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US 6,203,990 B1Granted
Method and system for pattern analysis, such as for analyzing oligonucleotide primer extension assay products
AssigneeMitoKor
InventorEoin David Fahy
Life of this patent
Estimating the term…
Abstract
A system and corresponding method analyzes data for patterns, such as data produced from DNA sequencers. An ASCII text file, generated by DNA sequencer software, is used as the input source for the pattern analysis software program. This text file contains peak intensity data, identified by gel-lane and mobility, for bands corresponding to 2 sequences of differing length. The software uses gel-mobility values of control DNA samples to identify bands of interest from test samples in the dataset. Spurious data point or artifacts are filtered out in this selection process. The selected data is then imported to a second software program that performs algorithms such as linear progression and curve fitting.
Claims35
A system for generating information based on biological samples, comprising:
- a biological assay device that analyzes a two dimensionally spaced set of biological samples and produces a set of data therefrom, wherein the biological samples include at least one control sample, wherein the set of data includes x-axis and y-axis spatial coordinate values and a quantitative value for each biological sample, and wherein the set of data may include unwanted values;
- and
- a computer having a processor and memory, wherein the computer receives the set of data from the biological assay device, stores the set of data in the memory, and wherein the processor:
- determines a two dimensional location of the at least one control sample based on the set of data;
- identifies x-axis and y-axis spatial coordinates for the biological samples in the set of data based on the determined two dimensional location of the at least one control sample;
- filters the quantitative values of for at least some of the biological samples, from the unwanted values, in the set of data, based on the identified x-axis and y-axis spatial coordinates;
- and
- analyzes the filtered quantitative values of each biological sample, respectively, by comparing the quantitative value of a first portion of the filtered quantitative values of each respective biological sample at a first pair of x-axis and y-axis spatial coordinates with a sum of the quantitative value of the first portion and the quantitative value of a second portion of the filtered quantitative values of each respective biological sample at a second pair of x-axis and y-axis spatial coordinates to produce a displayable report of the analyzed quantitative values.
5 more elements
The system of claim wherein the computer includes a web browser, and wherein the displayable report is provided to the web browser for transmission over the Internet.
A method for generating information based on biological samples, comprising:
- receiving a set of data produced from testing a set of biological samples, wherein the biological samples include test samples and at least one control sample related to at least some of the test samples by space, time or frequency, wherein the set of data includes first and second values and a quantitative value for each test sample;
- identifying first or second values corresponding to the control sample in the set of data;
- identifying first or second values for at least some of the test samples in the set of data based on the identified first or second values of the control sample and the spatial, temporal or frequency relationship between the control sample and the at least some of the test samples;
- filtering the quantitative values for the at least some of the test samples in the set of data based on the identified first or second values;
- and
- analyzing the filtered quantitative values of a selected test sample by comparing the quantitative value of a first portion of the filtered quantitative values of the selected test sample at a first pair of x-axis and y-axis spatial coordinates with a sum of the quantitative value of the first portion and the quantitative value of a second portion of the filtered quantitative values of the selected test sample at a second pair of x-axis and y-axis spatial coordinates.
3 more elements
A computer-readable medium for storing computer readable instructions, the instructions being capable of programming a computer to perform a method, the method comprising:
- receiving a set of data produced from testing a set of biological samples, wherein the biological samples include test samples and at least one control sample related to at least some of the test samples by space, time or frequency, wherein the set of data includes first and second values and a quantitative value for each test sample;
- identifying first or second values corresponding to the control sample in the set of data;
- identifying first or second values for at least some of the test samples in the set of data based on the identified first or second values of the control sample and the spatial, temporal or frequency relationship between the control sample and the at least some of the test samples;
- filtering the quantitative values for the at least some of the test samples in the set of data based on the identified first or second values;
- and
- analyzing the filtered quantitative values of a selected one of the test samples by comparing the quantitative value of a first portion of the filtered quantitative values of the selected test sample at a first pair of x-axis and y-axis spatial coordinates with a sum of the quantitative value of the first portion and the quantitative value of a second portion of the filtered quantitative values of the selected test sample at a second pair of x-axis and y-axis spatial coordinates.
3 more elements
A method for displaying to a user information from biological samples, comprising:
- receiving a set of data produced from testing a set of biological samples, wherein the biological samples include test samples and at least one control sample related to at least some of the test samples by space, time or frequency, and wherein the set of data includes first and second values and a quantitative value for each test sample;
- identifying first or second values corresponding to the control sample in the set of data;
- identifying first or second values for at least some of the test samples in the set of data based on the identified first or second values of the control sample and the spatial, temporal or frequency relationship between the control sample and the at least some of the test samples;
- filtering the quantitative values for the at least some of the test samples in the set of data based on the identified first or second values;
- analyzing each of the test samples by calculating a ratio of a quantitative value of a first component of the first or second value for each test sample to the sum of the quantitative value of the first component and a quantitative value of a second component of the first or second value for each respective test sample;
- and
- displaying the filtered quantitative values, so that only quantitative values for test samples of interest are displayed.
4 more elements
A method for generating information based on biological samples, comprising:
- receiving a set of data produced from testing a set of biological samples, wherein the biological samples includes a test sample;
- filtering the test sample to separate the test sample into at least first and second components;
- analyzing the test sample by calculating a ratio of the quantitative value of the first component to the quantitative value of a sum of the first and second components;
- and
- displaying results of the analysis.
2 more elements
Dependencies are inferred from the claim text.