IP Library › Granted Patent US 12,553,086
Granted Patent B2
US 12,553,086 · App. 17/505,588 · Granted Feb 17, 2026

Methods for simultaneous amplification of target loci

Inventors: Joshua Babiarz (Castro Valley, CA); Tudor Pompiliu Constantin (Berkeley, CA); Lane A. Eubank (San Carlos, CA); George Gemelos (Portland, OR); Matthew Micah Hill (Belmont, CA); Huseyin Eser Kirkizlar (Los Angeles, CA); Matthew Rabinowitz (San Francisco, CA); Onur Sakarya (Redwood City, CA); Styrmir Sigurjonsson (San Jose, CA); Bernhard Zimmermann (Manteca, CA)
Assignee: Natera, Inc.
C12Q1/6883C12Q1/6809C12Q1/6811C12Q1/6844C12Q1/6848C12Q1/6851C12Q1/6855C12Q1/6869C12Q1/6874C12Q2600/156
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Quick Facts
Patent No.
US 12,553,086
App. No.
17/505,588
Granted
Feb 17, 2026
Kind
B2
Abstract

The invention provides methods for simultaneously amplifying multiple nucleic acid regions of interest in one reaction volume as well as methods for selecting a library of primers for use in such amplification methods. The invention also provides library of primers with desirable characteristics, such as minimal formation of amplified primer dimers or other non-target amplicons.

Claims (21)

1 . A method for preparing a non-naturally occurring composition of amplified DNA derived from one or more fetal or embryonic cells of an unborn fetus or embryo useful for reconstructing at least a portion of the genome of the fetus or embryo, comprising:

(a) extracting genomic DNA from the one or more fetal or embryonic cells;

(b) preparing a non-naturally occurring composition of amplified DNA by amplification of at least 1,000 polymorphic loci from the genomic DNA extracted in (a) to obtain amplified DNA;

(c) analyzing the non-naturally occurring composition of amplified DNA obtained in (b) by high-throughput sequencing to obtain genetic data of the fetus or embryo at the polymorphic loci, and reconstructing at least a portion of the genome of the fetus or embryo using the genetic data of the fetus or embryo and haplotypes of at least one biological parent of the fetus or embryo at the polymorphic loci.

2 . The method of claim 1 , wherein the polymorphic loci are SNP loci.

3 . The method of claim 1 , wherein step (a) comprises extracting genomic DNA from one or more fetal cells.

4 . The method of claim 1 , wherein step (a) comprises extracting genomic DNA from one or more embryonic cells.

5 . The method of claim 1 , wherein step (a) comprises extracting genomic DNA from a single fetal or embryonic cell.

6 . The method of claim 1 , wherein step (b) comprises ligation of adaptors to the genomic DNA to obtain adaptor-ligated DNA and performing universal amplification on the adaptor-ligated DNA.

7 . The method of claim 1 , wherein step (b) comprises performing targeted multiplex amplification of the at least 1,000 polymorphic loci using at least 1,000 different target-specific primers.

8 . The method of claim 1 , wherein step (b) comprises barcoding PCR.

9 . The method of claim 1 , wherein step (c) comprises reconstructing at least a portion of the genome of the fetus or embryo using the genetic data of the fetus or embryo and haplotypes of both biological parents of the fetus or embryo at the polymorphic loci.

10 . The method of claim 1 , wherein the method further comprises measuring genetic data of at least one biological parent of the fetus or embryo, and phasing the genetic data to obtain haplotypes of the biological parent at the polymorphic loci.

11 . The method of claim 1 , wherein the method further comprises measuring genetic data of both biological parents of the fetus or embryo, and phasing the genetic data to obtain haplotypes of both biological parents at the polymorphic loci.

12 . The method of claim 1 , wherein a haplotype is determined for one or more chromosomes of the fetus or embryo.

13 . The method of claim 1 , wherein a haplotype is determined for at least 30% of the genome of the fetus or embryo.

14 . The method of claim 13 , wherein the haplotype determination of the fetus or embryo comprises identifying which allele is present for the at least 1,000 polymorphic loci.

15 . A method for preparing a non-naturally occurring composition of amplified DNA derived from one or more fetal or embryonic cells of an unborn fetus or embryo useful for reconstructing at least a portion of the genome of the fetus or embryo, comprising:

(a) extracting genomic DNA from the one or more fetal or embryonic cells;

(b) preparing a non-naturally occurring composition of amplified DNA by targeted multiplex amplification of 1,000 to 100,000 SNP loci from the genomic DNA extracted in (a) to obtain amplified DNA;

(c) analyzing the non-naturally occurring composition of amplified DNA obtained in (b) by high-throughput sequencing to obtain genetic data of the fetus or embryo at the SNP loci, and reconstructing at least a portion of the genome of the fetus or embryo using the genetic data of the fetus or embryo and haplotypes of both biological parents of the fetus or embryo at the SNP loci.

Assignments (1)
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Oct 20, 2021
From: BABIARZ, JOSHUA; CONSTANTIN, TUDOR POMPILIU; EUBANK, LANE A.; GEMELOS, GEORGE; HILL, MATTHEW; KIRKIZLAR, HUSEYIN ESER; RABINOWITZ, MATTHEW; SAKARYA, ONUR; ZIMMERMANN, BERNHARD; SIGURJONSSON, STYRMIR
To: NATERA, INC.
Reel/Frame 057861/0938 →
Continuity (29)
Continuation 16734814 · Jan 6, 2020
Continuation 16412331 · May 14, 2019
Continuation 16140298 · Sep 24, 2018
Continuation 14918544 · Oct 20, 2015
Continuation In Part 14877925 · Oct 7, 2015
Continuation In Part 14692703 · Apr 21, 2015
Continuation In Part 14538982 · Nov 24, 2014
Continuation In Part 14225356 · Mar 25, 2014
Continuation In Part 13780022 · Feb 28, 2013
Continuation In Part 13683604 · Nov 21, 2012
Continuation In Part PCTUS2012058578 · Oct 3, 2012
Continuation In Part 13683604 · Nov 21, 2012
Continuation In Part PCTUS2012058578 · Oct 3, 2012
Continuation In Part 13335043 · Dec 22, 2011
Continuation In Part 13300235 · Nov 18, 2011
Continuation In Part 13110685 · May 18, 2011
Provisional Application 62148173 · Apr 15, 2015
Provisional Application 62147377 · Apr 14, 2015
Provisional Application 62146188 · Apr 10, 2015
Provisional Application 62066514 · Oct 21, 2014
Provisional Application 61994791 · May 16, 2014
Provisional Application 61987407 · May 1, 2014
Provisional Application 61982245 · Apr 21, 2014
Provisional Application 61683331 · Aug 15, 2012
Provisional Application 61675020 · Jul 24, 2012
Provisional Application 61634431 · Feb 29, 2012
Provisional Application 61542508 · Oct 3, 2011
Provisional Application 61571248 · Jun 23, 2011
Related Publication 20220033909A1 · Feb 3, 2022
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