	US 12,116,628 B2
	Rapid aneuploidy detection
Bert Vogelstein, Baltimore, MD (US); Kenneth W. Kinzler, Baltimore, MD (US); Nickolas Papadopoulos, Towson, MD (US); and Isaac A. Kinde, Beaumont, CA (US)
Assigned to The Johns Hopkins University, Baltimore, MD (US)
Filed by The Johns Hopkins University, Baltimore, MD (US)
Filed on Sep. 23, 2021, as Appl. No. 17/483,537.
Application 17/483,537 is a continuation of application No. 14/792,716, filed on Jul. 7, 2015, abandoned.
Application 14/792,716 is a continuation of application No. 14/388,314, granted, now 10,053,729, issued on Aug. 21, 2018, previously published as PCT/US2013/033451, filed on Mar. 22, 2013.
Claims priority of provisional application 61/659,695, filed on Jun. 14, 2012.
Claims priority of provisional application 61/615,535, filed on Mar. 26, 2012.
Prior Publication US 2022/0010371 A1, Jan. 13, 2022
This patent is subject to a terminal disclaimer.
Int. Cl. C12Q 1/68 (2018.01); C12Q 1/6811 (2018.01); C12Q 1/6827 (2018.01); C12Q 1/6869 (2018.01); C12Q 1/6883 (2018.01)

CPC C12Q 1/6869 (2013.01) [C12Q 1/6811 (2013.01); C12Q 1/6827 (2013.01); C12Q 1/6883 (2013.01); C12Q 2600/112 (2013.01); C12Q 2600/156 (2013.01); C12Q 2600/16 (2013.01)]

12 Claims

1. A method of detecting the presence or absence of aneuploidy, comprising:

a) contacting a sample comprising plasma DNA from a human patient with a single primer pair, wherein said primer pair comprises a first primer and a second primer,

wherein both said first primer and said second primer are designed to anneal to long interspersed nucleotide elements (LINEs) present on a reference set of all twenty-two autosome human non-aneuploid chromosomes that would generate, during amplification, an expected distribution for said twenty-two autosome human non-aneuploid chromosomes,

wherein said plasma DNA comprises at least a portion of all twenty-two autosome patient chromosomes;

b) amplifying, using polymerase chain reaction, at least a portion of said plasma DNA using the single primer pair, whereby a plurality of amplicons from said LINEs are produced,

wherein said plurality of amplicons are distinct from one another,

wherein each of said plurality of amplicons is less than 180 bp in length; and

wherein said plurality of amplicons comprise at least two amplicons from each of said twenty-two autosome patient chromosomes;

c) sequencing at least 5 nucleotides of each of the amplicons in the plurality of amplicons;

d) aligning in silico the sequenced amplicons from each of said twenty-two autosome patient chromosomes to said reference set of all twenty-two autosome human non-aneuploid chromosomes in order to produce a query distribution for each of said twenty-two autosome patient chromosomes,

wherein said query distribution comprises a normalized count of the number of sequenced amplicons at each position where they align to said reference set of all twenty-two autosome human non-aneuploid chromosomes; and

e) identifying:

i) the presence of aneuploidy based upon finding at least one normalized count difference between said query distribution for at least one of said twenty-two autosome patient chromosomes and said expected distribution for a corresponding at least one of said twenty-two autosome human non-aneuploid chromosomes, or

ii) the absence of aneuploidy based upon not finding at least one normalized count different difference between said query distribution and said expected distribution.