Rare cell analysis using sample splitting and DNA tags

• US 8,372,584 B2
• Filed: 06/14/2007
• Issued: 02/12/2013
• 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, Toner, Mehmet, Kapur, Ravi, Stoughton, Roland
• Primary Examiner(s): WOOLWINE, SAMUEL C
• Application Number:
  US11/763,421
• Publication Number:
  US 20080220422A1
• Time in Patent Office: 2,070 Days
• Field of Search: None
• US Class Current: 435/6.1
• 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 of determining a presence or absence of a fetal aneuploidy in a fetus by analysis of a maternal blood sample obtained from a pregnant woman comprising a mixture of fetal and maternal cells, the method comprising:

(a) enriching a mixture of fetal and maternal cells of a maternal blood sample for fetal cells to obtain a mixed cell preparation enriched for fetal cells;

(b) splitting the mixed cell preparation of step (a) into at least 100 discrete portions and directing the discrete portions to different locations;

(c) identifying at least one location that contains a single fetal cell and obtaining genomic DNA from the single fetal cell at the at least one identified location;

(d) amplifying fetal genomic DNA obtained from the single fetal cell at the at least one identified location;

(e) sequencing the fetal genomic DNA of step (d) to generate sequence data; and

(f) determining the presence or absence of a fetal aneuploidy from the sequence data of step (e), wherein said determining comprises analyzing the sequence data using computer executable logic recorded on a computer readable medium.

2. The method of claim 1, wherein the fetal aneuploidy is trisomy of chromosome 21.

3. The method of claim 1, wherein the mixed cell preparation of step (a) is split into at least 200 discrete portions.

4. The method of claim 3, wherein the mixed cell preparation of step (a) is split into at least 1000 discrete portions.

5. The method of claim 1, wherein the locations are addressable locations on a matrix.

6. The method of claim 1, wherein the chromosome is selected from the group consisting of chromosome 21, chromosome 18, chromosome 13, chromosome X, and chromosome Y.

7. The method of claim 1, further comprising determining an abundance of alleles from the sequence data of step (e).

8. The method of claim 7, wherein the alleles comprise Short Tandem Repeat (STR) alleles.

9. The method of claim 7, wherein the alleles comprise Single Nucleotide Polymorphism (SNP) alleles.

10. The method of claim 1, wherein the fetal genomic DNA is amplified by whole genome amplification.

11. The method of claim 10, wherein the chromosome is selected from the group consisting of chromosome 21, chromosome 18, chromosome 13, chromosome X, and chromosome Y.

12. The method of claim 11, wherein the fetal aneuploidy is trisomy 21.

13. The method of claim 11, wherein the fetal aneuploidy is trisomy 18.

14. The method of claim 11, wherein the fetal aneuploidy is trisomy 13.

15. The method of claim 1, wherein step (d) comprises amplifying regions of fetal genomic DNA of a chromosome suspected of being aneuploid in the fetus and wherein analyzing the sequencing data of step (f) comprises quantifying the amplified DNA regions of the chromosome suspected of being aneuploid in the fetus.

16. The method of claim 15, wherein an aneuploidy region is an entire chromosome.

17. The method of claim 1, wherein said sequencing comprises single-molecule sequencing.

18. The method of claim 1, wherein said sequencing comprises sequencing-by-synthesis.

19. The method of claim 1, wherein the fetal aneuploidy is monosomy X.

20. The method of claim 1, wherein the fetal aneuploidy comprises monosomy, trisomy, tetrasomy, or pentasomy of one or more chromosomes.

21. The method of claim 1, wherein the fetal aneuploidy comprises segmental aneuploidy.