# US 11,306,358 B2 · Method for determining genetic condition of fetus

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- Number: US 11,306,358 B2
- Document ID: US11306358B2
- Status: Granted
- Kind: B2
- Application number: 15/712,785
- Filed: 2017-09-22
- Published: 2018-03-29
- Granted: 2022-04-19
- Earliest claimed: 2015-03-31
- Assignees: FUJIFILM Corporation
- Applicants: FUJIFILM Corporation
- Inventors: Aya Ouchi; Takayuki Tsujimoto; Masaya Nagase; Yasuyuki Ishii
- Web page: https://patentgrep.com/patent/US11306358B2

## CPC

- C12Q 1/6883: for diseases caused by alterations of genetic material
- C12N 15/1089: {Design, preparation, screening or analysis of libraries using computer algorithms}
- C12Q 1/6811: Selection methods for production or design of target specific oligonucleotides or binding molecules
- C12Q 1/6876: Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12N 15/09: Recombinant DNA-technology
- C12Q 2600/156: Polymorphic or mutational markers
- C12Q 2600/16: Primer sets for multiplex assays
- 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
- C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00)

## Abstract

Provided is a method for determining a genetic condition of a fetus, the method including: an objective region selection step of selecting an objective region for determining the genetic condition, from regions on a human genome; a step of isolating a single cell from a maternal blood sample; a step of extracting genomic DNA from the single cell; a step of performing PCR amplification on the objective region using a primer set designed so as to perform the PCR amplification on the objective region using genomic DNA extracted from the single cell as a template; and a DNA sequencing step of decoding a DNA base sequence of a PCR amplification product of the objective region, in which the primer set designed so as to perform the PCR amplification on the objective region is designed through a method for designing a primer set used for the polymerase chain reaction, the method for designing a primer set including a first stage selection step based on a local alignment score and a second stage selection step based on a global alignment score.

## Claims

### Claim 1

A method for determining a genetic condition of a fetus, the method comprising:
an objective region selection step of selecting an objective region for determining the genetic condition, from regions on a human genome;
a single cell isolation step of isolating a single cell from a maternal blood sample;
a genomic DNA extraction step of extracting genomic DNA from the single cell;
an amplification step performed through a polymerase chain reaction in which the objective region is amplified through the polymerase chain reaction using a primer set designed so as to amplify the objective region through the polymerase chain reaction using the genomic DNA extracted from the single cell as a template; and
a DNA sequencing step of decoding a DNA base sequence of an amplification product of the objective region obtained through the polymerase chain reaction,
wherein the objective region selection step is performed before or after both steps of the single cell isolation step and the genomic DNA extraction step, or performed in parallel with both steps of the single cell isolation step and the genomic DNA extraction step,
wherein the primer set designed so as to amplify the objective region through the polymerase chain reaction is designed through a method for designing a primer set used for the polymerase chain reaction, the method for designing a primer set including
a target region selection step of selecting a target region in which the primer set used for the polymerase chain reaction is designed, from the objective region,
a primer candidate base sequence generation step of generating at least one base sequence of a primer candidate for amplifying the target region based on each base sequence in vicinity regions at both ends of the target region on the genome,
a local alignment step of obtaining a local alignment score by performing pairwise local alignment on the base sequence of the primer candidate under a condition that a partial sequence to be subjected to comparison includes the 3′ terminal of the base sequence of the primer candidate,
a first stage selection step of performing first stage selection of the base sequence of the primer candidate based on the local alignment score obtained in the local alignment step,
a global alignment step of obtaining a global alignment score by performing pairwise global alignment on a base sequence which is of three base length and includes the 3′ terminal of the base sequence of the primer candidate,
a second stage selection step of performing second stage selection of a base sequence of the primer candidate based on the global alignment score obtained in the global alignment step, and
a primer employment step of employing the base sequence of the primer candidate which has been selected in both of the first stage selection step and the second stage selection step as a base sequence of a primer for amplifying the target region, and
wherein both steps of the local alignment step and the first stage selection step are performed before or after both steps of the global alignment step and the second stage selection step, or performed in parallel with both steps of the global alignment step and the second stage selection step, and
wherein the genetic condition is a numerical abnormality of a chromosome of the fetus,
an objective region for determining the genetic condition on at least one of chromosome 13, chromosome 18, and chromosome 21 is selected from regions on a human genome in the objective region selection step, and
the DNA base sequence of the amplification product of the objective region obtained through the polymerase chain reaction is decoded, a ratio of number of times of sequence reading of mother-derived amplification product to number of times of sequence reading of fetus-derived amplification product is obtained, and it is determined that the fetus has the numerical abnormality of the chromosome in a case where the ratio is greater than or equal to a predetermined cutoff value, in the DNA sequencing step.

### Claim 2 (depends on 1)

The method for determining a genetic condition of a fetus according to claim 1,
wherein the primer set designed so as to amplify the objective region through the polymerase chain reaction is designed through a method for designing a primer set used for the polymerase chain reaction, the method for designing a primer set including
a first target region selection step of selecting a first target region in which the primer set used for the polymerase chain reaction is designed, from the objective region,
a first primer candidate base sequence generation step of generating at least one base sequence of a primer candidate for amplifying the first target region based on each base sequence in vicinity regions at both ends of the first target region on the genome,
a first local alignment step of obtaining a local alignment score by performing pairwise local alignment on the base sequence of the primer candidate under a condition that a partial sequence to be subjected to comparison includes the 3′ terminal of the base sequence of the primer candidate,
a first step of first stage selection of performing first stage selection of the base sequence of the primer candidate based on the local alignment score obtained in the first local alignment step,
a first global alignment step of obtaining a global alignment score by performing pairwise global alignment on a base sequence which is of three base length and includes the 3′ terminal of the base sequence of the primer candidate,
a first step of second stage selection of performing second stage selection of the base sequence of the primer candidate based on the global alignment score obtained in the first global alignment step,
a first primer employment step of employing the base sequence of the primer candidate which has been selected in both of the first step of first stage selection and the first step of second stage selection as a base sequence of a primer for amplifying the first target region,
a second target region selection step of selecting a second target region in which the primer set used for the polymerase chain reaction is designed, from the objective region,
a second primer candidate base sequence generation step of generating at least one base sequence of each primer candidate for amplifying the second target region based on each base sequence in vicinity regions at both ends of the second target region on the genome,
a second local alignment step of obtaining a local alignment score by performing pairwise local alignment on the base sequence of the primer candidate for amplifying the second target region and the base sequence of the primer which has already been employed, under a condition that partial sequences to be subjected to comparison include the 3′ terminal of the base sequence of the primer candidate and the 3′ terminal of the base sequence of the primer which has already been employed,
a second step of first stage selection of performing first stage selection of the base sequence of the primer candidate for amplifying the second target region based on the local alignment score obtained in the second local alignment step,
a second global alignment step of obtaining a global alignment score by performing pairwise global alignment on base sequences which have a predetermined sequence length and include the 3′ terminal of the base sequence of the primer candidate for amplifying the second target region and the 3′ terminal of the base sequence of the primer which has already been employed,
a second step of second stage selection of performing second stage selection of the base sequence of the primer candidate for amplifying the second target region based on the global alignment score obtained in the second global alignment step, and
a second primer employment step of employing the base sequence of the primer candidate which has been selected in both of the second step of first stage selection and the second step of second stage selection as a base sequence of a primer for amplifying the second target region,
wherein both steps of the first local alignment step and the first step of first stage selection are performed before or after both steps of the first global alignment step and the first step of second stage selection, or performed in parallel with both steps of the first global alignment step and the first step of second stage selection,
wherein both steps of the second local alignment step and the second step of first stage selection are performed before or after both steps of the second global alignment step and the second step of second stage selection, or performed in parallel with both steps of the second global alignment step and the second step of second stage selection, and
wherein, in a case where there are three or more of the target regions, the steps from the second target region selection step to the second primer employment step are repeated with respect to all of the target regions until a base sequence of a primer for amplifying each target region is employed.

### Claim 3 (depends on 1)

The method for determining a genetic condition of a fetus according to claim 1,
wherein in case that the genetic condition of the fetus is not determined in the DNA sequencing step, the steps at least from the single cell isolation step to the DNA sequencing step are repeated until the genetic condition of the fetus can be determined.

### Claim 4 (depends on 2)

The method for determining a genetic condition of a fetus according to claim 2,
wherein in case that the genetic condition of the fetus is not determined in the DNA sequencing step, the steps at least from the single cell isolation step to the DNA sequencing step are repeated until the genetic condition of the fetus can be determined.

### Claim 5 (depends on 2)

The method for determining a genetic condition of a fetus according to claim 2,
wherein the genetic condition is a numerical abnormality of a chromosome of the fetus,
an objective region for determining the genetic condition on at least one of chromosome 13, chromosome 18, and chromosome 21 is selected from regions on a human genome in the objective region selection step, and
the DNA base sequence of the amplification product of the objective region obtained through the polymerase chain reaction is decoded, a ratio of number of times of sequence reading of mother-derived amplification product to number of times of sequence reading of fetus-derived amplification product is obtained, and it is determined that the fetus has the numerical abnormality of the chromosome in a case where the ratio is greater than or equal to a predetermined cutoff value, in the DNA sequencing step.

### Claim 6 (depends on 3)

The method for determining a genetic condition of a fetus according to claim 3,
wherein the genetic condition is a numerical abnormality of a chromosome of the fetus,
an objective region for determining the genetic condition on at least one of chromosome 13, chromosome 18, and chromosome 21 is selected from regions on a human genome in the objective region selection step, and
the DNA base sequence of the amplification product of the objective region obtained through the polymerase chain reaction is decoded, a ratio of number of times of sequence reading of mother-derived amplification product to number of times of sequence reading of fetus-derived amplification product is obtained, and it is determined that the fetus has the numerical abnormality of the chromosome in a case where the ratio is greater than or equal to a predetermined cutoff value, in the DNA sequencing step.

### Claim 7 (depends on 4)

The method for determining a genetic condition of a fetus according to claim 4,
wherein the genetic condition is a numerical abnormality of a chromosome of the fetus,
an objective region for determining the genetic condition on at least one of chromosome 13, chromosome 18, and chromosome 21 is selected from regions on a human genome in the objective region selection step, and
the DNA base sequence of the amplification product of the objective region obtained through the polymerase chain reaction is decoded, a ratio of number of times of sequence reading of mother-derived amplification product to number of times of sequence reading of fetus-derived amplification product is obtained, and it is determined that the fetus has the numerical abnormality of the chromosome in a case where the ratio is greater than or equal to a predetermined cutoff value, in the DNA sequencing step.

### Claim 8 (depends on 1)

The method for determining a genetic condition of a fetus according to claim 1, the method further comprising:
a magnetic bead purification step of purifying the amplification product of the objective region obtained through the polymerase chain reaction, using magnetic beads, between the amplification step performed through a polymerase chain reaction and the DNA sequencing step.

### Claim 9 (depends on 2)

The method for determining a genetic condition of a fetus according to claim 2, the method further comprising:
a magnetic bead purification step of purifying the amplification product of the objective region obtained through the polymerase chain reaction, using magnetic beads, between the amplification step performed through a polymerase chain reaction and the DNA sequencing step.

### Claim 10 (depends on 3)

The method for determining a genetic condition of a fetus according to claim 3, the method further comprising:
a magnetic bead purification step of purifying the amplification product of the objective region obtained through the polymerase chain reaction, using magnetic beads, between the amplification step performed through a polymerase chain reaction and the DNA sequencing step.

### Claim 11 (depends on 4)

The method for determining a genetic condition of a fetus according to claim 4, the method further comprising:
a magnetic bead purification step of purifying the amplification product of the objective region obtained through the polymerase chain reaction, using magnetic beads, between the amplification step performed through a polymerase chain reaction and the DNA sequencing step.

### Claim 12 (depends on 5)

The method for determining a genetic condition of a fetus according to claim 5, the method further comprising:
a magnetic bead purification step of purifying the amplification product of the objective region obtained through the polymerase chain reaction, using magnetic beads, between the amplification step performed through a polymerase chain reaction and the DNA sequencing step.