Methods for generating databases and databases for identifying polymorphic genetic markers

• US 20030190644A1
• Filed: 10/15/2002
• Published: 10/09/2003
• 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: Braun, Andreas, Ping, Yip
• Application Number:
  US10/272,756
• Publication Number:
  US 20030190644A1
• Time in Patent Office: Days
• US Class Current: 435/6.11
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6872 involving mass spectrometry
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2521/301 Endonuclease
• CPC Class Codes: C12Q 2535/125 Allele specific primer extension
• CPC Class Codes: C12Q 2561/125 Ligase Detection Reaction [LDR]
• CPC Class Codes: C12Q 2565/627 being a mass spectrometer
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: Y10T 436/24 Nuclear magnetic resonance, electron spin resonance or other spin effects or mass spectrometry

Abstract

A high throughput method of determining frequencies of genetic variations is provided. The method includes steps of selecting a healthy target population and a genetic variation to be assessed; pooling a plurality of samples of biopolymers obtained from members of the population; determining or detecting the biopolymer that comprises the variation by mass spectrometry; obtaining a mass spectrum or a digital representation thereof; and determining the frequency of the variation in the population.

Claims

1. A high throughput method of determining frequencies of genetic variations, comprising:

selecting a healthy target population and a genetic variation to be assessed;

pooling a plurality of samples of biopolymers obtained from members of the population;

determining or detecting the biopolymer that comprises the variation by mass spectrometry;

obtaining a mass spectrum or a digital representation thereof; and

determining the frequency of the variation in the population.

2. The method of claim 1, wherein:

the variation is selected from the group consisting of an allelic variation, a post-translational modification, a nucleic modification, a label, a mass modification of a nucleic acid and methylation; and

/or

the biopolymer is a nucleic acid, a protein, a polysaccharide, a lipid, a small organic metabolite or intermediate, wherein the concentration of biopolymer of interest is the same in each of the samples; and

/or

the frequency is determined by assessing the method comprising determining the area under the peak in the mass spectrum or digital representation thereof corresponding to the mass of the biopolymer comprising the genomic variation.

3. The method of claim 2, wherein the method for determining the frequency is effected by determining the ratio of the signal or the digital representation thereof to the total area of the entire mass spectrum, which is corrected for background.