Back to results
US 2023/0111097 A1Published application
Array-based methods for analysing mixed samples using different allele-specific labels, in particular for detection of fetal aneuploidies
AssigneeAffymetric, Inc.
InventorsJeanette SCHMIDT, Orna MIZRAHI MAN, Jiang LI
Life of this patent
Estimating the term…
Abstract
Provided includes methods and systems useful in array-based analysis of mixed nucleic acid populations, including for genotyping and copy number analysis of the various subpopulations of the mixed nucleic acid population. Also provided includes methods and systems useful in the diagnosis of genetic abnormalities in a mixed nucleic acid population taken from an organism.
Claims20
A system for analyzing a nucleic acid sample obtained from a pregnant female, the system comprising
- (a) a probe microarray comprising
- a plurality of probes configured to hybridize to a target nucleic acid from a target chromosome, the target nucleic acid comprising a polymorphic site, the plurality of probes comprising first probes configured to hybridize to a first allelic variant (“A allele”) of the target nucleic acid and comprising second probes configured to hybridize to a second allelic variant (“B allele”) of the target nucleic acid, wherein the polymorphic site can be homozygous for the A allele (“AA”), homozygous for the B allele (“BB”), or heterozygous (“AB”),
- the probe microarray being configured to generate first signals indicative of hybridization of one or more first probes to one or more target nucleic acids comprising the first allelic variant, and to generate second signals indicative of hybridization of one or more second probes to one or more target nucleic acids comprising the second allelic variant;
- (b) a scanner configured to detect the signals generated by the probe microarray according to a first channel for the first signals and a second channel for the second signals;
- and
- (c) a computer communicatively coupled to the scanner, the computer comprising a processor and memory, the memory encoded with instructions which are executable by the processor to cause the computer to at least:
- receive first signal and second signal data from the scanner, and
- determine, using the first signal and second signal data, one or more of:
- (i) a copy number of the target chromosome in a fetus,
- (ii) a fetal genotype for the SNP,
- (iii) a maternal genotype for the SNP, or
- (iv) a fetal fraction of the sample.
9 more elements
A system for analyzing a mixed nucleic acid sample comprising a major subpopulation and a minor subpopulation, the system comprising:
- (a) a probe microarray comprising:
- a plurality of probes configured to hybridize to a target nucleic acid from a target chromosome, the target nucleic acid comprising a polymorphic site, the plurality of probes comprising first probes configured to hybridize to a first allelic variant (“A allele”) of the target nucleic acid and comprising second probes configured to hybridize to a second allelic variant (“B allele”) of the target nucleic acid, wherein the polymorphic site can be homozygous for the A allele (“AA”), homozygous for the B allele (“BB”), or heterozygous (“AB”),
- the probe microarray being configured to generate first signals indicative of hybridization of one or more first probes to one or more target nucleic acids comprising the first allelic variant, and to generate second signals indicative of hybridization of one or more second probes to one or more target nucleic acids comprising the second allelic variant;
- (b) a scanner configured to detect the signals generated by the probe microarray according to a first channel for the first signals and a second channel for the second signals;
- and
- (c) a computer communicatively coupled to the scanner, the computer comprising a processor and memory, the memory encoded with instructions which are executable by the processor to cause the computer to at least:
- receive first signal and second signal data from the scanner, and
- determine the copy number of the target chromosome in the minor subpopulation using the first signal and the second signal.
5 more elements
Dependencies are inferred from the claim text.