DETECTION OF GENETIC ABNORMALITIES
First Claim
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1. An assay system for detection of the presence or absence of a fetal chromosomal abnormality comprising the steps of:
- providing a mixed sample comprising cell free DNA;
isolating two or more selected non-polymorphic nucleic acid regions from a first genomic region of interest in the mixed sample;
isolating two or more selected non-polymorphic nucleic acid regions from a second genomic region of interest in the mixed sample;
amplifying the selected nucleic acid regions from the first and second genomic regions using one or more rounds of amplification;
detecting the amplified nucleic acid regions;
quantifying a relative frequency of the selected nucleic acid regions from the first and second genomic regions of interest;
comparing the relative frequency of the selected nucleic acid regions from the first and second genomic regions of interest; and
identifying the presence or absence of a fetal chromosomal abnormality based on the compared relative frequency.
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Abstract
The present invention provides assay systems and related methods for determining genetic abnormalities in mixed samples comprising cell free DNA from both normal and putative genetically atypical cells. Exemplary mixed samples for analysis using the assay systems of the invention include samples comprising both maternal and fetal cell free DNA and samples that contain DNA from normal cells and circulating cancerous cells.
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Citations
48 Claims
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1. An assay system for detection of the presence or absence of a fetal chromosomal abnormality comprising the steps of:
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providing a mixed sample comprising cell free DNA; isolating two or more selected non-polymorphic nucleic acid regions from a first genomic region of interest in the mixed sample; isolating two or more selected non-polymorphic nucleic acid regions from a second genomic region of interest in the mixed sample; amplifying the selected nucleic acid regions from the first and second genomic regions using one or more rounds of amplification; detecting the amplified nucleic acid regions; quantifying a relative frequency of the selected nucleic acid regions from the first and second genomic regions of interest; comparing the relative frequency of the selected nucleic acid regions from the first and second genomic regions of interest; and identifying the presence or absence of a fetal chromosomal abnormality based on the compared relative frequency. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12)
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13. An assay system for detection of the presence or absence of a fetal aneuploidy comprising the steps of:
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providing a mixed sample comprising cell free DNA; isolating two or more selected non-polymorphic nucleic acid regions from a first chromosome of interest in the mixed sample; isolating two or more selected non-polymorphic nucleic acid regions from a second chromosome of interest in the mixed sample; amplifying the selected nucleic acid regions from the first and second chromosomes using one or more rounds of amplification; detecting the amplified nucleic acid regions; quantifying a relative frequency of the selected nucleic acid regions from the first and second chromosomes of interest; comparing the relative frequency of the selected nucleic acid regions from the first and second chromosomes of interest; and identifying the presence or absence of an aneuploidy based on the compared relative frequencies of the first and second chromosome of interest. - View Dependent Claims (14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25)
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26. An assay system for detection of the presence or absence of a fetal aneuploidy comprising the steps of:
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providing a maternal sample comprising maternal and fetal cell free DNA; selectively amplifying two or more nucleic acid regions from a first chromosome of interest in the maternal sample; selectively amplifying two or more nucleic acid regions from a second chromosome of interest in the maternal sample; detecting the amplified nucleic acid regions; quantifying a relative frequency of the selected nucleic acid regions from the first and second chromosomes of interest; comparing the relative frequency of the selected nucleic acid regions from the first and second chromosomes of interest; and identifying the presence or absence of a fetal aneuploidy based on the compared relative frequencies of the selected nucleic acid regions. - View Dependent Claims (27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38)
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39. An assay system for detection of the presence or absence of a fetal aneuploidy comprising the steps of:
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providing a maternal sample comprising maternal and fetal cell free DNA; selectively amplifying two or more nucleic acid regions from a chromosome of interest in the maternal sample; selectively amplifying two or more nucleic acid regions from a reference chromosome in the maternal sample; determining a relative frequency of the selected nucleic acid regions from the chromosomes of interest and the reference chromosome; comparing the relative frequency of the selected nucleic acid regions from the chromosomes of interest and the reference chromosome; and identifying the presence or absence of a fetal aneuploidy based on the compared relative frequencies of the selected nucleic acid regions. - View Dependent Claims (40, 41, 42, 43, 44, 45, 46, 47, 48)
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Specification