System and method for cleaning noisy genetic data and determining chromosome copy number
DCFirst Claim
1. A method for measuring the amounts of fetal chromosome segments in a maternal blood sample, comprising:
- obtaining cell-free DNA comprising fetal and maternal chromosome segments from the maternal blood sample;
performing universal amplification on the chromosome segments to generate amplified chromosome segments;
performing clonal amplification on the amplified chromosome segments to generate clonally amplified chromosome segments; and
measuring the amounts of clonally amplified fetal chromosome segments by performing next-generation sequencing.
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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.
302 Citations
13 Claims
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1. A method for measuring the amounts of fetal chromosome segments in a maternal blood sample, comprising:
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obtaining cell-free DNA comprising fetal and maternal chromosome segments from the maternal blood sample; performing universal amplification on the chromosome segments to generate amplified chromosome segments; performing clonal amplification on the amplified chromosome segments to generate clonally amplified chromosome segments; and measuring the amounts of clonally amplified fetal chromosome segments by performing next-generation sequencing. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13)
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Specification