Characterization of molecules in nanofluidics
Systems are provided for detecting and quantitating short nucleic acid molecules.
1. A system for characterizing a sample, comprising:
one or more regions for labeling sample nucleic acid molecules of less than 550 nucleotides in length;
a fluidic nanochannel for translocating the labeled sample nucleic acid molecules, wherein the fluidic nanochannel is configured to elongate at least a portion of the sample nucleic acid molecules, and wherein the fluidic nanochannel has a length of at least 10 nm and a cross-sectional diameter of less than 1000 nm; and
a device configured to detect physical counts of signals arising from the labeled sample nucleic acid molecules of less than 550 nucleotides in length in the fluidic channels, said signals comprising patterns,
wherein the system is configured to:
align positions of the patterns to a reference genome, thereby ascertaining a coverage depth over the reference genome, and
compare coverage depth of the sample nucleic acid molecules to coverage depth for reference molecules so as to determine copy number for the sample nucleic acid molecules.
2. The system of claim 1 , wherein the sample is selected from the group consisting of a bacterium, a virion, a DNA molecule, an RNA molecule, a nucleic acid polymer.
3. The system of claim 1 , wherein the sample is derived from maternal blood, and wherein the reference molecules are derived from a maternal sample other than blood.
4. The system of claim 1 , wherein the labeling comprises labeling the nucleic acid molecules with at least two labels are located at either end of a zone of interest in the nucleic acid molecule.
5. The system of claim 1 , wherein the label is selected from the group consisting of a fluorescent label, a magnetic label.
6. The system of claim 1 , wherein the detecting comprises optical inspection comprising determining the physical count, the intensity, the wavelength, or the size of the labels.
7. The system of claim 1 , wherein the detecting comprises optical inspection comprising determining the length of at least one labeled region in the sample.
8. The system of claim 1 , wherein correlating the signals comprises determining the signals arising from a pool of samples or a pool of portions of a sample.
9. The system of claim 1 , wherein the system is configured to correlate the signals comprises using the ratio (K) between the signal arising from a plurality of samples or sample portions (S1, S2 . . . Sn) and the signal arising from the reference (C):
K1=S1/C, K2=S2/C . . . Kn=Sn/C
10. The system of claim 9 , wherein a difference between K1 and Kn is used to determine the presence of a genetic abnormality in the sample.
11. The system of claim 10 , wherein the genetic abnormality is a translocation, addition, amplification, transversion, inversion, or aneuploidy.
12. The system of claim 1 , wherein the reference is derived from a known diploid or haploid chromosome.
13. The system of claim 1 , wherein the signals from the sample are correlated with the population distribution from a metagenomic or microbiome study.
14. The system of claim 1 , wherein the fluidic channel is a nanochannel.
15. The system of claim 1 , wherein the fluidic channel is disposed parallel to a surface of a substrate.
16. The system of claim 1 , wherein the system is configured to generate a histogram distribution to reflect coverage depth for the sample.
17. The system of claim 1 , wherein the sample comprises circulating fetal cells, circulating tumor cells, or body fluids or tissues.
18. The system of claim 1 , wherein the translocating comprises subjecting the labeled sample to a motivating force selected from the group consisting of a fluid flow, an electroosmotic force, an electrophoretic force, an electrokinetic force, a temperature gradient, a surface property gradient, a capillary flow, a pressure gradient, a magnetic field, an electric field, a receding meniscus, a surface tension, a thermal gradient, a pulling force, a pushing force.
19. The system of claim 1 , wherein signal from the reference molecules comprises an electronically or optically stored value or set of values.
20. A system for characterizing a sample, comprising:
a region for labeling a plurality of sequence-specific locations on a sample DNA of less than 550 nucleotides in length;
a region for linearizing at least a portion of the labeled sample DNA; and
a device for quantifying the signal arising from the labels on the labeled sample DNA, the quantifying comprising detecting physical counts of signals arising from the labeled sample DNA of less than 550 nucleotides in length in the fluidic channels,
wherein the system is configured to compare coverage depth of the sample DNA molecules to coverage depth for labeled reference molecules so as to determine copy number for the sample nucleic acid molecules.
21. The system of claim 1 , wherein the fluidic nanochannel is configured to elongate at least a portion of a labeled reference molecule.
22. The system of claim 21 , wherein the fluidic nanochannel is configured to flow the labeled sample molecule and the labeled reference molecule in individual fluidic nanochannels.
23. The system of claim 21 , wherein the fluidic nanochannel is configured to flow the labeled sample molecule and the labeled reference molecule in the same fluidic nanochannel.
24. The system of claim 20 , wherein a quantity of signal from the reference molecules comprises an electronically or optically stored value or set of values.