Methods and compositions for identifying a fetal cell

• US 20100304978A1
• Filed: 01/26/2010
• Published: 12/02/2010
• Est. Priority Date: 01/26/2009
• Status: Abandoned Application

• Current Assignee: Verinata Health Incorporated (Illumina Incorporated)
• Original Assignee: Verinata Health Incorporated (Illumina Incorporated)
• Inventors: Robbins, David L., Bao, Yun, Chuu, Yue-Jen, Shoemaker, Daniel, Deng, David Xingfei
• Application Number:
  US12/657,723
• Publication Number:
  US 20100304978A1
• Time in Patent Office: Days
• US Class Current: 506/7
• CPC Class Codes: C12Q 1/6841 In situ hybridisation
• CPC Class Codes: C12Q 1/6879 for sex determination
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays

Abstract

The present invention provides methods and compositions for specifically identifying a fetal cell. An initial screening of approximately 400 candidate genes by digital PCR in different fetal and adult tissues identified a subset of 24 gene markers specific for fetal nucleated RBC and trophoblasts. The specific expression of those genes was further evaluated and verified in more defined tissues and isolated cells through quantitative RT-PCR using custom Taqman probes specific for each gene. A subset of fetal cell specific markers (FCM) was tested and validated by RNA fluorescent in situ hybridization (FISH) in blood samples from non-pregnant women, and pre-termination and post-termination pregnant women. Applications of these gene markers include, but are not limited to, distinguishing a fetal cell from a maternal cell for fetal cell identification and genetic diagnosis, identifying circulating fetal cell types in maternal blood, purifying or enriching one or more fetal cells, and enumerating one or more fetal cells during fetal cell enrichment.

Claims

1. A method for identifying a fnRBC comprising detecting transcript or protein expression of a HBE, AFP, AHSG, or J42-4-d gene.

2. The method of claim 1, wherein said detecting comprises using at least two primers and at least one probe that anneals to a cDNA generated from a transcript expressed by said HBE, AFP, AHSG, or J42-4-d gene.

3. A method for identifying a trophoblast comprising detecting transcript or protein expression of a KISS1, LOC90625, AFP, hPL, beta-hCG, or FN1 gene.

4. The method of claim 3, wherein said detecting comprises using at least two primers and at least one probe that anneals to a cDNA generated from a transcript expressed by said KISS1, LOC90625, AFP, hPL, beta-hCG, or FN1 gene.

5. A method for identifying a fetal cell in a maternal sample comprising detecting transcript or protein expression by a cell of one or more of the KISS1, LOC90625, FN1, or AHSG genes to distinguish said fetal cell from a maternal cell.

7. The method of claim 5 or 6, wherein the maternal sample is a maternal blood sample, amniocentesis sample, or cervical swab.

8. The method of claim 5 or 6, wherein said fetal cell is a fetal nucleated RBC or a placental cell.

9. The method of claim 7, wherein said sample is taken in the 1^st or early 2^nd trimester.

10. The method of claim 7, wherein said sample is taken in the 2^nd trimester.

11. The method of claim 5, wherein said fetal cell is a fetal nucleated red blood cell and said gene is AHSG.

12. The method of claim 5, wherein said fetal cell is a trophoblast and said gene is FN1.

13. The method of claim 5 or 6, wherein said detecting comprises RNA FISH, RNA-FISH with a molecule beacon probe, RT-PCR, Q-PCR, digital mRNA profiling, Northern blotting, ribonuclease protection assay, or RNA expression profiling using microarrays.

14. The method of claim 5 or 6, wherein said detecting comprises binding a protein with one or more binding moieties.

15. The method of claim 14, wherein said one or more binding moieties is an antibody, Fab fragment, Fc fragment, scFv fragment, peptidomimetic, or peptoid.

6. A method for identifying a fetal cell in a maternal sample comprising detecting transcript or protein expression by a cell of three or more of the hPL, KISS1, LOC90625, FN1, PSG9, HBE, AFP, beta-hCG, AHSG or J42-4-d genes to distinguish said fetal cell from a maternal cell.

16. A method for identifying a fetal cell in a maternal sample, comprising:

a. enriching a fetal cell, and

b. detecting protein or transcript expression of one or more genes by said fetal cell, wherein said expression of said one or more genes distinguishes said fetal cell from a maternal cell, wherein said one or more genes is hPL, CHS2, KISS1, GDF15, CRH, TFP12, CGB, LOC90625, FN1, COL1A2, PSG9, PSG1, AFP, APOC3, SERPINC1, AMBP, CPB2, ITIH1, APOH, HPX, beta-hCG, AHSG, APOB, or J42-4-d.

17. The method of claim 16, wherein the step of enriching a fetal cell comprises one or more steps of density centrifugation, size based separation, affinity separation, magnetic separation, microfluidic fluorescent cell sorting, dielectrophoretic enrichment, or antibody separation.

18. The method of claim 16, wherein the sample is a maternal blood sample, amniocentesis sample, or cervical swab.

19. The method of claim 16, wherein said cell is a fetal nucleated RBC or a placental cell.

20. The method of claim 16, further comprising enriching a fetal nucleated RBC by magnetic enrichment.

21. The method of claim 16, further comprising enriching one or more fetal nucleated RBCs by anti-CD71 or anti-GLA selection.

22. The method of claim 16, further comprising enriching one or more trophoblasts by anti-HLA-G or anti-EGFR selection.

23. The method of claim 16, wherein said cell is a fetal nucleated RBC and said one or more genes is AFP, AHSG, or J42-4-d.

24. The method of claim 16, wherein said cell is a trophoblast and said one or more genes is KISS1, LOC90625, AFP, hPL, beta-hCG, or FN1.

25. The method of claim 16, wherein said detecting is by RNA FISH, RNA-FISH with a molecule beacon probe, RT-PCR, Q-PCR, digital mRNA profiling, Northern blotting, ribonuclease protection assay, or RNA expression profiling using microarrays.

26. The method of claim 16, wherein said fetal cell is from a maternal sample obtained in the 1^st trimester or 2^nd trimester of pregnancy.

27. The method of claim 16, wherein said detecting protein expression comprises binding a protein with a binding moiety.

28. The method of claim 27, wherein said binding moiety is an antibody, Fab fragment, Fc fragment, scFv fragment, peptidomimetic, or peptoid.

29. A method for identifying a fetal cell specific transcript comprising

a. isolating a transcript from a sample containing a fetal cell and a transcript from a sample lacking fetal cells;

b. producing cDNAs of said transcripts;

c. performing quantitative PCR on said cDNAs; and

d. comparing results of said quantitative PCR between samples to identify a marker transcript with higher expression in a fetal cell relative to a non-fetal cell.

30. The method of claim 29, wherein said fetal cell is first enriched from a maternal sample by size based separation.

31. The method of claim 29, further comprising a verifying step comprising detecting a marker transcript by quantitative PCR.