Methods for generating databases and databases for identifying polymorphic genetic markers

• US 8,818,735 B2
• Filed: 06/28/2012
• Issued: 08/26/2014
• Est. Priority Date: 10/13/1999
• Status: Expired due to Fees

• Current Assignee: Sequenom Incorporated (Laboratory Corporation Of America Holdings)
• Original Assignee: Sequenom Incorporated (Laboratory Corporation Of America Holdings)
• Inventors: Braun, Andreas, Kster, Hubert, Van Den Boom, Dirk Johannes, Yip, Ping, Rodi, Charles, He, Liyan, Chiu, Norman, Jurinke, Christian
• Primary Examiner(s): Clow, Lori A
• Application Number:
  US13/536,807
• Publication Number:
  US 20120301882A1
• Time in Patent Office: 789 Days
• US Class Current: 702/19
• 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

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.

Claims

1. A method for determining whether a polymorphism correlates with susceptibility to morbidity, early mortality, or morbidity and early mortality, comprising:

identifying a polymorphism, wherein said polymorphism has not previously been correlated with susceptibility to morbidity, early mortality, or morbidity and early mortality;

obtaining samples from healthy individuals within more than one age range;

pooling the samples from healthy individuals within each age range, wherein healthy individuals are selected only on the basis of being healthy;

determining the frequency of the identified polymorphism in each sample pool using mass spectrometry, which includes identifying the appearance or disappearance of the polymorphism with increasing age; and

correlating said frequency of the appearance or disappearance of the polymorphism with increasing age in the healthy population with susceptibility to morbidity, early mortality, or morbidity and early mortality in said healthy population.

2. 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 populations.

3. The method of claim 1, wherein the polymorphism comprises a SNP.

4. 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.

5. The method of claim 1, wherein said sample comprises body tissue or fluid from said individual.

6. The method of claim 1, wherein said sample comprises DNA.

7. The method of claim 1, wherein said method comprises obtaining genomic nucleic acid from a sample from a healthy individual.

8. The method of claim 1, further comprising amplifying a portion of the genomic nucleic acid to produce amplified fragments thereof.

9. The method of claim 1, wherein the polymorphism is identified by a method comprising primer oligo base extension.

10. The method of claim 9, 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.

11. The method of claim 9, 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.

12. 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.

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 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.

14. The method of claim 1, wherein the samples are pooled within an age range and within a gender.

15. The method of claim 14, wherein the appearance or disappearance of a polymorphism is identified with increasing age within one gender and not within the other.

16. The method of claim 15, wherein the appearance or disappearance of the polymorphism is correlated with susceptibility to morbidity, early mortality, or morbidity and early mortality in males and not females.

17. The method of claim 15, wherein the appearance or disappearance of the polymorphism is correlated with susceptibility to morbidity, early mortality, or morbidity and early mortality in females and not males.