Fetal aneuploidy detection by sequencing

Patent metadata

Field	Value
Publication number	US-11674176-B2
Application number	US-202016917185-A
Country	US
Kind code	B2
Filing date	Jun 30, 2020
Priority date	Jun 14, 2006
Publication date	Jun 13, 2023
Grant date	Jun 13, 2023

Abstract

The present invention provides apparatus and methods for enriching components or cells from a sample and conducting genetic analysis, such as SNP genotyping to provide diagnostic results for fetal disorders or conditions.

First claim

What is claimed is:

1. A method for determining a ratio of signal intensities of amplification products for a maternal allele in a first genomic region on a first chromosome suspected of being aneuploid and for a maternal allele in a second genomic region on a second chromosome that is not aneuploid or not suspected of being aneuploid in a mixed sample comprising a mixture of fetal and maternal cells, the method comprising:
a. enriching the mixed sample for fetal cells to produce an enriched sample comprising fetal and maternal cells having an increased concentration of fetal cells relative to maternal cells before enrichment, and lysing cells in the enriched sample to obtain genomic DNA (gDNA);
b. hybridizing probes to each of a plurality of loci in the gDNA on at least two different chromosomes to produce hybridized probes;
c. ligating the hybridized probes at each locus to each other to create an amplification template specific to each locus;
d. amplifying the amplification template specific to each locus to create amplification products;
e. hybridizing the amplification products to probes on a microarray; and
f. detecting, among the amplification products hybridized to probes on the microarray, a first signal intensity of the amplification products for a maternal allele in a first genomic region on a first chromosome suspected of being aneuploid and a second signal intensity of the amplification products for a maternal allele in a second genomic region on a second chromosome that is not aneuploid or not suspected of being aneuploid, and determining a ratio of the first signal intensity to the second signal intensity.

2. The method of claim 1 , wherein the mixed sample comprises a maternal blood sample from a pregnant woman within a first or second trimester.

3. The method of claim 1 , further comprising attaching the gDNA to a solid support.

4. The method of claim 3 , wherein the solid support comprises a paramagnetic particle.

5. The method of claim 3 , wherein the solid support comprises streptavidin.

6. The method of claim 3 , wherein the gDNA is biotin-labeled.

7. The method of claim 1 , wherein three oligonucleotide probes are provided for each locus.

8. The method of claim 1 , wherein the gDNA is attached to a particle and the ligation occurs while the gDNA is attached to the particle, thereby forming an amplification template annealed to the gDNA attached to the particle.

9. The method of claim 8 , further comprising releasing the amplification template from the gDNA attached to the particle.

10. The method of claim 1 , wherein the amplification template comprises universal polymerase chain reaction (PCR) primer sites and the amplification comprises hybridization of universal primers to the universal PCR primer sites.

11. The method of claim 1 , wherein the microarray is a DNA microarray.

Assignees

• Verinata Health Inc
• Massachusetts Gen Hospital
• Gpb Scientific Llc

Inventors

• Stoughton Roland
• Kapur Ravi
• Cohen Barb Ariel
• Toner Mehmet

Classifications

• C12Q1/6883 Primary

  for diseases caused by alterations of genetic material · CPC title

• C12Q2600/156

  Polymorphic or mutational markers · CPC title

• C12Q1/6874 Primary

  involving nucleic acid arrays, e.g. sequencing by hybridisation · CPC title