Dual-mode microfluidic genetics testing platforms and methods of dual-mode genetics testing using same

Abstract

Dual mode genetics testing systems are devised about a single element testing platform. A microfluidic network and system of interconnected receiving cells and reaction vessels supports at the same time genotyping and copy number analysis where the platform may be subject to a common thermal cycle schedule to cause the proper reactions (DNA replication) necessary in both test types. Further, the microfluidic platform which includes reaction vessels for genotyping which are spatially removed from reaction vessels for copy number analysis, is coupled to optical scanner and detection systems specifically arranged to apply test specific detection routines on each of these distinct regions or portions of the dual mode test platform.

1 - 12 . (canceled) 
     
     
         13 . A dual mode genetic testing method comprising:
 a) providing a plurality of reaction vessels in two distinct test modules with TaqMan reagent chemistry, said two distinct test modules comprising a genotyping module and a copy number analysis module;   b) providing at least one DNA sample in a plurality of reaction vessels of two distinct test modules comprising a genotyping module and a copy number analysis module;   c) mixing the provided TaqMan reagents with the provided DNA;   d) executing a repeated thermal cycle to induce replication of the provided DNA, wherein the thermal cycle includes comprises:
 i) heating the provided DNA in the reaction vessels to cause denaturing of the DNA; 
   ii) cooling the denatured DNA in the reaction vessels to cause annealing and DNA replication;   iii) illuminating the copy number analysis module with high energy light to stimulate fluorescence in the reaction cells thereof;   iv) capturing optical return signal from the copy number analysis module; and   v) determining whether the last executed cycle is a final cycle of a prescribed thermal cycle schedule;   e) illuminating the genotyping module with high energy light to stimulate fluorescence in the reaction cells thereof; and   f) capturing a spatially distributed optical signal from the genotyping module.   
     
     
         14 . The dual mode genetic testing method of  claim 13 , said “providing TaqMan reagent chemistry” step comprises loading the reaction vessels of a copy number analysis module with a TaqMan chemistry; and loading the reaction vessels of a genotyping module with another TaqMan chemistry. 
     
     
         15 . The dual mode genetic testing method of  claim 14 , said “loading the reaction vessels of a copy number analysis module” comprises providing a composition of PCR reagents configured for a copy number analysis type genetic testing and a contrast enhancing reagent. 
     
     
         16 . The dual mode genetic testing method of  claim 13 , said “providing at least one DNA sample” comprises providing a reference oligonucleotide in at least one reaction vessel of the copy number analysis module. 
     
     
         17 . The dual mode genetic testing method of  claim 13 , said “capturing optical return signal from the copy number analysis module” comprises capturing a plurality of signals over the course of a thermal cycle schedule to form a plot of return signal intensity as a function of thermal cycles applied from which a copy number determination may be based. 
     
     
         18 . The dual mode genetic testing method of  claim 13 , said “capturing an optical return signal from the genotyping module” comprises capturing and thresholding an optical signal at the end of a thermal cycle schedule from which a genotype determination may be based. 
     
     
         19 . The dual mode genetic testing method of  claim 17 , said capturing an optical signal from the genotyping module comprises capturing a bi-color signal whereby a determination of allele identity and/or zygosity of a locus of interest may be made. 
     
     
         20 . The dual mode genetic testing method of  claim 13 , said “providing at least one DNA sample” step comprises placing a DNA sample from a single organism in at least one reaction vessel of the genotyping module and at least one reaction vessel of the copy number analysis module. 
     
     
         21 . A dual mode genetic testing method comprising:
 providing a microfluidic platform comprising a first test module and a second test module, the first test module comprising a plurality of first reaction vessels each comprising a first composition of PCR reagents configured for a copy number analysis type genetic testing, and the second test module comprising a plurality of second reaction vessels each comprising a second composition of PCR reagents configured for a genotype testing;   obtaining a genomic DNA sample from a test subject;   dispensing the genomic DNA sample into at least one of the first reaction vessels and at least one of the second reaction vessel of the microfluidic platform;   simultaneously subjecting the microfluidic platform to a prescribed set of thermal cycles, wherein the microfluidic platform remains in physical contact with a thermocycler system throughout the prescribed set of thermal cycles;   capturing a plurality of discrete optical signals from each of the first reaction vessels whereby determining copy number of a locus of interest; and   capturing a single optical signal from each of the second reaction vessels at a discrete moment in time whereby determining allele identity and/or zygosity of a genetic polymorphism of interest.   
     
     
         22 . The dual mode genetic testing method of  claim 21 , wherein capturing a plurality of discrete optical signals from each of the first reaction vessels comprises optically coupling each of the first reaction vessels to a first channel of a multi-channel optical detector, and capturing the plurality of discrete optical signals from each of the first reaction vessels over the course of an extended period of time to form a plot of captured signal intensity as a function of thermal cycles applied. 
     
     
         23 . The dual mode genetic testing method of  claim 21 , wherein capturing a single optical signal from each of the second reaction vessels comprises optically coupling each of the second reaction vessels to a second channel of a multi-channel optical detector. 
     
     
         24 . The dual mode genetic testing method of  claim 21 , wherein each of the first reaction vessels further comprises a contrast enhancing reagent. 
     
     
         25 . The dual mode genetic testing method of  claim 21 , wherein each of the second reaction vessels further comprises at least two optically activated markers each being indicative of a specific allele of the genetic polymorphism of interest, whereby a determination of allele identity and/or zygosity of a genetic polymorphism of interest may be made. 
     
     
         26 . The dual mode genetic testing method of  claim 22 , wherein said first channel is further arranged with driver electronics which enable the optical detector to detect return optical signal of intensities which range over at least two orders of magnitude. 
     
     
         27 . The dual mode genetic testing method of  claim 23 , wherein said second channel is further arranged with driver electronics operable for capturing optical signals of a plurality of wavelength. 
     
     
         28 . The dual mode genetic testing method of  claim 21 , wherein the microfluidic platform further comprises optically activated markers attached to a genetic fragment, wherein nucleotide sequence of the genetic fragment corresponds to a gene of particular interest and wherein the optically activated markers' reemission spectra are affected by proximity of the markers to one another. 
     
     
         29 . The dual mode genetic testing method of  claim 28 , wherein the microfluidic platform comprises a first and a second optically activated markers,
 said first optically activated marker attached to a first genetic fragment having a sequence which selectively anneals to a first allele at a locus of interest, said second optically activated marker attached to a second genetic fragment having a sequence which selectively anneals to a region of variable copy number.   
     
     
         30 . The dual mode genetic testing method of  claim 29 , wherein said second test module further comprises a reference nucleic acid molecule capable of annealing with said second genetic fragment to produce an optical signal by which a comparison may be made with respect to alleles under test. 
     
     
         31 . The dual mode genetic testing method of  claim 29 , wherein said first optically activated marker attached to a first genetic fragment having a sequence which selectively anneals to an allele of a locus of interest is provided with a third optically activated marker attached to a third genetic fragment having a sequence which selectively anneals to a second allele of a locus of interest, and wherein said third optically active marker possess an optical property which is detectably different from said first optically active marker. 
     
     
         32 . The dual mode genetic testing method of  claim 21 , wherein at least one of said first reaction vessels and at least one of said second reaction vessels are provided with a common nucleic acid sample. 
     
     
         33 . The dual mode genetic testing method of  claim 32 , wherein first optically activated marker fluoresces at a first wavelength, wherein said third optically activated marker fluoresces at a third wavelength, and wherein said multi-channel optical detector is configured to distinctly detect said first wavelength and said third wavelength. 
     
     
         34 . The dual mode genetic testing method of  claim 21 , wherein said contrast enhancing reagent specifically enhances optical signals captured from the reactions vessels of the first test module. 
     
     
         35 . The dual mode genetic testing method of  claim 21 , wherein said first channel of the multi-channel detector is color blind.