Methods for generating databases and databases for identifying polymorphic genetic markers

Abstract

Processes and methods for creating a database of genomic samples from healthy human donors, methods that use the database to identify and correlate polymorphic genetic markers and other markers with diseases and conditions are provided.

What is claimed is: 
     
         1 . A method for determining whether a polymorphism correlates with a gene or pathway involved in the onset and progression of disease in males or females, comprising:
 a) obtaining samples from healthy male and female individuals;   b) pooling the samples from healthy male individuals within an age range to obtain pools from younger and older male populations;   c) pooling the samples from healthy female individuals within an age range to obtain pools from younger and older female populations;   d) determining the frequency of the polymorphism in said pooled samples using a mass spectrometer;   e) determining a difference in frequency of the polymorphism in the pooled samples obtained from younger and older female populations or younger and older male populations;   f) determining a difference in the frequency of the polymorphism of step e) between male and female populations; and   g) associating the polymorphism with a disease or a biochemical pathway that occurs with high frequency in younger or older male or female populations.   
     
     
         2 . The method of  claim 1 , wherein the mass spectrometric format is selected from the group consisting of Matrix Assisted Laser Desorption/Ionization, Time of Flight (MALDI TOF), Electrospray (ES); IR-MALDI, Ion Cyclotron Resonance (ICR), Fourier Transform, and combinations thereof. 
     
     
         3 . The method of  claim 1 , wherein the frequency of the polymorphism in said samples is in a database, and said database is sorted to identify correlations between the frequency of said polymorphism in older and younger male and female populations. 
     
     
         4 . The method of  claim 1 , wherein the polymorphism comprises a SNP. 
     
     
         5 . The method of  claim 1 , further comprising identifying the locus of said polymorphism and assessing or deducing the function of a gene at said locus. 
     
     
         6 . The method of  claim 1 , wherein said sample comprises body tissue or fluid from said individual. 
     
     
         7 . The method of  claim 1 , wherein said sample comprises DNA. 
     
     
         8 . The method of  claim 1 , wherein said method comprises obtaining genomic nucleic acid from a sample from a healthy individual. 
     
     
         9 . The method of  claim 1 , further comprising amplifying a portion of the genomic nucleic acid to produce amplified fragments thereof. 
     
     
         10 . The method of  claim 1 , wherein the polymorphism is identified by a method comprising primer oligo base extension. 
     
     
         11 . The method of  claim 10 , wherein the primer oligo base extension comprises hybridizing a nucleic acid molecule from a sample from a healthy individual with a primer oligonucleotide that is complementary to the nucleic acid molecule at a site adjacent to the polymorphic marker. 
     
     
         12 . The method of  claim 11 , further comprising optionally immobilizing the nucleic acid molecule onto a solid support, to produce an immobilized nucleic acid molecule; contacting the optionally-immobilized nucleic acid molecule with a composition comprising a dideoxynucleoside triphosphate or a 3′-deoxynucleoside triphosphate and a polymerase, so that only a dideoxynucleoside or 3′-deoxynucleoside triphosphate that is complementary to the polymorphic marker is extended onto the primer; and detecting the extended primer, thereby identifying the polymorphism. 
     
     
         13 . The method of  claim 1 , wherein the polymorphism is identified by a method comprising:
 identifying samples by sorting a database comprising datapoints representative of a plurality of individuals from whom biological samples are obtained, wherein each datapoint is associated with data representative of the organism type and other identifying information, wherein said database is sorted according to a selected parameter to identify samples that match the selected parameter;   isolating a nucleic acid molecule from each identified sample;   pooling each isolated nucleic acid molecule; and   identifying the polymorphism in the nucleic acid molecule by a method comprising primer oligo base extension.   
     
     
         14 . The method of  claim 1 , wherein the polymorphism is identified by a method comprising:
 identifying samples by sorting a database comprising datapoints representative of a plurality of individuals from whom biological samples are obtained, wherein each datapoint is associated with data representative of the organism type and other identifying information, wherein said database is sorted according to a selected parameter to identify samples that match the selected parameter;   isolating a biopolymer from each identified sample;   pooling each isolated biopolymer;   cleaving the pooled biopolymers to produce fragments thereof;   obtaining a mass spectrum of the resulting fragments and comparing the mass spectrum with a control mass spectrum to identify differences between the spectra and thereby identifying any polymorphisms; wherein:   the control mass spectrum is obtained from either   
       samples represented by datapoints in said database that were not selected by sorting said database; or 
       samples identified by sorting said database according to a different selected parameter. 
     
     
         15 . The method of  claim 1 , wherein the polymorphism is identified by a method comprising:
 isolating a biopolymer from samples of body tissue or fluid from older and younger male and female populations;   pooling each isolated biopolymer;   cleaving the pooled biopolymers to produce fragments thereof;   obtaining a mass spectrum of the resulting fragments;   determining a frequency of each fragment, whereby an average frequency is calculated; and   comparing the frequency of each fragment to identify fragments present in amounts lower than the average frequency, thereby identifying the polymorphism.   
     
     
         16 . The method of  claim 14 , wherein the biopolymers comprise genomic nucleic acid molecules.