Prenatal Diagnosis Using Cell-Free Fetal DNA in Amniotic Fluid
First Claim
1. A method of prenatal diagnosis comprising steps of:
- providing a sample of amniotic fluid fetal DNA;
analyzing the amniotic fluid fetal DNA by hybridization to obtain fetal genomic information; and
based on the fetal genomic information obtained, providing a prenatal diagnosis.
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Abstract
The present invention relates to improved methods of prenatal diagnosis, screening, monitoring and/or testing. The inventive methods include the analysis by array-based hybridization of cell-free fetal DNA isolated from amniotic fluid. In addition to allowing the prenatal diagnosis of a variety of diseases and conditions, and the assessment of fetal characteristics such as fetal sex and chromosomal abnormalities, the new inventive methods provide substantially more information about the fetal genome in less time than it takes to perform a conventional metaphase karyotype analysis. In particular, the enhanced molecular karyotype methods provided by the present invention allow the detection of chromosomal aberrations that are not often detected prenatally such as microdeletions, microduplications and subtelomeric rearrangements.
253 Citations
137 Claims
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1. A method of prenatal diagnosis comprising steps of:
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providing a sample of amniotic fluid fetal DNA;
analyzing the amniotic fluid fetal DNA by hybridization to obtain fetal genomic information; and
based on the fetal genomic information obtained, providing a prenatal diagnosis. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42)
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43. A method of prenatal diagnosis performed by analyzing amniotic fluid fetal DNA by array-based comparative genomic hybridization, the method comprising steps of:
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providing a test sample of amniotic fluid fetal DNA, wherein the test sample comprises a plurality of nucleic acid segments comprising a substantially complete first genome with an unknown karyotype and labeled with a first detectable agent;
providing a reference sample, wherein the reference sample comprises a plurality of nucleic acid segments comprising a substantially complete second genome with a known karyotype and labeled with a second detectable agent;
providing an array comprising a plurality of genetic probes, wherein each genetic probe is immobilized to a discrete spot on a substrate surface to form the array and wherein together the genetic probes comprise a substantially complete third genome or a subset of a third genome;
contacting the array simultaneously with the test and reference samples under conditions wherein the nucleic acid segments in the samples can specifically hybridize to the genetic probes on the array;
determining the binding of the individual nucleic acids of the test sample and reference sample to the individual genetic probes immobilized on the array to obtain a relative binding pattern; and
based on the relative binding pattern obtained, providing a prenatal diagnosis. - View Dependent Claims (44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83)
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84. A method of testing amniotic fluid fetal DNA by array-based comparative genomic hybridization comprising steps of:
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providing a test sample of amniotic fluid fetal DNA, wherein the test sample comprises a plurality of nucleic acid segments comprising a substantially complete first genome with a chromosomal micro-abnormality and labeled with a first detectable agent;
providing a reference sample of control genomic DNA, wherein the reference sample comprises a plurality of nucleic acid segments comprising a substantially complete second genome with a known karyotype and labeled with a second detectable agent;
providing an array comprising a plurality of genetic probes, wherein each genetic probe is immobilized to a discrete spot on a substrate surface to form the array and wherein together the genetic probes comprise a substantially complete third genome or a subset of a third genome;
contacting the array simultaneously with the test sample and reference sample under conditions wherein the nucleic acid segments of the test and reference samples can specifically hybridize to the genetic probes immobilized on the array;
using a computer-assisted imaging system capable of acquiring multicolor fluorescence images to obtain a fluorescence image of the array after hybridization;
using a computer-assisted image analysis system to analyze the fluorescence image obtained, to interpret data imaged from the array and to display results as genome copy number ratios as a function of genomic locus in the third genome;
determining the karyotype of the first genome by FISH analysis; and
comparing the results displayed as genome copy number ratios to the karyotype of the first genome determined by FISH. - View Dependent Claims (85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103)
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104. A method for identifying a chromosomal abnormality by analyzing amniotic fluid fetal DNA by array-based comparative genomic hybridization, the method comprising steps of:
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providing a test sample of amniotic fluid fetal DNA, wherein the amniotic fluid fetal DNA originates from a fetus determined to have multiple congenital anomalies by sonographic examination, and wherein the test sample comprises a plurality of nucleic acid segments comprising a substantially complete first genome with a normal karyotype and labeled with a first detectable agent;
providing a reference sample of control amniotic fluid fetal DNA, wherein the control amniotic fluid fetal DNA originates from a fetus determined to have no congenital anomalies by sonographic examination, and wherein the reference sample comprises a plurality of nucleic acid segments comprising a substantially complete second genome with a normal karyotype and labeled with a second detectable agent;
providing an array comprising a plurality of genetic probes, wherein each genetic probe is immobilized to a discrete spot on a substrate surface to form the array and wherein together the genetic probes comprise a substantially complete third genome or a subset of a third genome;
contacting the array simultaneously with the test sample and reference sample under conditions wherein the nucleic acid segments in the samples can specifically hybridize to the genetic probes immobilized on the array;
using a computer-assisted imaging system capable of acquiring multicolor fluorescence images to obtain a fluorescence image of tie array after hybridization;
using a computer-assisted image analysis system to analyze the fluorescence image obtained, to interpret data imaged from the array and to display results as genome copy number ratios as a function of genomic locus in the third genome; and
analyzing the results displayed to detect and identify any chromosomal abnormality present. - View Dependent Claims (105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137)
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Specification