Devices, systems and methods for ultra-low volume liquid biopsy

Abstract

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.

What is claimed is: 
     
         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.