Fetal cell analysis using sample splitting

• US 8,168,389 B2
• Filed: 09/02/2008
• Issued: 05/01/2012
• Est. Priority Date: 06/14/2006
• Status: Active Grant

• Current Assignee: Verinata Health Incorporated (Illumina Incorporated), Mehmet Toner, ZEON Corporation
• Original Assignee: Gpb Scientific, LLC, Verinata Health Incorporated (Illumina Incorporated), The General Hospital Corporation (Mass General Brigham, Inc.)
• Inventors: Shoemaker, Daniel, Kapur, Ravi, Toner, Mehmet, Stoughton, Roland, Davis, Ronald W.
• Primary Examiner(s): Woolwine, Samuel
• Application Number:
  US12/230,628
• Publication Number:
  US 20100136529A1
• Time in Patent Office: 1,337 Days
• Field of Search: None
• US Class Current: 435/6.12
• CPC Class Codes: B01L 3/502761 specially adapted for handling suspended solids or molecules independently from the bulk fluid flow, e.g. for trapping or sorting beads, for physically stretching molecules investigating characteristics of particles G01N15/00
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• 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 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 2015/1006 for cytology
• CPC Class Codes: G01N 2015/1029 Particle size
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

The present invention provides systems, apparatuses, and methods to detect the presence of fetal cells when mixed with a population of maternal cells in a sample and to test fetal abnormalities, e.g. aneuploidy. The present invention involves labeling regions of genomic DNA in each cell in said mixed sample with different labels wherein each label is specific to each cell and quantifying the labeled regions of genomic DNA from each cell in the mixed sample. More particularly the invention involves quantifying labeled DNA polymorphisms from each cell in the mixed sample.

Claims

1. A method for performing prenatal diagnosis of a fetal aneuploidy in a blood sample from a human suspected of being pregnant, who is pregnant, or who has been pregnant, the method comprising:

obtaining a mixture of fetal and maternal cells from a blood sample obtained from a human suspected of being pregnant, who is pregnant, or who has been pregnant;

enriching the mixture of cells for fetal cells to obtain a mixed cell preparation enriched for fetal cells;

distributing the enriched mixed cell population into individual reaction samples at discrete addressable locations such that a portion of the reaction samples contain single fetal cells;

identifying reaction samples containing a single fetal cell;

obtaining nucleic acids from the single fetal cells;

sequencing the nucleic acids to produce partial or complete genome sequences;

based on the sequences, quantifying DNA regions from a chromosome suspected of being aneuploid in the fetus; and

determining the presence or absence of a fetal aneuploidy from the quantitation of the chromosomal DNA regions.

2. The method of claim 1, wherein said sequencing is ultra-deep sequencing, wherein said ultra-deep sequencing comprises amplifying the nucleic acids obtained from the single fetal cells to produce at least one million copies of individual nucleic acid molecules and sequencing said at least one million copies of individual nucleic acid molecules in parallel.

3. The method of claim 2, wherein DNA amplification is conducted prior to the ultra-deep sequencing.

4. The method of claim 3, wherein DNA amplification is whole genome amplification.

5. The method of claim 4, wherein the fetal aneuploidy is aneuploidy of a chromosome selected from a group consisting of chromosome 21, chromosome 18, chromosome 13, chromosome X, or chromosome Y.

6. The method of claim 2, wherein the fetal aneuploidy is trisomy of chromosome 18.

7. The method of claim 2, wherein the fetal aneuploidy is trisomy of chromosome 13.

8. The method of claim 2, wherein the fetal aneuploidy is trisomy of chromosome X.

9. The method of claim 2, wherein the fetal aneuploidy is trisomy of chromosome 21.

10. The method of claim 2, wherein the fetal aneuploidy is aneuploidy of chromosome X or chromosome Y.

11. The method of claim 2, wherein the fetal aneuploidy is trisomy XXY.

12. The method of claim 2, wherein the fetal aneuploidy is trisomy XYY.

13. The method of claim 2, wherein the fetal aneuploidy is a monosomy of one or more chromosomes.

14. The method of claim 2, wherein said sequencing is sequencing-by-synthesis.

15. The method of claim 1, wherein the fetal aneuploidy is trisomy of a chromosome selected from a group consisting of chromosome 21, chromosome 18, chromosome 13, and chromosome X.

16. The method of claim 15, wherein the fetal aneuploidy is trisomy of chromosome 21.

17. The method of claim 1, wherein quantifying DNA regions further comprises determining abundance of selected alleles.

18. The method of claim 17, wherein the selected alleles are Short Tandem Repeat (STR) alleles.

19. The method of claim 17, wherein the selected alleles are Single Nucleotide Polymorphism (SNP) alleles.

20. The method of claim 17, further comprising:

obtaining genomic DNA from a sample of maternal cells; and

determining abundance of selected alleles in the maternal genomic DNA.