

• US 20120322670A1
• Filed: 08/26/2010
• Published: 12/20/2012
• Est. Priority Date: 08/28/2009
• Status: Active Grant

• Current Assignee: FUJIFILM Cellular Dynamics, Inc. (Fujifilm Holdings Corporation)
• Original Assignee: Cellular Dynamics International, Inc. (Fujifilm Holdings Corporation)
• Inventors: Thomson, James, Seay, Nicholas
• Granted Patent: US 9,506,114 B2
• Time in Patent Office: Days
• US Class Current: 506/7
• CPC Class Codes: C12Q 1/6881 for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
• CPC Class Codes: C12Q 2600/154 Methylation markers
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/158 Expression markers

Abstract

Methods for the determination of tissue-specific genetic variation are provided. For example, in certain aspects methods for using iPS cell-derived specific cell types for differential molecular analysis of tissue-specific genetic variation are described.

Claims

1. A method for determining the presence of a tissue-specific genetic variation in a test subject relative to a selected control genetic structure, comprising:

a) obtaining genetic material of a differentiated cell of a selected tissue, the cell having been prepared by differentiating an induced pluripotent stem (iPS) cell obtained by reprogramming a somatic cell of the subject; and

b) testing the genetic material of said differentiated cell to compare one or more genetic structure of said genetic material with one or more control genetic structures to determine the presence of such a genetic variation in cells of the tissue of the subject.

2. The method of claim 1, wherein the subject has or is suspected of having a genetic abnormality or genetic disease.

3. The method of claim 1, wherein said selected tissue is retina.

4. The method of claim 3, wherein said differentiated cell is a neural retina cell.

5. The method of claim 3, wherein said differentiated cell is a retina pigment epithelium (RPE) cell.

6. The method of claim 1, wherein said testing comprises RNA or DNA sequencing.

7. The method of claim 1, wherein said testing employs microarray analysis.

8. The method of claim 1, wherein said genetic material comprises RNA or DNA.

9. The method of claim 1, wherein said genetic structure is a nucleotide sequence.

10. The method of claim 1, wherein said genetic structure is represented by an expression profile on RNA level or protein level.

11. The method of claim 1, wherein said genetic variation is a polymorphism.

12. The method of claim 11, wherein said genetic variation is a single nucleotide polymorphism variation.

13. The method of claim 1, wherein said genetic variation is a gene mutation.

14. The method of claim 1, wherein said genetic variation is represented by differential expression on RNA level or protein level.

15. The method of claim 1, wherein said genetic variation is variation of one or more coding sequences.

16. The method of claim 1, wherein said genetic variation is variation of one or more gene regulatory elements.

17. The method of claim 16, wherein said gene regulatory element is a promoter, enhancer, silencer or responsive element.

18. The method of claim 16, wherein said gene regulatory element is microRNA.

19. The method of claim 1, wherein said genetic variation is epigenetic variation.

20. The method of claim 19, wherein said genetic variation is variation in methylation of the genetic structure.

21. The method of claim 1, wherein the control genetic structure is one known not to have a selected genetic variation.

22. The method of claim 21, wherein the control genetic structure is comprised in genetic material from a normal tissue.

23. The method of claim 1, wherein the control genetic structure is comprised in genetic material, wherein the genetic material is from a selected normal cell prepared by differentiating an iPS cell obtained by reprogramming a normal somatic cell of a control subject.

24. The method of claim 23, wherein the selected normal cell is of the same tissue type as the selected tissue of the test subject.

25. The method of claim 1, wherein the control genetic structure is of a control subject being a relative of the test subject.

26. The method of claim 25, wherein the control subject is a sibling of the test subject.

27. The method of claim 22, wherein the normal tissue is of the same tissue type as the selected tissue of the test subject.