US 10,119,167 B2Granted

Non-invasive prenatal diagnosis of fetal genetic condition using cellular DNA and cell free DNA

AssigneeIllumina, Inc.

InventorsAnupama Srinivasan, Darya I. Chudova, Richard P. Rava

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Abstract

Disclosed are methods for determining at least one sequence of interest of a fetus of a pregnant mother. In various embodiments, the method can determine one or more sequences of interest in a test sample that comprises a mixture of maternal cellular DNA and mother-and-fetus cfDNA. In some embodiments, methods are provided for determining whether the fetus has a genetic disease. In some embodiments, methods are provided for determining whether the fetus is homozygous in a disease causing allele when the mother is heterozygous of the same allele. In some embodiments, methods are provided for determining whether the fetus has a copy number variation (CNV) or a non-CNV genetic sequence anomaly.

Claims41

Dependent claims

A method for determining at least one sequence of interest of a fetus of a pregnant mother, the method comprising:

(a) obtaining mother-only cellular DNA of the pregnant mother, wherein the mother-only cellular DNA has a sequence that maps to the at least one sequence of interest;
(b) obtaining mother-and-fetus mixed cfDNA from the pregnant mother, wherein the mother-and-fetus mixed cfDNA has a sequence that maps to the at least one sequence of interest;
(c) applying a first index sequence to the mother-only cellular DNA and a second index sequence to the cfDNA, wherein
the first index sequence and the second index sequence are different,
the first index sequence specifies a source of DNA as being from the mother-only cellular DNA from the pregnant mother, and
the second index sequence specifies a source of DNA as being from the cfDNA from the pregnant mother;
(d) combining the mother-only cellular DNA and the cfDNA to provide a sample of combined cellular DNA and cfDNA;
(e) sequencing said sample of combined cellular and cfDNA to provide a plurality of sequence reads and mapping the plurality of sequence reads to a reference sequence;
and
(f) analyzing the mapped sequence reads to determine the presence and/or abundance of the at least one sequence of interest in the fetus's DNA, wherein at least a portion of the mapped sequence reads maps to the at least one sequence of interest.

7 more elements

Dependencies are inferred from the claim text.

Facts

Application: 14/802,936Filed 17 Jul 2015 · us provisional application
Priority: 18 Jul 2014
Published: US 2016/0017412 A121 Jan 2016
Granted: 6 Nov 2018
Term ends: Not estimatedThe source records don’t support an estimate.

Classification11 codes

C12Q 1/6874
Methods for sequencing: involving nucleic acid arrays, e.g. sequencing by hybridisation
C12Q 1/6827
Hybridisation assays: for detection of mutation or polymorphism
C12Q 1/6869
Involving nucleic acids: methods for sequencing
G16B 20/10
ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations: ploidy or copy number detection

Family

Application62/026,548Us provisional application · filed 18 Jul 2014
US 2016/0017412 A1Pre-grant publication · published 21 Jan 2016
US 10,119,167 B2This patent

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

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