DIAGNOSIS OF FETAL ABNORMALITIES USING POLYMORPHISMS INCLUDING SHORT TANDEM REPEATS

• US 20080050739A1
• Filed: 06/14/2007
• Published: 02/28/2008
• Est. Priority Date: 06/14/2006
• Status: Abandoned Application

• Current Assignee: Verinata Health Incorporated (Illumina Incorporated)
• Original Assignee: Verinata Health Incorporated (Illumina Incorporated)
• Inventors: Cohen, Barb, Stoughton, Roland, Kapur, Ravi
• Application Number:
  US11/763,426
• Publication Number:
  US 20080050739A1
• Time in Patent Office: Days
• US Class Current: 435/6
• 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: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/10 Ploidy or copy number detection
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection

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, i.e. aneuploidy. In addition, the present invention provides methods to determine when there are insufficient fetal cells for a determination and report a non-informative case. The present invention involves quantifying regions of genomic DNA from a mixed sample. More particularly the invention involves quantifying DNA polymorphisms from the mixed sample.

Claims

1. A method for diagnosing a fetal abnormality comprising:

enriching one or more fetal cells from a maternal blood sample using size-based separation,

analyzing one or more regions of genomic DNA from said fetal cells for STRs, and

determining a fetal abnormality based on the STR analysis.

2. The method of claim 1, wherein said enriching comprises applying said sample to a device comprising an array of obstacles on a substrate.

3. The method of claim 1, wherein said enriching comprises applying said sample into a system that separates a first component of said mixed sample in a first direction and a second component of said mixed sample in a second direction, and wherein said first component has a larger hydrodynamic size than said second component.

4. The method of claim 1, wherein said enriching step further comprises performing magnetic separation on the mixed sample.

5. The method of claim 1, wherein said enriching step further comprises performing FACS on the mixed sample.

6. The method of claim 1, wherein said enriching step further comprises performing laser microdissection on the mixed sample.

7. The method of claim 1, wherein said enriching step further comprises performing a magnetic separation on the mixed sample.

8. The method of claim 1, wherein said fetal abnormality is aneuploidy.

10. The method of claim 8, wherein said aneuploidy is trisomy selected from the group consisting of:

trisomy 13, trisomy 18, trisomy 21 (Down Syndrome), Klinefelter Syndrome (XXY), other irregular number of sex or autosomal chromosomes, and a combination thereof.

11. The method of claim 8, wherein whether said aneuploidy is maternally or paternally derived is determined.

12. The method of claim 1, wherein the fetal abnormality is a segmental aneuploidy.

13. The method of claim 1, wherein said fetal abnormality is a condition associated with said regions of genomic DNA.

14. The method of claim 1, wherein said analyzing involves the amplification of one or more regions of genomic DNA by PCR.

15. The method of claim 14, further comprising a pre-PCR step comprising multiple displacement amplification.

16. The method of claim 1, wherein said analyzing of genomic DNA regions is performed by CGE or qPCR.

18. The method of claim 1, wherein said regions of genomic DNA are localized in a specific chromosome.

19. The method of claim 18, wherein said chromosome is selected from the group consisting of:

X chromosome, Y chromosome, chromosome 21, chromosome 13 and chromosome 18.

20. The method of claim 1, wherein said obtaining further comprises enriching fetal cells in said maternal blood sample.

21. The method of claim 20, wherein said enriched fetal cells constitute less than 50% of total cells.

23. The method of claim 1, wherein said determining further comprises inputting data from said comparing step into a predetermined data model for the association of DNA quantity with maternal and non-maternal alleles.

9. (canceled)

17. (canceled)

22. (canceled)

24. A method for diagnosing a fetal abnormality comprising:

enriching one or more fetal cells from a maternal blood sample, wherein said sample is applied to a device comprising an array of obstacles on a substrate,

analyzing one or more regions of genomic DNA from said fetal cells, and

determining a fetal abnormality from the analyzed regions.

25-46. -46. (canceled)

47. A method comprising

comparing levels of genomic DNA from a control sample and a mixed sample comprising at least one fetal cell, wherein the control sample comprises a dilution of said mixed maternal blood sample, and

determining a fetal abnormality from said comparison

48-69. -69. (canceled)

70. A computer program product comprising a computer readable medium having a computer executable logic recorded thereon for enabling a processor to diagnose a fetal abnormality comprising a receiving procedure for receiving data from one of more DNA genomic regions from a mixed sample containing at least one fetal cell,

computer assisted logic for analyzing a fetal abnormality from said received data;

and

an output procedure for generating an output indicating the presence, absence or kind of said fetal abnormality.

71-92. -92. (canceled)

93. A method for determining a fetal condition comprising:

comparing the level of polymorphisms of at least two alleles at two or more loci in a control sample and a test sample comprising fetal cells, wherein said test sample is enriched for fetal cells using size-based separation from a maternal blood sample.

99. The method of claim 93, further comprising

(a) estimating the relative number of fetal and maternal cells in said control sample and said test sample,

(b) relating said level of polymorphisms of at least two alleles at two or more loci to said relative number of maternal and fetal cells, and

(c) determining the presence or absence of trisomy in the sample enriched in fetal cells based on the comparison.

94-98. -98. (canceled)

100-101. -101. (canceled)