Automated sample-to-microarray apparatus and method

Patent metadata

Field	Value
Publication number	US-8965710-B2
Application number	US-55951306-A
Country	US
Kind code	B2
Filing date	Nov 14, 2006
Priority date	Jul 2, 2004
Publication date	Feb 24, 2015
Grant date	Feb 24, 2015

Abstract

An apparatus having within or as part of a housing; a sample port; a microarray port; a lysis module; a purification module for containing a solid phase for binding of oligonucleotides; a thermocycling module for containing a polymerase chain reaction; a fragmentation module; and a microarray module for holding a microarray and a liquid in contact with the microarray. The apparatus is configured to be coupled to a device for: pumping a liquid through, in order, the lysis, purification, thermocycling, fragmentation, and microarray modules; sonicating any contents of the lysis module; thermocycling the thermocycling module to perform the polymerase chain reaction; heating the fragmentation module to fragment any oligonucleotides contained therein; circulating a fluid over the surface of the microarray; and performing one or more washing or staining steps on the microarray.

First claim

What is claimed is:

1. An apparatus comprising:
a housing;
a sample port for placing a liquid biological sample into the housing;
a microarray port for inserting a microarray having oligonucleotide probes thereon into the housing;
a lysis module within the housing and coupled to the sample port;
a purification module within the housing coupled to the lysis module and containing a solid phase comprising covalently immobilized capture probes that are capable of capturing 80% of human genomic DNA;
a thermocycling module within the housing coupled to the purification module and capable of containing a polymerase chain reaction;
a fragmentation module within the housing coupled to the thermocycling module; and
a microarray module within the housing coupled to the fragmentation module and capable of holding the microarray and a liquid in contact with the microarray;
wherein the apparatus is configured to be coupled to a device capable of:
pumping a liquid through, in order, the lysis module, the purification module, the thermocycling module, the fragmentation module, and the microarray module;
sonicating any contents of the lysis module;
thermocycling the thermocycling module to perform the polymerase chain reaction;
heating the fragmentation module to fragment any oligonucleotides contained therein;
circulating a fluid over the surface of the microarray; and
performing one or more washing or staining steps on the microarray.

2. The apparatus of claim 1 , further comprising:
a lysis reagent reservoir coupled to the lysis module.

3. The apparatus of claim 1 , wherein the thermocycling module is capable of containing a reverse transcriptase reaction.

4. The apparatus of claim 1 , further comprising:
a restriction enzyme reservoir coupled to the fragmentation module.

5. The apparatus of claim 1 , further comprising:
a biotin reservoir coupled to the fragmentation module.

6. The apparatus of claim 1 , further comprising:
a lyophilized restriction enzyme within the fragmentation module.

7. The apparatus of claim 1 , further comprising:
one or more wash or stain reservoirs coupled to the microarray module.

8. A method comprising:
providing an apparatus comprising:
a housing;
a sample port for placing a liquid biological sample into the housing;
a microarray port for inserting a microarray having oligonucleotide probes thereon into the housing;
a lysis module within the housing and coupled to the sample port;
a purification module within the housing coupled to the lysis module and containing a solid phase comprising covalently immobilized capture probes that are capable of capturing 80% of human genomic DNA;
a thermocycling module within the housing coupled to the purification module and capable of containing a polymerase chain reaction;
a fragmentation module within the housing coupled to the thermocycling module; and
a microarray module within the housing coupled to the fragmentation module and capable of holding the microarray and a liquid in contact with the microarray;

inserting the microarray into the microarray port;
inserting the sample through the sample port and into the lysis module; and
coupling the apparatus to a device, the device performing a process comprising:
sonicating the sample in the lysis module;
pumping the product of the sonication into the purification module;
hybridizing 80% of the human genomic DNA in the product of the sonication to the capture probes to produce a purified product;
pumping the purified product to the thermocycling module;
introducing a set of PCR primers into the thermocycling module;
performing a polymerase chain reaction within the thermocycling module to produce a product of the polymerase chain reaction containing PCR-produced oligonucleotides;
pumping the product of the polymerase chain reaction into the fragmentation module;
introducing a restriction enzyme into the fragmentation module;
heating the contents of the fragmentation module to cause fragmentation of the PCR-produced oligonucleotides to produce fragmented oligonucleotides;
pumping the product of the fragmentation into the microarray module;
circulating the product of the fragmentation over the microarray to allow hybridization of the fragmented oligonucleotides to the probes on the microarray; and
performing one or more washing or staining steps on the hybridized microarray.

9. The method of claim 8 , further comprising:
mixing the sample with a lysis reagent.

10. The method of claim 8 , further comprising:
performing a reverse transcriptase reaction in the thermocycling module before performing the polymerase chain reaction.

11. The method of claim 8 , further comprising:
biotinylating the product of the fragmentation.

12. The method of claim 8 , further comprising:
removing the apparatus from the device; and
coupling a second instance of the apparatus to the device.

Assignees

• Ligler Frances S
• Stenger David A
• Erickson Jeff
• Archer Marie
• Us Navy

Inventors

• Ligler Frances S
• Stenger David A
• Erickson Jeff
• Archer Marie

Classifications

• B01L2200/10

  Integrating sample preparation and analysis in single entity, e.g. lab-on-a-chip concept · CPC title

• G01N2035/00158

  Elements containing microarrays, i.e. "biochip" · CPC title

• B01L2400/0487

  fluid pressure, pneumatics · CPC title

• B01L2300/1827

  using resistive heater · CPC title

• B01L2300/087

  Multiple sequential chambers · CPC title