System, method and apparatus for transgenic and targeted mutagenesis screening
AssigneeTransnetyx, Inc.
InventorsTimothy A. Hodge, Shawn O'Malley
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Abstract
The present invention provides a method and apparatus for to conduct transgenic and targeted mutagenesis screening of genomic DNA. This invention also provides a system for screening DNA for a designated genetic sequence. The system includes a computer having a processor, memory and web browser, wherein the computer receives instructions concerning the designated genetic sequence and other screening parameter selection from a remote user via a form of electronic communication, and an automatic screening device that analyzes samples of genomic DNA for the designated sequence.
Claims195
A method to detect a designated genetic sequence in a sample of genomic DNA, comprising:
- (a) depositing genomic DNA on a substrate;
- (b) adding at least one labeled probe specific for a portion of said designated genetic sequence;
- (c) detecting the signal from said at least one labeled probe specific for a portion of said designated genetic sequence to detect said designated genetic sequence in said sample of genomic DNA.
A method to detect a designated genetic sequence in a sample of genomic DNA, by comparing said sample with a designated control sample of genomic DNA, the method comprising the steps of:
- (a) depositing said genomic DNA from said sample at a first location on a substrate;
- (b) depositing said genomic DNA from said designated control sample at a second location on said substrate;
- (c) adding at least one labeled probe specific for a portion of said designated genetic sequence to said first and second locations on said substrate;
- (d) detecting the signal from said at least one labeled probe, specific for a portion of said designated genetic sequence at said first and second locations on said substrate, and
- (e) comparing the signal from said first and second locations on said substrate to detect a designated genetic sequence in said sample of genomic DNA.
A method to detect a designated genetic sequence in a sample of tissue by comparing said sample to a designated control sample of tissue, this method comprising the steps of:
- (a) treating said sample of tissue and said designated control sample of tissue with a sufficient amount of a lysis buffer to obtain cellular debris including genomic DNA;
- (b) separating the genomic DNA from the cellular debris for said sample of tissue and said designated control sample of tissue;
- (c) depositing the genomic DNA from said sample at a first location on a substrate;
- (d) depositing the genomic DNA from said designated control sample at a second location on said substrate;
- (e) adding at least one labeled probe specific for a portion of said designated genetic sequence to said first and second locations on said substrate;
- (f) detecting the signal from said at least one labeled probe, specific for a portion of said designated genetic sequence, at said first and second locations on said substrate, and
- (g) comparing the signal from said first and second locations on said substrate to detect a designated genetic sequence in said sample of tissue.
A method to detect a designated genetic sequence in a sample of tissue by comparing said sample with a designated control sample of tissue, this method comprising the steps of:
- (a) treating said sample of tissue and said designated control sample of tissue with a sufficient amount of a lysis buffer to obtain cellular debris including genomic DNA;
- (b) separating the genomic DNA from the cellular debris for said sample of tissue and said designated control sample of tissue using magnetic particles;
- (c) depositing genomic DNA from said sample at a first location on a substrate;
- (d) depositing genomic DNA from said designated control sample at a second location on said substrate;
- (e) adding at least one labeled probe specific for a portion of said designated genomic sequence to said first and second locations on said substrate;
- (f) detecting the signal from said at least one labeled probe, specific for a portion of said designated genetic sequence at said first and second locations on said substrate, and
- (g) comparing the signal from said first and second locations on said substrate to detect said designated genetic sequence in said sample of tissue.
A method to detect a designated genetic sequence in a sample of tissue by comparing said sample with a designated control sample of tissue, this method comprising the steps of:
- (a) treating said sample of tissue and said designated control sample of tissue with a sufficient amount of a lysis buffer to obtain cellular debris including genomic DNA;
- (b) separating the genomic DNA from the cellular debris for said sample of tissue and said designated control sample of tissue using magnetic particles;
- (c) adjusting genomic DNA concentration to facilitate detection of said designated genetic sequence;
- (d) depositing genomic DNA from said sample at a first location on said substrate;
- (e) depositing genomic DNA from said designated control sample at a second location on said substrate;
- (f) adding at least one labeled probe specific for a portion of said designated genomic sequence to said first and second locations on said substrate;
- (g) detecting the signal from said at least one labeled probe, specific for a portion of said designated genetic sequence at said first and second locations on said substrate, and
- (h) comparing the signal from said first and second locations on said substrate to detect said designated genetic sequence in said sample of tissue.
A method of screening a sample of for a designated genetic sequence by comparing said sample with a designated control sample of tissue said screening method using at least one labeled target binding probe and at least one labeled reference binding probe, the method comprising the steps of:
- (a) treating said sample of tissue and said designated control sample of tissue with a sufficient amount of a lysis buffer to obtain cellular debris including genomic DNA;
- (b) separating the genomic DNA from the cellular debris for said sample of tissue and said designated control sample of tissue using magnetic particles;
- (c) depositing genomic DNA from said sample at a first location on a substrate;
- (d) depositing genomic DNA from said designated control sample at a second location on said substrate;
- (e) adding at least one labeled probe specific for a portion of said designated genetic sequence to said first and second locations on said substrate;
- (f) adding at least one labeled reference binding probe to said first and second locations on said substrate;
- (g) detecting the signal from said at least one labeled probe, specific for a portion of said designated genetic sequence at said first and second locations on said substrate,
- (h) detecting the signal from at least one labeled reference binding probe at said first and second locations on said substrate;
- (e) comparing the signal from said first and second locations on said substrate to screen a sample for said designated genetic sequence.
A method of screening a sample of tissue for a designated genetic sequence, by comparing said sample with a designated control sample of tissue, wherein said tissue samples, including said genomic DNA, are sent by a remote user to a screening laboratory;
- this method comprising the steps of:
- (a) facilitating the extraction of genomic DNA from a tissue sample by providing a lysis buffer to a remote user;
- (b) treating said sample of tissue and said designated control sample of tissue with a sufficient amount of said lysis buffer to obtain cellular debris including genomic DNA;
- (c) transmitting said tissue samples in said lysis buffer from said remote user to said screening laboratory;
- (d) receiving the lysed tissue samples at said screening laboratory from the remote user;
- (e) separating the genomic DNA from the cellular debris for said sample of tissue and said designated control sample of tissue using magnetic particles;
- (f) depositing genomic DNA from said sample at a first location on a substrate;
- (g) depositing genomic DNA from said designated control sample at a second location on said substrate;
- (h) adding at least one labeled probe specific for a portion of said designated genomic sequence to said first and second locations on said substrate;
- (i) detecting the signal from said at least one labeled probe, specific for a portion of said designated genetic sequence at said first and second locations on said substrate, and
- (j) comparing the signal from said first and second locations on said substrate to screen said tissue sample for said designated genetic sequence.
A method of screening genomic DNA, in at least one sample, sent by a remote user to a screening laboratory, for a designated genomic DNA sequence, said remote user providing screening parameters via an electronic communications link to said screening laboratory and a supplier, the method comprising:
- (a) transmitting an access request from a remote user to a screening laboratory via an electronic communications link;
- (b) transmitting an access enabling response from said screening laboratory to said remote user via an electronic communications link, said access enabling response including said screening parameters;
- (c) selecting screening parameters by said remote user;
- (d) transmitting said selected screening parameter selections from said remote user to said screening laboratory via an electronic communications link;
- (e) receiving screening parameter selections from said remote user by said screening laboratory via said communications link;
- (f) transmitting a request from said remote user via an electronic communications link to a supplier to obtain probes conforming to selected screening parameters;
- (g) receiving said probes by said laboratory
- (h) transmitting said sample from said remote user to said screening laboratory;
- (i) conducting screening of said sample, according to said selected screening parameters, to obtain data;
- and
- (j) transmitting said data to said remote user via an electronic communications link.
A method of screening genomic DNA, in at least one sample, sent by a remote user to a screening laboratory for a designated genetic DNA sequence, said remote user providing screening parameters via an electronic communications link to the screening, the method comprising:
- (a) transmitting an access request from a remote user to a screening laboratory via an electronic communications link;
- (b) transmitting an access enabling response from said screening laboratory to said remote user via an electronic communications link, said access enabling response including said screening parameters;
- (c) selecting screening parameters by said remote user;
- (d) transmitting said selected screening parameter selections from said remote user to said screening laboratory via an electronic communications link;
- (e) receiving screening parameter selections from said remote user by said screening laboratory via said communications link;
- (f) transmitting a request from said screening laboratory via an electronic communications link to a supplier to obtain probes conforming to selected screening parameters;
- (g) receiving said probes by said screening laboratory;
- (h) transmitting said sample from said remote user to said screening laboratory;
- (i) conducting screening of said sample, according to said selected screening parameters, to obtain data;
- and
- (j) transmitting said data to said remote user via an electronic communications link.
A method of screening genomic DNA, in at least one sample, sent by a remote user to a screening laboratory for a designated genomic DNA sequence, said remote user providing screening parameters via an electronic communications link to the screening, the method comprising:
- (a) transmitting an access request from a remote user to a screening laboratory via an electronic communications link;
- (b) transmitting an access enabling response from said screening laboratory to said remote user via an electronic communications link, said access enabling response including said screening parameters;
- (c) selecting screening parameters by said remote user;
- (d) transmitting said selected screening parameter selections from said remote user to said screening laboratory via an electronic communications link;
- (e) receiving selected screening parameter selections from said remote user by said screening laboratory via said communications link;
- (f) transmitting a request from said screening laboratory via an electronic communications link to a supplier to obtain probes conforming to selected screening parameters;
- (g) receiving said probes by said screening laboratory;
- (h) transmitting a sample of tissue in a lysis buffer from said remote user to said screening laboratory, said lysis buffer formulated to lysis said tissue in said sample during transit time between said remote user and said screening laboratory
- (i) conducting screening of said sample, according to said selected screening parameters, to obtain data;
- and
- (j) transmitting said data to said remote user via an electronic communications link.
An automated apparatus for high volume screening and targeted mutagenesis screening of tissue samples sent by a remote user to a screening laboratory;
- comprising:
- (a) means for transmitting an access request from a remote user to a screening laboratory via an electronic communications link;
- (b) means for transmitting an access enabling response from said screening laboratory, to said remote user via an electronic communications link with screening parameters;
- (c) means for transmitting screening parameter selections from said remote user to said screening laboratory;
- (d) means for transmitting said sample from said remote user to said screening laboratory;
- (e) means for isolating genomic DNA from said sample;
- (f) means for depositing said genomic DNA on to a substrate;
- (g) means for screening genomic DNA;
- and
- (h) means for transmitting said data to said remote user.
A high volume apparatus for screening a tissue sample for modified or mutated genomic DNA according to screening parameter selections made by a remote user, comprising:
- (a) an automated accessioning station for removing liquid from a first well plate to a second well plate;
- (b) an isolation station for isolating genomic DNA in said second well plate;
- (c) an optical standardization station for adjusting DNA concentration in said second well plate;
- (d) an arraying station for depositing said genomic DNA from said second testing plate on to a substrate;
- (e) a hybridization station for hydridizing labeled probes that bind to the portions of the genomic DNA;
- (f) a detection station for detecting the bound labeled probes;
- (g) means for making screening parameter selections by a remote user, the remote user communicating with the apparatus through electronic communications link;
- and
- (h) means for communicating screening results to the remote user through an electronic communications link.
A system of screening genomic DNA in a sample for a designated genomic DNA sequence comprising:
- (a) computer having a processor, memory and web browser wherein the computer is adapted to receive the screening parameter selections from a remote user;
- and
- (b) a work station that analyzes samples of genomic DNA for said screening parameter selections wherein said workstation includes a microarray imager.
Dependencies are inferred from the claim text.