# US 11,306,359 B2 · System and method for cleaning noisy genetic data from target individuals using genetic data from genetically related individuals

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- Number: US 11,306,359 B2
- Document ID: US11306359B2
- Status: Granted
- Kind: B2
- Application number: 16/288,690
- Filed: 2019-02-28
- Published: 2019-07-11
- Granted: 2022-04-19
- Earliest claimed: 2005-11-26
- Assignees: Natera, Inc.
- Applicants: Natera, Inc.
- Inventors: Matthew Rabinowitz; Milena Banjevic; Zachary Demko; David Johnson
- Web page: https://patentgrep.com/patent/US11306359B2

## CPC

- C12Q 1/6883: for diseases caused by alterations of genetic material
- C12Q 1/6827: for detection of mutation or polymorphism
- C12Q 1/6876: 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, e.g. genotype-phenotype associations
- G16B 20/20: Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
- G16B 20/40: Population genetics; Linkage disequilibrium
- G16B 25/00: ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
- G16B 30/00: ICT specially adapted for sequence analysis involving nucleotides or amino acids
- G16B 40/00: ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
- C12Q 2600/118: Prognosis of disease development
- C12Q 2600/156: Polymorphic or mutational markers
- C12Q 2600/158: Expression markers
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY

## 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.

## Claims

### Claim 1

A method for preparing a preparation of amplified DNA from a sample comprising cell-free DNA derived from a fetus and mother of the fetus useful for detecting the presence or absence of a chromosomal abnormality in the fetus, the method comprising:
(a) extracting cell-free DNA from a blood, serum or plasma sample of the mother of the fetus;
(b) preparing a preparation of amplified DNA by performing targeted multiplex amplification on the cell-free DNA obtained in (a) or DNA derived therefrom to amplify at least 70 target loci on a chromosome or chromosome segment of interest in a single reaction to obtain amplicons;
(c) analyzing the preparation of amplified DNA obtained in (b) by microarray or sequencing to detect amplified DNA to measure the amounts of genetic material at the target loci, wherein the target loci have alleles with 100% penetrance in the population; and determining the presence or absence of a chromosomal abnormality in the fetus based on the measured amounts of genetic material at the target loci.

### Claim 2 (depends on 1)

The method of claim 1, wherein microarray is used to measure the amounts of genetic material at the target loci.

### Claim 3 (depends on 1)

The method of claim 1, wherein sequencing is used to measure the amounts of genetic material at the target loci.

### Claim 4 (depends on 1)

The method of claim 1, wherein the chromosome or chromosome segment of interest is selected from the group consisting of chromosome 13, chromosome 18, chromosome 21, X chromosome, Y chromosome, and combinations thereof, and wherein the chromosomal abnormality is selected from the group consisting of monosomy, uniparental disomy, trisomy, other aneuploidies, unbalanced translocations, insertions, deletions, and combinations thereof.

### Claim 5 (depends on 1)

The method of claim 1, wherein the chromosomal abnormality is trisomy of chromosome 13, chromosome 18, or chromosome 21.

### Claim 6 (depends on 1)

The method of claim 1, wherein the determining is performed by comparing the amounts of genetic material at the target loci to an expected amount, wherein the expected amount is a mean value of genetic material at multiple loci for a reference chromosome or chromosome segment expected to be disomic.

### Claim 7 (depends on 1)

The method of claim 1, wherein the method further comprises determining the probability of aneuploidy in the fetus by comparing the measured amounts of genetic material at the target loci to an expected amount for a particular copy number of a chromosome or chromosome segment of interest.

### Claim 8 (depends on 1)

The method of claim 1, wherein the amplification comprises ligating oligonucleotides that hybridize to target sequences comprising the target loci and amplifying the ligated oligonucleotides by PCR.

### Claim 9 (depends on 8)

The method of claim 8, wherein the PCR is performed using universal primer sequences.

### Claim 10

A method for preparing a preparation of amplified DNA from a sample comprising cell-free DNA derived from a fetus and mother of the fetus useful for detecting the presence or absence of a chromosomal abnormality in the fetus, the method comprising:
(a) extracting cell-free DNA from a blood, serum or plasma sample of the mother of the fetus;
(b) preparing a preparation of amplified DNA by performing targeted multiplex amplification on the cell-free DNA obtained in (a) or DNA derived therefrom to amplify at least 70 target loci on a chromosome or chromosome segment of interest in a single reaction to obtain amplicons;
(c) analyzing the preparation of amplified DNA obtained in (b) by microarray or sequencing to detect amplified DNA to measure the amounts of genetic material at the target loci, wherein the amounts of genetic material at the target loci are measured irrespective of the identity of alleles at each locus; and determining the presence or absence of a chromosomal abnormality in the fetus based on the measured amounts of genetic material at the target loci.

### Claim 11 (depends on 10)

The method of claim 10, wherein microarray is used to measure the amounts of genetic material at the target loci.

### Claim 12 (depends on 10)

The method of claim 10, wherein sequencing is used to measure the amounts of genetic material at the target loci.

### Claim 13 (depends on 10)

The method of claim 10, wherein the chromosome or chromosome segment of interest is selected from the group consisting of chromosome 13, chromosome 18, chromosome 21, X chromosome, Y chromosome, and combinations thereof, and wherein the chromosomal abnormality is selected from the group consisting of monosomy, uniparental disomy, trisomy, other aneuploidies, unbalanced translocations, insertions, deletions, and combinations thereof.

### Claim 14 (depends on 10)

The method of claim 10, wherein the chromosomal abnormality is trisomy of chromosome 13, chromosome 18, or chromosome 21.

### Claim 15 (depends on 10)

The method of claim 10, wherein the determining is performed by comparing the amounts of genetic material at the target loci to an expected amount, wherein the expected amount is a mean value of genetic material at multiple loci for a reference chromosome or chromosome segment expected to be disomic.

### Claim 16 (depends on 10)

The method of claim 10, wherein the method further comprises determining the probability of aneuploidy in the fetus by comparing the measured amounts of genetic material to an expected amount for a particular copy number of a chromosome or chromosome segment of interest.

### Claim 17 (depends on 10)

The method of claim 10, wherein the amplification comprises ligating oligonucleotides that hybridize to target sequences comprising the target loci and amplifying the ligated oligonucleotides by PCR.

### Claim 18 (depends on 17)

The method of claim 17, wherein the PCR is performed using universal primer sequences.