Methods for the detection of nucleic acids

• US 6,203,993 B1
• Filed: 04/04/2000
• Issued: 03/20/2001
• Est. Priority Date: 08/14/1996
• Status: Expired due to Term

• Current Assignee: Esoterix Genetic Laboratories LLC (Laboratory Corporation Of America Holdings)
• Original Assignee: Exact Sciences Corporation, Whitehead Institute for Biomedical Research
• Inventors: Shuber, Anthony P., Daley, George Q., Lapidus, Stanley N.
• Primary Examiner(s): Houtteman, Scott W.
• Application Number:
  US09/542,103
• Time in Patent Office: 350 Days
• Field of Search: 435/6, 536/23.3
• US Class Current: 435/6.11
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 2535/125 Allele specific primer extension
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids

Abstract

Methods are provided for identifying nucleic acids. Methods of the invention are useful for identifying and analyzing nucleic acids, especially variants of single nucleotide polymorphisms, that are indicative of disease or the predisposition for disease.

Claims

1. A method for determining the severity of a disease of a patient, the method comprising the steps of:

(a) determining a number of a genomic polymorphic variant, the presence of which is a diagnostic disease marker, at a single base polymorphic locus in a genomic DNA sample obtained from the patient;

(b) applying to said number a predetermined statistical relationship, said statistical relationship correlating numbers of said genomic polymorphic variants in a sample comprising pooled genomic DNA obtained from members of a population of having said disease, with the clinical severity of said disease; and

(c) determining the clinical severity of said disease of the patient.

2. A method for identifying a single base polymorphic locus as a marker for a disease treatment, the method comprising the steps of:

(a) obtaining a first sample comprising pooled genomic DNA from members of an organism population, said members having undergone a successful treatment of said disease;

(b) obtaining a second sample comprising pooled genomic DNA from members of said population, said members having undergone an unsuccessful treatment of said disease;

(c) determining whether a statistically-significant difference exists between an enumerated number of a single base polymorphic variant at a single base polymorphic locus in said first sample and an enumerated number of a single base polymorphic variant at said locus in said second sample,

said difference being indicative that said locus is a marker for a disease treatment.

3. A method for identifying a combination of nucleic acid variants, the presence of said combination being indicative of a marker for a disease treatment, said combination comprising one or more of said variants, the method comprising the steps of:

(a) determining a first set of numbers, said first set comprising an enumerated number for each of said one or more of said variants in a sample obtained from members of a population having undergone a successful treatment for a disease;

(b) determining a second set of numbers, said second set comprising an enumerated number for each of said one or more of said variants in a sample obtained from members of said population having undergone an unsuccessful treatment for said disease; and

(c) determining whether there is a statistically-significant difference between said first set of numbers and said second set of numbers, the presence of said difference being indicative that said combination of nucleic acid variants is indicative of a disease treatment.

4. A method for identifying a single base polymorphic locus as a marker for toxicity of a pharmaceutical compound, the method comprising the steps of:

(a) obtaining a first sample comprising pooled genomic DNA from members of an organism population, said members having been administered a pharmaceutical compound without displaying an indication of a toxic effect;

(b) obtaining a second sample comprising pooled genomic DNA from members of said population, said members having been administered a pharmaceutical compound and having displayed an indication of a toxic effect;

(c) determining whether a statistically-significant difference exists between an enumerated number of a single base polymorphic variant at a single base polymorphic locus in said first sample and an enumerated number of a single base polymorphic variant at said locus in said second sample,

said difference being indicative that said locus is a marker for toxicity of a pharmaceutical compound.