Process for specimen handling for analysis of nucleic acids

Claim 1

A process for handling a single specimen for the analysis of nucleic acid sequences, comprising: (a) immobilizing said specimen in a device comprising a top cover portion and a bottom housing portion, said top cover portion hingedly moved to a closed position; said bottom housing portion having an extended area on a first side of said bottom housing portion extending beyond said top cover portion; wherein said bottom housing portion has edges defining a space, said space comprises a fluid receiving area in the extended area and a thin, flat matrix and specimen holding area; said fluid receiving area being in fluid communication with said matrix and specimen holding area; wherein immobilizing the specimen in the matrix and specimen holding area is by means selected from the group consisting of standard fixatives and gel matrix materials; which matrix and specimen holding area is defined by the top cover portion when said top cover portion is in a closed position; (b) adding a first treatment fluid to said fluid receiving area wherein the first treatment fluid fills said matrix and specimen holding area forming a liquid film in contact with the top cover portion and the matrix and specimen, said treatment fluids selected from the group consisting of lysing and denaturing solutions, wash and rinse solutions, amplification, hybridization and detection reagents and electrophoresis buffers; wherein said treatment fluids are added to the device so that the nucleic acids of the immobilized specimen are treated in place on the device; wherein the top cover portion is in said closed position during amplification; (c) controlling the temperature of the carrier device for incubating a treatment fluid with the specimen at a desired temperature for a desired time period, said temperature control selected from the group consisting of maintaining and changing the temperature of the device; (d) adding a volume of a second treatment fluid equal to the volume of the first treatment fluid wherein the first fluid volume exits the matrix and specimen holding area opposite where the fluids are added; (e) repeating the addition of fluids sufficient to rinse away the prior treatment fluid and bring the next treatment fluid into contact with the specimen in the matrix and specimen holding area; wherein the detection reagents are used to visualize and enumerate individual locations of the nucleic acids in place within the specimen.