Non-invasive method for isolation and detection of fetal DNA

• US 5,641,628 A
• Filed: 11/14/1994
• Issued: 06/24/1997
• Est. Priority Date: 11/13/1989
• Status: Expired due to Term

• Current Assignee: Children's Medical Center Corporation
• Original Assignee: Children's Medical Center Corporation
• Inventors: Bianchi, Diana W.
• Primary Examiner(s): Zitomer, Stephanie W.
• Assistant Examiner(s): MYERS, CARLA J
• Application Number:
  US08/338,279
• Time in Patent Office: 953 Days
• Field of Search: 435/6, 435/91.2, 435/7.24, 435/7.25, 935/77, 935/78, 536/24.31, 536/25.4, 436/63
• US Class Current: 435/6.11
• CPC Class Codes: C12Q 1/6804 Nucleic acid analysis using immunogens immunoassay G01N33/53
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6841 In situ hybridisation
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 1/6876 Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• CPC Class Codes: C12Q 1/6879 for sex determination
• CPC Class Codes: C12Q 1/6881 for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2543/10 the purpose being "in situ" analysis
• CPC Class Codes: C12Q 2545/113 with an external standard/control, i.e. control reaction is separated from the test/target reaction
• CPC Class Codes: C12Q 2547/00 Reactions characterised by the features used to prevent contamination
• CPC Class Codes: C12Q 2565/137 Chromatographic separation
• CPC Class Codes: C12Q 2565/626 being a flow cytometer
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: G01N 2015/1006 for cytology
• CPC Class Codes: G01N 33/5002 Partitioning blood components
• CPC Class Codes: G01N 33/56966 Animal cells
• CPC Class Codes: G01N 33/56972 White blood cells
• CPC Class Codes: G01N 33/56977 HLA or MHC typing
• CPC Class Codes: G01N 33/80 involving blood groups or blood types or red blood cells white blood cells G01N33/56972

Abstract

A method of detecting the presence or absence of a fetal DNA sequence of interest in fetal DNA derived from a sample of peripheral blood obtained from a pregnant woman is described. The method involves obtaining a sample of peripheral blood from a pregnant woman, treating the sample of peripheral blood such that the fetal DNA present in the fetal nucleated cells is made available for detection and detecting the presence or absence of the fetal DNA sequence of interest in the available fetal DNA. The proportion of fetal nucleated cells present in the sample of peripheral blood can be increased forming a sample enriched in fetal nucleated cells prior to the detection step. The fetal DNA sequence of interest can be detected by treating the peripheral blood sample such that fetal DNA present in the sample is made available for hybridization with a DNA probe and subsequently contacting the available fetal DNA with a DNA probe hybridizable to fetal DNA of interest under hybridization conditions. The presence or absence of hybridization between the DNA probe and the fetal DNA of interest is detected as an indication of the presence or absence of the fetal DNA of interest.

Claims

1. A noninvasive method for facilitating prenatal diagnosis of a chromosomal abnormality in a fetus, comprising:

obtaining a peripheral blood sample from a pregnant woman;

treating the peripheral blood sample to produce an enriched blood sample enriched in fetal nucleated erythrocytes; and

performing in situ hybridization on the enriched blood sample with a chromosome specific probe or a probe specific for abnormal chromosomal DNA to generate spatially resolved signals in individual chromosomes of interphase cells such that diagnosis of a chromosomal abnormality in the fetus is facilitated on the basis of the generated signals.

2. The method of claim 1 wherein the chromosomal abnormality is an aneuploidy.

3. The method of claim 1 wherein the in situ hybridization is fluorescent in situ hybridization.

4. The method of claim 1 wherein the probe is hybridizable to fetal DNA of interest contained in a chromosome selected from the group consisting of chromosomes 13, 18, 21, X, and Y.

5. The method of any one of claims 1-4 wherein the sample is treated in a multistep enrichment process for fetal nucleated erythrocytes.

6. The method of claim 1 wherein the multistep enrichment includes the separation of non-nucleated cells from nucleated cells in the peripheral blood sample from the pregnant woman forming a nucleated cell enriched sample and the treatment of the nucleated cell enriched sample such that the proportion of fetal cells in the sample is increased with respect to the proportion of cells from the pregnant woman forming a sample enriched in fetal nucleated erythrocytes.

7. The method of claim 1 wherein the peripheral blood sample from the pregnant woman is enriched in fetal nucleated cells using density gradient centrifugation.

8. The method of claim 1 wherein the peripheral blood sample from the pregnant woman is enriched in fetal nucleated cells by lysing nonnucleated cells.

9. The method of claim 1 wherein the peripheral blood sample from the pregnant woman is treated for enrichment for fetal nucleated erythrocytes using only a single fetal-specific monoclonal antibody.

10. The method of claim 1 wherein the peripheral blood sample from the pregnant woman is treated for enrichment for fetal nucleated erythrocytes using at least one fetal-specific monoclonal antibody.

11. The method of claim 1 wherein in situ hybridization is performed on a solid support.

12. The method of claims 1 wherein the peripheral blood sample from the pregnant woman is treated by contacting it with a first monoclonal antibody which recognizes fetal nucleated erythrocytes but not cells derived from the peripheral blood sample from the pregnant woman and/or a second monoclonal antibody which recognizes cells derived from the peripheral blood sample from the pregnant woman but not fetal nucleated erythrocytes, under conditions appropriate for antibody binding thereby producing fetal nucleated erythrocyte-first monoclonal antibody complexes and/or pregnant woman cell-second monoclonal antibody complexes, respectively, and

separating fetal nucleated erythrocyte-first monoclonal antibody complexes from pregnant woman cells and/or separating pregnant woman cell-second monoclonal antibody complexes from fetal nucleated erythrocytes thereby separating fetal nucleated erythrocytes from cells derived from the peripheral blood sample from the pregnant woman.

13. The method of claim 12 wherein the first and/or second monoclonal antibody are attached to a solid support.

14. The method of claim 12 wherein the peripheral blood sample from the pregnant woman is obtained when the gestational age of the fetus is about fifteen to seventeen weeks.

15. The method of claim 14 wherein the peripheral blood sample from the pregnant woman is obtained when the gestational age of the fetus is about sixteen weeks.

16. The method of claim 13 wherein the solid support is a magnetizable bead.

17. The method of any of claims 1, 3 or 5-16, wherein the probe is hybridizable to fetal DNA of interest contained in a Y chromosome.

18. The method of any of claims 1, 3 or 5-16, wherein the probe is hybridizable to fetal DNA of interest which is associated with a disease.

19. The method of claim 18 wherein the disease is cystic fibrosis.

20. The method of claim 18 wherein the disease as Duchenne muscular dystrophy.

21. The method of claim 18 wherein the disease is hemophilia A.

22. The method of claim 18 wherein the disease is Gaucher'"'"'s disease.

23. The method of claim 18 wherein the disease is sickle cell anemia.

24. The method of claim 18 wherein the disease is β

thalassemia.

25. The method of claim 18 wherein the disease phenylketonuria.

26. The method of claim 5, wherein the probe is hybridizable to fetal DNA of interest contained in a Y chromosome.