Identifying genetic variation in affected tissues
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.
1. A method for determining the presence of a tissue-specific genetic variation in a test subject, wherein the test subject has a disease of unknown genetic cause that affects a retinal tissue, the method comprising:
a) creating an induced pluripotent stem (iPS) cell from somatic cells from a sample taken from said test subject;
b) making a differentiated retinal cell using the iPS cell of step a);
c) sequencing a first nucleic acid from said differentiated retinal cell; and
d) comparing said first nucleic acid sequence with a second nucleic acid sequence from a cell from a control individual, thereby determining the presence of tissue-specific genetic variation in the subject.
2. The method of claim 1 , wherein said differentiated cell is a neural retina cell.
3. The method of claim 1 , wherein said differentiated cell is a retina pigment epithelium (RPE) cell.
4. The method of claim 1 , wherein said sequencing comprises DNA sequencing.
5. The method of claim 1 , wherein the control individual is one known not to have a selected genetic variation.
6. The method of claim 5 , wherein the control cell is from a normal tissue.
7. The method of claim 1 , wherein the control cell is prepared by differentiating an iPS cell obtained by reprogramming a normal somatic cell of a control subject.
8. The method of claim 7 , wherein the control cell is a retinal cell.
9. The method of claim 1 , wherein the control cell is a retinal cell.
10. The method of claim 1 , wherein said sequencing comprises RNA sequencing.