US6054268

Method and system for genotyping

The present invention pertains to a process which can be fully automated for accurately determining the alleles of genetic markers. More specifically, the present invention is related to performing PCR amplification on locations of DNA to generate a reproducible pattern, labeling the PCR products, converting the labels into a signal, operating on the signal, and then determining the genotype of the location of the DNA. An amplification can include multiple locations from the DNA of one or more individuals. The invention also pertains to genetics applications and systems which can effectively use this genotyping information.

1. A method for determining where a lane or DNA fragment size is located in an image of DNA fragments comprising the steps:
   1. obtaining labeled DNA fragments that include size standard fragments;
   2. separating the labeled DNA fragments by size to form a lane;
   3. detecting labeled DNA fragments to form part of an image represented as a set of signals in the memory of a computing device;
   4. obtaining expected locations of the size standard fragments in the image;
   5. operating a processor of a computing device with memory on the image and the expected locations to form a comparison; and
   6. determining from said comparison where a lane or DNA fragment size is located in the image.
2. A method as described in claim 1 wherein the operating step simultaneously processes two dimensions in the image.
3. A method as described in claim 1 wherein the labeled DNA fragments include a labeled DNA sample fragment derived from a DNA sample, and after the determining step there are the steps of:
   7. detecting a labeled DNA sample fragment in the image to form a second set of signals in the memory of a computing device;
   8. operating a processor of a computing device on the second set of signals and on the determined location of a lane or DNA fragment size in the image to form a second comparison; and
   9. estimating from the second comparison a physical property of the labeled DNA sample fragment corresponding to a DNA size or a DNA concentration.
4. A method as described in claim 3 wherein the estimated physical property of the labeled DNA sample fragment corresponds to a DNA size or a DNA concentration.
5. A method as described in claim 3 wherein after the estimating step (i) there is the step of using the estimated property in a genetic analysis to identify a gene.
6. A method for genotyping comprised of the steps:
   1. obtaining DNA or RNA material from a genome;
   2. amplifying an STR genetic marker at a location of the material to produce an amplified product having a reproducible pattern;
   3. labeling the amplified product with labels;
   4. converting the labels with a sensing device which produces a first electrical signal;
   5. operating on the first electrical signal with a second electrical signal corresponding to the reproducible pattern to form a third electrical signal; and
   6. producing from the third electrical signal a genotype of the material at the location.
7. A method as described in claim 6 wherein after the producing step there is the step of identifying and isolating a gene by positional cloning.
8. A method as described in claim 7 wherein after the identifying and isolating step there is the step of determining the DNA sequence of the gene.
9. A method as described in claim 8 wherein after the determining step there is the step of purifying derivatives of the gene.
10. A method as described in claim 1 wherein the step of separating the labeled fragments is performed by gel electrophoresis.