US5541067

Method and system for genotyping

The present invention pertains to a process which can be fully automated for accurately determining the alleles of STR genetic markers. More specifically, the present invention is related to performing PCR amplification on locations of DNA, labelling the PCR products, converting the labels into a signal, removing a reproducible PCR stutter pattern from the signal by means of a computational device, 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 genotyping comprised of the steps:
   1. obtaining DNA or RNA material from a genome;
   2. amplifying locations of the material, with the length of the location not exceeding fifty kilobases and the location containing a polynucleotide repeat region;
   3. labelling the amplified material with labels;
   4. converting the labels with a sensing device which produces a first electrical signal;
   5. removing a reproducible pattern of the amplification from the first electrical signal to form a third electrical signal; and
   6. producing from the third electrical signal a genotype of the material at the locations.
2. A method as described in claim 1 wherein the reproducible pattern of the amplification corresponds to a PCR stutter artifact of the location.
3. A method as described in claim 1 wherein the step of removing the reproducible pattern from the first electrical signal includes the step of a deconvolution procedure.
4. A method as described in claim 1 wherein the step of removing the reproducible pattern from the first electrical signal includes the step of deconvolving with a second electrical signal related to the reproducible pattern of the amplification.
5. A method as described in claim 1 wherein the step of removing the reproducible pattern includes the step of deconvolving with matrix processing of the electrical signals.
6. A method as described in claim 1 wherein the determination of the second set of electrical signals of the location is comprised of the steps:
   1. obtaining DNA or RNA material from a genome;
   2. amplifying locations of the material, with the length of the location not exceeding fifty kilobases and the location containing a polynucleotide repeat region;
   3. labelling the amplified material with labels;
   4. converting the labels with a sensing device which produces a first electrical signal; and
   5. operating on the first set of electrical signals produced from the amplified material to produce a second set of electrical signals corresponding to reproducible patterns of the locations.
7. A method as described in claim 1 wherein the obtaining step pools DNA or RNA from one or more individuals.
8. A method as described in claim 1 wherein the amplifying step includes more than one polynucleotide repeat location.
9. A method as described in claim 1 wherein the amplifying step includes more than one polynucleotide repeat location, and the size properties of these locations may overlap.
10. A method as described in claim 1 wherein the amplifying step includes more than one polynucleotide repeat location, the size properties of these locations may overlap, and the reproducible patterns of the different locations include bands of the same size.
11. A method as described in claim 1 wherein the amplifying step includes more than one polynucleotide repeat location, the size properties of these locations may overlap, the reproducible patterns of the different locations include bands of the same size, and the reproducible patterns of the different locations are used in genotyping the locations.
12. A method as described in claim 1 wherein the removing step combines the first electrical signal with a second set of electrical signals corresponding to reproducible patterns of the locations.
13. A system for genotyping comprising:
    1. means for obtaining nucleic acid material from a genome;
    2. means for amplifying locations of the material, said amplifying means in communication with the nucleic acid material;
    3. means for assaying the amplified material based on size and concentration, said assaying means in communication with amplifying means;
    4. means for converting the assayed amplified material into a first set of electrical signals corresponding to size and concentration of the amplified material at the locations, said converting means in communication with the assaying means; and
    5. means for removing a reproducible pattern of amplification from the first electrical signal with a second electrical signal to form a third electrical signal, said means in communication with the sets of electrical signals.
14. A system as described in claim 13 wherein:
    1. the amplifying means includes polymerase chain reaction, or harvesting cloned cells;
    2. the assaying means includes gel or ultrathin gel electrophoresis, or mass spectroscopy, or denaturing gradient gel electrophoresis, or differential hybridization, or sequencing by hybridization;
    3. the converting means employs labeling with detection including radioactivity, or fluorescence, or phosphorescence, or chemiluminescence, or visible light, or ions, or pH, or electricity, or resistivity, or biotinylation, or antibodies; and includes the detecting means which includes a photomultiplier tube; a radioactivity counter, a resistivity sensor, a pH meter, or an optical detector; and
    4. the operating means includes statistical moment determinations, or Fourier transformation, or optimal filtering, or polynomial calculations, or matrix computations.
15. A method for analyzing genetic material of an organism comprising the steps of:
    1. obtaining DNA or RNA material from the organism;
    2. amplifying locations of the material, with the average length of the locations not exceeding fifty kilobases and each location including a polynucleotide repeat region;
    3. labelling the amplified material with labels;
    4. converting the labels with a sensing device which produces a first electrical signal; and
    5. producing the genotype of an amplified location of the genetic material in an electronic acquisition system comprising a region having a radius of less than five feet at a rate exceeding 100 genotypes per hour.
16. A method as described in claim 1 wherein in the removing step there is the step of removing a plurality of reproducible patterns of the amplification.