System and method for cleaning noisy genetic data and determining chromosome copy number
First Claim
1. A method of detecting aneuploidy of one or more chromosomes of interest in a fetus, the method comprising:
- obtaining fetal and maternal chromosome segments from cell-free DNA in a maternal blood sample comprising chromosome segments from the one or more chromosomes of interest and chromosome segments from one or more reference chromosomes;
ligating at least one adapter comprising a universal amplification sequence to the chromosome segments to obtain adapter-ligated chromosome segments;
performing universal amplification of the adapter-ligated chromosome segments to generate amplified chromosome segments;
measuring the amounts of the amplified chromosome segments; and
detecting aneuploidy of the one or more chromosomes of interest using the amounts of amplified chromosome segments from the one or more chromosomes of interest and the amounts of amplified chromosome segments from the one or more reference chromosomes.
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Abstract
Disclosed herein is a system and method for increasing the fidelity of measured genetic data, for making allele calls, and for determining the state of aneuploidy, in one or a small set of cells, or from fragmentary DNA, where a limited quantity of genetic data is available. Poorly or incorrectly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target genome and the genome of genetically related individuals. In accordance with one embodiment, incomplete genetic data from an embryonic cell are reconstructed at a plurality of loci using the more complete genetic data from a larger sample of diploid cells from one or both parents, with or without haploid genetic data from one or both parents. In another embodiment, the chromosome copy number can be determined from the measured genetic data, with or without genetic information from one or both parents.
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Citations
11 Claims
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1. A method of detecting aneuploidy of one or more chromosomes of interest in a fetus, the method comprising:
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obtaining fetal and maternal chromosome segments from cell-free DNA in a maternal blood sample comprising chromosome segments from the one or more chromosomes of interest and chromosome segments from one or more reference chromosomes; ligating at least one adapter comprising a universal amplification sequence to the chromosome segments to obtain adapter-ligated chromosome segments; performing universal amplification of the adapter-ligated chromosome segments to generate amplified chromosome segments; measuring the amounts of the amplified chromosome segments; and detecting aneuploidy of the one or more chromosomes of interest using the amounts of amplified chromosome segments from the one or more chromosomes of interest and the amounts of amplified chromosome segments from the one or more reference chromosomes. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11)
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Specification