DEVICES, SYSTEMS AND METHODS FOR ULTRA-LOW VOLUME LIQUID BIOPSY
Provided herein are devices, systems, kits and methods for obtaining genetic information from cell-free fetal nucleic acids in ultra-low amounts of biological samples. Due to the convenience of obtaining ultra-low amounts of samples, devices, systems, kits and methods can be at least partially employed at a point of need.
1 ) A method comprising:
a) obtaining capillary blood from a subject, wherein the capillary blood comprises cell-free nucleic acids;
b) optionally amplifying the cell-free nucleic acids;
c) tagging at least a portion of the cell-free nucleic acids to produce a library of tagged cell-free nucleic acids;
d) optionally amplifying the tagged cell-free nucleic acids;
e) sequencing at least a portion of the tagged cell-free nucleic acids; and
f) detecting a normal representation, an overrepresentation or an underrepresentation of at least one target sequence in the at least a portion of the tagged cell-free nucleic acids.
2 ) The method of claim 1 , comprising producing a library having an efficiency of at least 0.5.
3 ) The method of claim 1 , comprising amplifying the cell-free nucleic acids or tagged cell-free nucleic acids in the presence of a crowding agent.
4 ) The method of any one of claim 1 , comprising repairing ends of the cell-free nucleic acids.
5 ) The method of claim 1 , wherein obtaining capillary blood comprises obtaining not more than 1 milliliter of blood.
6 ) The method of claim 1 , wherein obtaining capillary blood comprises obtaining not more than 100 microliters of blood.
7 ) The method of claim 1 , wherein obtaining capillary blood comprises obtaining not more than 40 microliters of blood.
8 ) The method of claim 1 , wherein the target cell-free nucleic acids are cell-free nucleic acids from a tumor.
9 ) The method of claim 1 , wherein the target cell-free nucleic acids are cell-free nucleic acids from a fetus.
10 ) The method of claim 1 , wherein the target cell-free nucleic acids are cell-free nucleic acids from a transplanted tissue or organ.
11 ) A method comprising:
a) obtaining a biological sample from a subject, wherein the biological sample contains up to about 10 9 cell-free nucleic acid molecules;
b) sequencing at least a portion of the cell-free nucleic acid molecules to produce sequencing reads;
c) measuring at least a portion of sequencing reads corresponding to at least one chromosomal region; and
d) detecting a normal representation, an overrepresentation or an underrepresentation of the at least one chromosomal region.
12 ) The method of claim 11 , wherein the biological sample is a biological fluid having a volume of less than about 500 μl.
13 ) The method of claim 11 , wherein the biological sample is a biological fluid having a volume of about 1 μL to about 100 μl.
14 ) The method of claim 11 , wherein the biological sample is a biological fluid having a volume of about 5 μL to about 80 μl.
15 ) The method of claim 11 , wherein the biological sample comprises blood, plasma, serum, urine, interstitial fluid, vaginal cells, vaginal fluid, buccal cells, or saliva.
16 ) The method of claim 11 , wherein the biological sample is serum or plasma.
17 ) The method of claim 11 , further comprising separating the plasma or serum from a blood sample.
18 ) The method of claim 17 , wherein separating comprises filtering the blood sample to remove cells, cell fragments, microvesicles, or a combination thereof, from the blood sample to produce the plasma sample.
19 ) The method of claim 17 , wherein obtaining the blood sample comprises pricking a finger.
20 ) The method of claim 11 , wherein the biological sample contains about 10 4 to about 10 9 cell-free nucleic acid molecules.
21 ) The method of claim 11 , wherein the biological sample contains about 10 4 to about 10 7 cell-free nucleic acid molecules.
22 ) The method of claim 11 , wherein the biological sample contains less than 300 pg of cell-free nucleic acid molecules.
23 ) The method of claim 11 , wherein the biological sample contains less than 3 ng of cell-free nucleic acid molecules.
24 ) The method of claim 11 , wherein the subject is a pregnant subject and the cell-free nucleic acid molecules comprise cell-free fetal nucleic acid molecules.
25 ) The method of claim 11 , wherein the cell-free nucleic acids comprise nucleic acids from a tumor in a tissue.
26 ) A system comprising:
a) a sample collector configured to collect a fluid sample of a subject;
b) a sample processor that is configured to isolate a sample component from the fluid sample;
c) a nucleic acid detector that is configured to detect nucleic acids in the fluid sample or the sample component; and
d) a nucleic acid information output.
27 ) The system of claim 26 , wherein the sample collector comprises a transdermal puncture device.
28 ) The system of claim 27 , wherein the transdermal puncture device comprises at least one of a needle, a lancet, a microneedle, a vacuum, and a microneedle array.
29 ) The system of claim 26 , wherein the sample component is selected from a cell, a carbohydrate, a phospholipid, a protein, a nucleic acid, and a microvesicle.
30 ) The system of claim 26 , wherein the sample component is a blood cell.
31 ) The system of claim 26 , wherein the sample component does not comprise a cell-free nucleic acid.
32 ) The system of claim 26 , wherein the sample component comprises a cell-free nucleic acid.
33 ) The system of claim 26 , wherein the sample component is plasma or serum.
34 ) The system of claim 33 , wherein the sample purifier is configured to isolate plasma from less than 1 milliliter of blood.
35 ) The system of claim 33 , wherein the sample purifier is configured to isolate plasma from less than 250 μl of blood.
36 ) The system of claim 26 , wherein the nucleic acid detector comprises a nucleic acid sequencer.
37 ) The system of claim 26 , wherein the system is configured to label nucleic acids of interest in the fluid sample, and the nucleic acid detector comprises a counting system that counts the labels to detect a representation of the nucleic acids of interest in the sample.
38 ) The system of claim 26 , comprising at least one nucleic acid amplification reagent and at least one crowding agent.
39 ) The system of claim 26 , comprising at least a first label for producing a library of cell-free nucleic acids from the fluid sample, and at least one amplification reagent.
40 ) The system of claim 26 , wherein the nucleic acid sequence output is selected from a wireless communication device, a wired communication device, a cable port, and an electronic display.
41 ) The system of claim 26 , wherein all components of the system are present in a single location.
42 ) The system of claim 26 , wherein all components of the system are housed in a single device.
43 ) The system of claim 26 , wherein the sample collector is located at a first location and at least one of the sample purifier and nucleic acid detector are second location.
44 ) The system of claim 26 , wherein the sample collector and at least one of the sample purifier and nucleic acid detector are at the same location.
45 ) The system of claim 26 , wherein the sample purifier comprises a filter.
46 ) The system of claim 45 , wherein the filter has a pore size of about 0.05 microns to about 2 microns.
47 ) The system of claim 26 , comprising a transport or storage compartment for transporting or storing at least a portion of the fluid sample.
48 ) The system of claim 47 , wherein the transport or storage compartment comprises an absorption pad, a fluid container, a sample preservative, or a combination thereof.