Granted Patent B2

US 12,744,126 · App. 17/365,786 · Granted Sep 22, 2026

Inventors: Allison Ryan (Belmont, CA); Katie Kobara (San Francisco, CA); Zachary Demko (San Francisco, CA); Susan J. Gross (Bronx, NY)

Assignee: Natera, Inc.

G16H50/30G16H50/70C12Q1/6869C12Q1/6883G16B20/10

Abstract

Claims (28)

1 . A method for preparing a non-naturally occurring composition of amplified DNA derived from a target sample of maternal blood or plasma useful for determining an aneuploidy risk score, comprising:

a) extracting cell-free DNA from the target sample of maternal blood or plasma comprising both maternal and fetal cell-free DNA, wherein the target sample has been determined to have a fetal fraction of 0.037 or less;

b) preparing a non-naturally occurring composition of amplified DNA, wherein step (b) comprises amplifying a plurality of targeted single nucleotide polymorphism (SNP) loci from the DNA extracted in (a) to obtain amplified DNA derived from said targeted SNP loci, and performing a barcoding PCR to append a sample barcode onto the amplified DNA; and

c) analyzing the non-naturally occurring composition of amplified cell-free DNA by performing high-throughput sequencing or a microarray assay on the amplified DNA obtained in (b) to determine an aneuploidy risk score for the cell-free DNA having a fetal fraction of 0.037 or less.

2 . The method of claim 1 , wherein step (c) comprises measuring genetic data of the target sample from the non-naturally occurring composition of amplified DNA by high throughput sequencing.

3 . The method of claim 1 , wherein step (c) comprises measuring genetic data of the target sample from the non-naturally occurring composition of amplified DNA by performing a microarray assay.

4 . The method of claim 1 , wherein step (c) comprises:

(i) receiving, by one or more processors, known genetic data from at least 50 known noninvasive prenatal testing samples, wherein gestational age and maternal weight are known for the 50 known noninvasive prenatal testing samples;

(ii) receiving, by the one or more processors, the genetic data for the target sample measured by high throughput sequencing or the microarray assay, and a gestational age, a maternal weight, and a fetal fraction associated with the target sample;

(iii) determining, by the one or more processors, a fetal fraction distribution for the received known genetic data based on the gestational age and the maternal weight associated with the target sample;

(iv) generating, by the one or more processors, a model for a plurality of ploidy states based on a fixed rate reduction of the determined fetal fraction distribution compared to an expected average fetal fraction for the gestational age and the maternal weight associated with the target sample;

(v) determining, by the one or more processors, a fetal fraction based data likelihood for the target sample for each of the plurality of ploidy states using the generated model and the fetal fraction associated with the target sample;

(vi) applying, by the one or more processors, a Bayesian probability determination to combine each fetal fraction based data likelihood with a previously determined risk score as a conditional value; and

(vii) outputting, by the one or more processors, the aneuploidy risk score for the target sample based on the applying.

5 . The method of claim 4 , wherein the previously determined risk score is a SNP based risk score.

6 . The method of claim 4 , further comprising: transforming the determined fetal fraction distribution to logarithm space, wherein a logarithm of the fetal fraction is assumed Gaussian distributed with a mean and standard deviation that are a function of gestational age and maternal weight for the known prenatal testing samples.

7 . The method of claim 4 , wherein determining a fetal fraction based data likelihood for the target sample comprises determining an integral of a probability density function of the generated model.

8 . The method of claim 4 , wherein the generated model is associated with trisomy 13.

9 . The method of claim 4 , wherein the generated model is associated with trisomy 18.

10 . The method of claim 4 , wherein the generated model is associated with maternal triploidy.

11 . The method of claim 4 , wherein determining a fetal fraction distribution for the received known genetic data comprises: grouping the genetic data for the at least 50 known prenatal testing samples into sets according to gestational age and maternal weight; and generating a grid of distribution parameters corresponding to each set, wherein the distribution parameters include average fetal fraction and standard deviation.

12 . The method of claim 4 , wherein the fixed rate reduction in the average fetal fraction correspond to a constant subtracted offset as determined by analysis of empirical data.

13 . The method of claim 1 , wherein the fetal fraction of cell-free DNA is between 0.013 and 0.037.

14 . A method for preparing a non-naturally occurring composition of amplified DNA derived from a target sample of maternal blood or plasma useful for determining an aneuploidy risk score, comprising:

(a) obtaining a target sample of maternal blood or plasma comprising both maternal and fetal cell-free DNA that has been determined to have a fetal fraction of 0.037 or less;

(b) extracting cell-free DNA from the target sample;

(c) preparing a non-naturally occurring composition of amplified DNA, wherein step (c) comprises amplifying a plurality of targeted single nucleotide polymorphism (SNP) loci from the DNA extracted in (b) to obtain amplified DNA derived from said targeted SNP loci, and performing a barcoding PCR to append a sample barcode onto the amplified DNA; and

(d) analyzing the non-naturally occurring composition of amplified cell-free DNA by performing high-throughput sequencing or a microarray assay on the amplified DNA obtained in (c).

Assignments (1)

Continuity (3)

References Cited (400)