Methods for the diagnosis of fetal abnormalities

• US 10,435,751 B2
• Filed: 07/26/2018
• Issued: 10/08/2019
• Est. Priority Date: 06/14/2006
• Status: Active Grant

• Current Assignee: Gpb Scientific, LLC, The General Hospital Corporation (Mass General Brigham, Inc.)
• Original Assignee: Verinata Health Incorporated (Illumina Incorporated)
• Inventors: Kapur, Ravi, Toner, Mehmet, Wang, Zihua, Fuchs, Martin
• Primary Examiner(s): Thomas, David C
• Application Number:
  US16/046,047
• Publication Number:
  US 20180327847A1
• Time in Patent Office: 439 Days
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• 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
• CPC Class Codes: G01N 1/30 Staining; Impregnating ; Fixation; Dehydration; Multistep processes for preparing samples of tissue, cell or nucleic acid material and the like for analysis
• CPC Class Codes: G01N 2800/385 Congenital anomalies
• CPC Class Codes: G01N 33/6893 related to diseases not provided for elsewhere

Abstract

The present invention relates to methods for detecting, enriching, and analyzing rare cells that are present in the blood, e.g. fetal cells. The invention further features methods of analyzing rare cell(s) to determine the presence of an abnormality, disease or condition in a subject, e.g. a fetus by analyzing a cellular sample from the subject.

Claims

1. A method for determining the presence or absence of a fetal aneuploidy using a maternal blood sample comprising a mixture of fetal and maternal genomic nucleic acids, the method comprising:

a. obtaining a test sample comprising a mixture of fetal and maternal genomic nucleic acids from a maternal blood sample;

b. selectively amplifying a plurality of target nucleic acids from the test sample and a plurality of target nucleic acids from a reference sample using primers labeled with a unique label for each target region, thereby generating amplification products, wherein the target nucleic acids are selected from one or more chromosomes to be tested for aneuploidy, and wherein the reference sample is diploid for the one or more chromosomes to be tested for aneuploidy;

c. amplifying the amplification products using universal primers;

d. detecting the amplified target nucleic acids from the test sample and from the reference sample;

e. quantifying the detected amplified target nucleic acids from the test sample and from the reference sample;

f. analyzing the test sample for the presence or absence of a fetal aneuploidy by comparing the quantity of the detected amplified target nucleic acids obtained from the test sample for the one or more chromosomes tested for aneuploidy to the quantity of the detected amplified target nucleic acids obtained from the reference sample for the one or more chromosomes tested for aneuploidy; and

g. generating a report on the presence or absence of aneuploidy in the maternal blood sample.

2. The method of claim 1, wherein the target nucleic acids are selected from one or more of chromosomes X, Y, 13, 18, and 21.

3. The method of claim 1, wherein the target nucleic acid sequences are quantified by chromatography, electrophoresis, comparative genomic hybridization (CGH), microarrays, or bead arrays.

4. The method of claim 3, wherein the chromatography is selected from gas chromatography, supercritical fluid chromatography, and liquid chromatography.

5. The method of claim 3, wherein the electrophoresis is selected from capillary electrophoresis, capillary zone electrophoresis, capillary isoelectric focusing, capillary electrochromatography, micellar electrokinetic capillary chromatography, isotachophoresis, transient isotachophoresis, and capillary gel electrophoresis.

6. The method of claim 1, wherein the target nucleic acid sequences are quantified using molecular inversion probes (MIPs).

7. The method of claim 3, wherein the target nucleic acid sequences are quantified using a microarray.

8. The method of claim 7, wherein the microarray is used to detect at least 5, 10, 20, 50, 100, 500, 1,000, 2,000, 5,000, 10,000, 20,000, 50,000, 100,000, 200,000, or 500,000 different target nucleic acids.

9. The method of claim 1, wherein the chromosomes are tested for any one or more of fetal trisomy 13, trisomy 18, or trisomy 21.

10. The method of claim 1, wherein the target nucleic acids are single nucleotide polymorphisms (SNPs), short tandem repeats (STRs), or RNA transcripts.

11. The method of claim 1, wherein the amplification comprises:

hybridizing one set of oligonucleotides per target nucleic acid, wherein each set comprises two or more oligonucleotides that each hybridize to different regions within the target nucleic acid

ligating the two or more hybridized oligonucleotide probes for each of the target nucleic acids to create amplification templates for each of the target nucleic acids; and

amplifying the amplification templates.

12. The method of claim 11, further comprising attaching biotin to the target nucleic acids to generate biotin-labeled target nucleic acids.

13. The method of claim 12, further comprising attaching the biotin-labeled target nucleic acids to a streptavidin coated solid support.

14. The method of claim 1, wherein quantifying the target nucleic acids further comprises determining a gene or allele copy number or both a gene copy number and an allele copy number.

15. The method of claim 14, further comprising determining fetal trisomy or monosomy based on the gene or allele copy number or the gene copy number and the allele copy number determination.

16. A method of determining the presence or absence of a fetal aneuploidy using a maternal blood sample comprising a mixture of fetal and maternal genomic nucleic acids, the method comprising:

a. obtaining a mixture of fetal and maternal genomic nucleic acids from a maternal blood sample;

b. hybridizing genomic nucleic acids with one set of oligonucleotides per target nucleic acid, wherein each set comprises two or more oligonucleotides that each hybridize to different regions within the target nucleic acid and wherein each oligonucleotide comprises a universal polymerase chain reaction (PCR) primer site to produce hybridization products;

c. processing the hybridization products to provide a template for amplification;

d. amplifying the hybridization products using primers with a unique label for each target region, thereby generating amplification products;

e. amplifying the amplification products using universal primers;

f. hybridizing the single-stranded, labeled nucleic acids to complementary nucleic acids on an array or bead;

g. detecting labels on the array or beads and analyzing the labels to determine genotypes of the nucleic acids; and

h. generating a report on the presence or absence of aneuploidy in the maternal blood sample based on the genotype analysis.

17. The method of claim 16, wherein the genomic nucleic acids are from one or more of chromosomes X, Y, 13, 18, and 21.

18. The method of claim 16, wherein the fetal aneuploidy is a trisomy or a monosomy.

19. The method of claim 18, wherein the trisomy is trisomy 13, trisomy 18, or trisomy 21.

20. The method of claim 16, further comprising enriching the mixture of fetal and maternal genomic nucleic acids for fetal genomic nucleic acids.

21. The method of claim 16, further comprising labeling the fetal and maternal genomic nucleic acids with biotin and immobilizing the biotin-labeled genomic nucleic acids to a solid support prior to step b.

22. The method of claim 21, wherein the solid support comprises a streptavidin coating.

23. The method of claim 21, wherein the solid support is a bead or particle.

24. The method of claim 16, wherein the array is a microarray.

25. The method of claim 24, wherein the microarray is used to detect at least 5, 10, 20, 50, 100, 500, 1,000, 2,000, 5,000, 10,000, 20,000, 50,000, 100,000, 200,000, or 500,000 different labeled nucleic acids.

26. The method of claim 16, wherein the labeled nucleic acids are quantified using molecular inversion probes (MIPs).