US 10,240,202 B2 · System and method for cleaning noisy genetic data from target individuals using genetic data from genetically related individuals

Abstract

A system and method for determining the genetic data for one or a small set of cells, or from fragmentary DNA, where a limited quantity of genetic data is available, are disclosed. Genetic data for the target individual is acquired and amplified using known methods, and poorly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target genome and the genome of genetically related subjects. In accordance with one embodiment of the invention, incomplete genetic data is acquired from embryonic cells, fetal cells, or cell-free fetal DNA isolated from the mother's blood, and the incomplete genetic data is reconstructed using the more complete genetic data from a larger sample diploid cells from one or both parents, with or without genetic data from haploid cells from one or both parents, and/or genetic data taken from other related individuals.

Claims20

Dependent claims

A method for detecting aneuploidy in a fetus, the method comprising:

(a) measuring the amounts of genetic material at multiple loci on a chromosome or chromosome segment of interest in a sample comprising cell-free DNA derived from the fetus and from the mother of the fetus, wherein the measuring comprises amplifying at least 70 loci in a single reaction and using microarray or sequencing to detect amplified reaction products, and wherein the amount of genetic material at a particular locus is determined irrespective of the identity of the alleles at that locus;
(b) determining, on a computer, the probability of aneuploidy in the fetus by comparing the measured amounts of genetic material to an expected amount for a particular copy number;
and
(c) outputting the selected probability as an indication of whether the fetus has aneuploidy.

1 more element

Dependencies are inferred from the claim text.

Facts

Application

15/191,197Filed 23 Jun 2016 · continuation

Priority

26 Nov 2005

Published

US 2016/0369345 A122 Dec 2016

Granted

26 Mar 2019

Term ends

Not estimatedThe source records don’t support an estimate.

Classification14 codes

C12Q 1/6883
Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes: for diseases caused by alterations of genetic material
C12Q 1/6827
Hybridisation assays: for detection of mutation or polymorphism
C12Q 1/6876
Involving nucleic acids: nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
G16B 20/00
Ict specially adapted for functional genomics or proteomics

Family

Application60/739,882Us provisional application · filed 26 Nov 2005

Application60/846,610Us provisional application · filed 22 Sep 2006

Application11/603,406Parent of this continuation · filed 22 Nov 2006

Application13/793,133Parent of this continuation · filed 11 Mar 2013

US 2016/0369345 A1Pre-grant publication · published 22 Dec 2016

US 9,424,392 B2Parent of this continuation

US 8,532,930 B2Parent of this continuation

US 2007/0184467 A1Published application

US 2013/0253369 A1Published application

US 10,240,202 B2This patent

From the US filing history. Foreign family members aren’t listed.

System and method for cleaning noisy genetic data from target individuals using genetic data from genetically related individuals

Life of this patent

System and method for cleaning noisy genetic data from target individuals using genetic data from genetically related individuals

Life of this patent

Abstract

Claims20