US 9,809,855 B2
Characterization of molecules in nanofluidics
Han Cao, San Diego, CA (US); Alex R. Hastie, San Diego, CA (US); and Ernest Tsz-Tsun Lam, San Diego, CA (US)
Assigned to BIONANO GENOMICS, INC., San Diego, CA (US)
Appl. No. 14/768,422
Filed by BioNano Genomics, Inc., San Diego, CA (US)
PCT Filed Feb. 19, 2014, PCT No. PCT/US2014/017226
§ 371(c)(1), (2) Date Aug. 17, 2015,
PCT Pub. No. WO2014/130589, PCT Pub. Date Aug. 28, 2014.
Claims priority of provisional application 61/767,219, filed on Feb. 20, 2013.
Prior Publication US 2016/0046992 A1, Feb. 18, 2016
Int. Cl. C12Q 1/68 (2006.01); C12M 1/34 (2006.01); C07H 21/04 (2006.01); C40B 40/06 (2006.01); G01N 31/22 (2006.01); G01N 33/50 (2006.01); B01L 3/00 (2006.01); G06F 19/22 (2011.01)
CPC C12Q 1/6883 (2013.01) [B01L 3/5027 (2013.01); C12Q 1/6809 (2013.01); G01N 33/5091 (2013.01); G06F 19/22 (2013.01); B01L 2200/10 (2013.01); B01L 2300/0627 (2013.01); C12Q 2600/166 (2013.01)] 15 Claims
 
1. A method of characterizing a sample comprising polynucleotide sequences, the method comprising:
labeling a plurality of sample nucleic acid molecules, each of about 10 base pairs to about 500 base pairs, with at least a first label, wherein the sample nucleic acid molecules comprise polynucleotide sequences of a genome or a fragment or fragments thereof, wherein the polynucleotide sequences of the sample nucleic acid molecules are from the sample;
providing a plurality of labeled control nucleic acid molecules, each of about 10 base pairs to about 500 base pairs, wherein the control nucleic acid molecules comprise polynucleotide sequences of the genome or fragment or fragments thereof;
translocating the plurality of labeled sample nucleic acid molecules through one or more fluidic nanochannels having a length of at least 10 nm and a cross-sectional diameter of less than 1000 nm;
translocating the labeled control nucleic acid molecules through one or more fluidic nanochannels having a length of at least 10 nm and a cross-sectional diameter of less than 1000 nm;
detecting physical counts of signals from the labeled sample nucleic acid molecules, said signals comprising patterns characteristic of the genome or fragment or fragments thereof; detecting physical counts of signals from the labeled control nucleic acid molecules, said signals comprising patterns characteristic of the genome or fragment or fragments thereof; and
aligning the patterns to a reference of the genome or fragment or fragments thereof, thereby ascertaining:
a coverage depth for the sample nucleic acid molecules over the reference of the genome or fragment or fragments; and
a coverage depth for the control nucleic acid molecules over the reference genome or fragment or fragments; and
determining a copy number of the genome or fragment or fragments thereof in the sample.