Diagnosis of fetal abnormalities using polymorphisms including short tandem repeats

• US 10,591,391 B2
• Filed: 03/14/2013
• Issued: 03/17/2020
• Est. Priority Date: 06/14/2006
• Status: Active Grant

• Current Assignee: Gpb Scientific, LLC, Verinata Health Incorporated (Illumina Incorporated), The General Hospital Corporation (Mass General Brigham, Inc.)
• Original Assignee: Verinata Health Incorporated (Illumina Incorporated)
• Inventors: Stoughton, Roland, Kapur, Ravi, Cohen, Barb Ariel, Shoemaker, Daniel, Davis, Ronald W., Toner, Mehmet
• Primary Examiner(s): Strzelecka, Teresa E
• Application Number:
  US13/830,871
• Publication Number:
  US 20130280709A1
• Time in Patent Office: 2,560 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: 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 of analyzing a fetal blood cell in a maternal blood sample obtained from a pregnant human female, the method comprising:

(a) obtaining the maternal blood sample;

(b) enriching the maternal blood sample for fetal blood cells to produce an enriched sample comprising fetal blood cells and maternal blood cells, wherein the enrichment increases the ratio of fetal cells to maternal cells to about 1/10,000 to about 1/10;

(c) binning fetal blood cells and maternal blood cells from the enriched sample by serial dilution, wherein the binning results in at least one bin containing an individual fetal blood cell from the enriched sample;

(d) identifying bins that contain at least one fetal blood cell using one or more fetal blood cell biomarkers;

(e) lysing fetal blood cells in the identified bins;

(f) amplifying the genomes of the lysed fetal blood cells in the identified bins to produce amplified nucleic acids; and

(g) analyzing the amplified nucleic acids in bins that contain at least one fetal cell for aneuploidy using ultra-deep sequencing.

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

3. The method of claim 2, wherein the fetal aneuploidy is a fetal aneuploidy of a chromosome selected from the group consisting of chromosome 13, chromosome 18, chromosome 21, chromosome X, and chromosome Y.

4. The method of claim 2, wherein the fetal aneuploidy comprises trisomy or monosomy.

5. The method of claim 4, wherein the fetal aneuploidy comprises trisomy, and wherein the trisomy comprises trisomy 13, trisomy 18, or trisomy 21.

6. The method of claim 4, wherein the fetal aneuploidy comprises monosomy X and the chromosome suspected of being aneuploid comprises chromosome X.

7. The method of claim 1, wherein the fetal aneuploidy comprises XXX, XXY, or XYY.

8. The method of claim 1, wherein the ultra-deep sequencing produces partial genome sequences for analysis.

9. The method of claim 1, wherein the ultra-deep sequencing produces complete genome sequences for analysis.

10. The method of claim 1, wherein the whole genomes of the lysed fetal blood cells are amplified.

11. The method of claim 1, wherein the binning comprises use of a nanofluidic system.

12. The method of claim 11, wherein the nanofluidic system separates samples into droplets.

13. The method of claim 1, wherein the binning is preceded by positive selection for fetal cells.

14. The method of claim 1, wherein the binning is preceded by negative selection for non-target cells.

15. The method of claim 1, wherein the enrichment increases the ratio of fetal cells to maternal cells to about 1/100 to about 1/10.

16. The method of claim 1, wherein the enrichment increases the ratio of fetal cells to maternal cells to about 1/50 to about 1/10.

17. The method of claim 1, wherein the enrichment increases the ratio of fetal cells to maternal cells to about 1/10.