Methods for analyzing rare circulating cells

1. A method for analyzing rare circulating cells (RCCs) in a non-enriched blood sample, comprising: (a) detecting RCCs in the non-enriched blood sample, comprising i) determining presence or absence of one or more immunofluorescent RCC detection markers in nucleated cells in the non-enriched blood sample, and ii) assessing the morphology of the nucleated cells, wherein RCCs are detected among the nucleated cells based on a combination of distinct immunofluorescent staining and morphological characteristics; (b) quenching the immunofluorescence of the one or more immunofluorescent RCC detection markers comprising contacting the RCCs with a quenching buffer, wherein the immunofluorescence is quenched by more than 50%, 60%, 70%, 80%, 90%, 95%, 99%, 99.9% or 99.99%; and (c) analyzing the detected RCCs, comprising determining presence or absence of one or more fluorescent RCC analysis markers.

2. The method of claim 1 , wherein the fluorescent RCC analysis markers are fluorescence in situ hybridization (FISH) markers.

3. The method of claim 1 , wherein more than 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 99% of RCCs detected in (a) are retained in (c).

4. The method of claim 1 , wherein the fluorescent RCC analysis markers are positive control markers.

5. The method of claim 4 , wherein the positive control markers are present in more than 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 99% of RCCs analyzed in (c).

6. The method of claim 4 , wherein the positive control markers are chromosomal markers.

7. The method of claim 4 , wherein the positive control markers are centromere markers or telomere markers.

8. The method of claim 1 , wherein the RCC analysis markers are genetic mutations selected from the group consisting of gene translocation, gene amplification gene deletion, gene aneuploidy and chromosomal aneuploidy.

9. The method of claim 1 , wherein analyzing the detected RCCs further comprises assessing the morphology of the detected RCCs.

10. The method of claim 1 , wherein the RCCs are circulating tumor cells (CTCs).

11. The method of claim 1 , wherein the RCCs are circulating epithelial cells (CECs).

12. The method of claim 1 , wherein the RCCs are CTC mimics.

13. The method of claim 1 , wherein the RCCs are CTC candidates.

14. The method of claim 1 , wherein the quenching buffer comprises a chaotropic agent.

15. The method of claim 14 , wherein the concentration of the chaotropic agent is at least 2M, 3M or 4M.

16. The method of claim 1 , wherein the quenching buffer comprises a chaotropic salt.

17. The method of claim 1 , wherein the quenching buffer comprises guanidine or a guanidinium salt.

18. The method of claim 1 , wherein the quenching buffer comprises guanidinium thiocyanate (guanidine thiocyanate) or guanidinium chloride (guanidine hydrochloride).

19. The method of claim 1 , wherein the RCCs were contacted with the quenching buffer for a period of time of more than 1 minute, 2 minutes, 3 minutes, 4 minutes, 5 minutes, 6 minutes, 7 minutes, 8 minutes, 9 minutes, 10 minutes, 15 minutes or more than 20 minutes.

20. The method of claim 1 , wherein the analyzed RCCs comprise RCC aggregates.

21. The method of claim 1 , wherein the RCCs are detected on a solid support.

22. The method of claim 1 , wherein the method is performed by fluorescent scanning microscopy.

23. The method of claim 22 , wherein the microscopy provides a field of view comprising more than 2, 5, 10, 20, 30, 40 or 50 RCCs, wherein each RCC is surrounded by more than 10, 50, 100, 150 or 200 WBCs.

24. The method of claim 1 , wherein determining presence or absence of the immunofluorescent RCC detection markers comprises comparing the distinct immunofluorescent staining of RCCs with distinct immunofluorescent staining of WBCs.

25. The method of claim 1 , wherein determining presence or absence of immunofluorescent RCC analysis markers comprises comparing the distinct fluorescent staining of RCCs with distinct fluorescent staining of WBCs.

26. The method of claim 1 , wherein the immunofluorescent RCC detection markers are immunofluorescent CTC detection markers.

27. The method of claim 1 , wherein the immunofluorescent RCC detection markers comprise a cytokeratin (CK).

28. The method of claim 1 , wherein the immunofluorescent RCC detection markers are immunofluorescent CEC detection markers.

29. The method of claim 1 , wherein the immunofluorescent RCC detection markers comprise Von Willebrand Factor (vWF).

30. The method of claim 1 , wherein (a) further comprises determining presence or absence of one or more immunofluorescent sample cell markers in the nucleated cells.

31. The method of claim 30 , wherein the immunofluorescent sample cell markers are specific for white blood cells (WBCs).

32. The method of claim 30 , wherein the immunofluorescent sample cell markers comprise CD 45.

33. The method of claim 1 , wherein assessing the morphology of the nucleated cells comprises comparing the morphological characteristics of RCCs with the morphological characteristics of surrounding WBCs.

34. The method of claim 1 , wherein the morphological characteristics comprise nucleus size, nucleus shape, cell size, cell shape, or nuclear to cytoplasmic ratio.

35. The method of claim 1 , wherein assessing the morphology of the nucleated cells comprises assessing the nucleated cell by nuclear detail, nuclear contour, presence or absence of nucleoli, quality of cytoplasm, quantity of cytoplasm, or immunofluorescent staining patterns.

36. The method of claim 1 , further comprising the initial step of obtaining a blood sample from a patient.

37. The method of claim 1 , wherein the blood sample was obtained from a non-small cell lung cancer (NSCLC) patient.

38. The method of claim 1 , wherein the non-enriched blood sample is a plurality of non-enriched blood samples.

39. The method of claim 1 , wherein the plurality of non-enriched blood samples was obtained from a plurality of patients.