Methods for generating databases and databases for identifying polymorphic genetic markers

• US 20030207297A1
• Filed: 10/15/2002
• Published: 11/06/2003
• Est. Priority Date: 10/13/1999
• Status: Abandoned Application

• Current Assignee: Sequenom Incorporated (Laboratory Corporation Of America Holdings)
• Original Assignee: Sequenom Incorporated (Laboratory Corporation Of America Holdings)
• Inventors: Yip, Ping, Braun, Andreas, Koster, Hubert, He, Liyan, Chiu, Norman, Rodi, Charlie, Jurinke, Christian, Boom, Dirk Van Den
• Application Number:
  US10/273,228
• Publication Number:
  US 20030207297A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/683 involving restriction enzymes, e.g. restriction fragment length polymorphism [RFLP]
• CPC Class Codes: C12Q 2537/143 Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
• CPC Class Codes: C12Q 2565/627 being a mass spectrometer

Abstract

A method for discovery of a polymorphism in a population is provided. The method includes the steps of obtaining samples of body tissue or fluid from a plurality of organisms; isolating a biopolymer from each sample; pooling each isolated biopolymer; optionally amplifying the amount of biopolymer; cleaving the pooled biopolymers to produce fragments thereof; obtaining a mass spectrum of the resulting fragments; and comparing the frequency of each fragment to identify fragments present in amounts lower than the average frequency, thereby identifying any polymorphisms.

Claims

1. A method for discovery of a polymorphism in a population, comprising:

obtaining samples of body tissue or fluid from a plurality of organisms;

isolating a biopolymer from each sample;

pooling each isolated biopolymer;

optionally amplifying the amount of biopolymer;

cleaving the pooled biopolymers to produce fragments thereof;

obtaining a mass spectrum of the resulting fragments; and

comparing the frequency of each fragment to identify fragments present in amounts lower than the average frequency, thereby identifying any polymorphisms.

2. The method of claim 1, wherein cleaving is effected by contacting the biopolymer with an enzyme.

3. The method of claim 2, wherein the enzyme is selected from the group consisting of nucleotide glycosylase, a nickase and a type IIS restriction enzyme.

4. The method of claim 1, wherein the biopolymer is a nucleic acid or a protein.

5. The method of claim 1, wherein the mass spectrometric format is selected from among Matrix-Assisted Laser Desorption/Ionization, Time-of-Flight (MALDI-TOF), Electrospray (ES), IR-MALDI, Ion Cyclotron Resonance (ICR), Fourier Transform and combinations thereof.

6. The method of claim 1, wherein the samples are obtained from healthy subjects.