METHOD TO ESTIMATE AGE OF INDIVIDUAL BASED ON EPIGENETIC MARKERS IN BIOLOGICAL SAMPLE

• US 20140228231A1
• Filed: 05/18/2012
• Published: 08/14/2014
• Est. Priority Date: 05/20/2011
• Status: Active Grant

• Current Assignee: Regents of the University of California (University of California)
• Original Assignee: Regents of the University of California (University of California)
• Inventors: Bocklandt, Sven, Vilain, Eric, Horvath, Steve, Sinsheimer, Janet
• Granted Patent: US 10,435,743 B2
• Time in Patent Office: Days
• US Class Current: 506/9
• CPC Class Codes: C12Q 1/6876 Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2600/154 Methylation markers

Abstract

The invention provides methods and materials that use observation of DNA characteristics to obtain information relating to the age of individuals. The instant disclosure identifies 88 sites in or near 80 genes for which the degree of cytosine methylation in epithelial and/or white blood cells is significantly correlated with age. In illustrative embodiments of the invention, cytosine methylation patterns the promoters of the EDARADD, TOMILI, and NPTX2 genes are used to predict the age of an individual with a high degree of accuracy.

Claims

1. A method of obtaining information useful to determine an age of an individual, the method comprising the steps of:

(a) obtaining a biological sample derived from an individual comprising genomic DNA from white blood cells or epithelial cells; and

(b) observing a pattern of cytosine methylation of at least one genomic DNA sequence selected from the group consisting of Edaradd (SEQ ID NO;

     1), TomL1 (SEQ ID NO;

     2), NPTX2 (SEQ ID NO;

     3) and ELN (SEQ ID NO;

     4);

so that information useful to determine the age of the individual is obtained.

2. The method of claim 1, wherein cytosine methylation is observed in:

(a) Edaradd (SEQ ID NO;

     1) and TomL1 (SEQ ID NO;

     2); and

/or

(b) Edaradd (SEQ ID NO;

     1) and NPTX2 (SEQ ID NO;

     3).

3. The method of claim 1, wherein cytosine methylation is observed in at least two genomic DNA sequences including ELN (SEQ ID NO:

4).

4. The method of claim 1, wherein a bisulfate conversion process is performed so that cytosine residues in the genomic DNA are transformed to uracil, while 5-methylcytosine residues in the genomic DNA are not transformed to uracil.

5. The method of claim 1, wherein the genomic DNA is hybridized to a complimentary sequence disposed on a microarray.

6. The method of claim 1, wherein the genomic DNA is amplified by a polymerase chain reaction process.

7. The method of claim 1, wherein cytosine methylation is observed one or more cytosine residues having a CG locus designation:

cg09809672, cg27210390, cg12799895 or cg05822532.

8. The method of claim 1, wherein the individual'"'"'s identity is unknown.

9. The method of claim 1, further comprising performing a DNA fingerprinting analysis on the genomic DNA.

10. The method of claim 1, further comprising using the information in a forensic investigation.

11. The method of claim 1, further comprising correlating the pattern of cytosine methylation observed with a predicted age of the individual.

12. The method of claim 1, further comprising comparing the predicted age of the individual with the actual chronological age of the individual, wherein the comparison comprises a diagnostic procedure for an age associated pathology.

13. The method of claim 11, wherein a regression analysis is used to correlate the pattern of cytosine methylation observed with the predicted age of the individual.

14. A method of obtaining information useful to determine an age of an individual, the method comprising the steps of:

(a) obtaining genomic DNA from white blood cells or epithelial cells derived from the individual; and

(b) observing cytosine methylation of at least two CG loci in the genomic DNA selected from the group consisting of CG locus designation;

cg27553955, cg12799895, cg21296230, cg04084157, cg25148589, cg17861230, cg03734874, cg18236477, cg27320127, cg07621046, cg14456683, cg21801378, cg00107187, cg05508084, cg07533148, cg03975694, cg19945840, cg00399483, cg06291867, cg24826867, cg06092815, cg19885761, cg24199834, cg04528819, cg13434842, cg02008154, cg25044651, cg02994956, cg20366906, cg27389185, cg14826456, cg12111714, cg12457773, cg11981599, cg00059225, cg06572160, cg08668790, cg12782180, cg20134215, cg13921352, cg13614181, cg23563234, cg00201234, cg21992250, cg00911351, cg19594666, cg15425280, cg06156376, cg19831077, cg27409364, cg15747595, cg02154186, cg20616414, cg10235817, cg16232126, cg24646414, cg17241310, cg10031651, cg23290344, cg06908778, cg02844545, cg14614211, cg25511429, cg15201635, cg19246110, cg06760035, cg13603171, cg13282837, cg20792062, cg02228185, cg13547237, cg09809672, cg01293143, cg05822532, cg07408456, cg08468689, cg27210390, cg01820374, cg17589341, cg19761273, cg03440846, cg08909157, cg11136562, cg16464322, cg08872742, cg18328933, cg15784615 and cg23282949;

so that information useful to determine the age of the individual is obtained.

15. The method of claim 14, further comprising correlating cytosine methylation observed in the CG loci with a predicted chronological age of the individual.

16. A kit for obtaining information useful to determine the age of an individual, the kit comprising:

A plurality of primers or probes specific for at least two genomic DNA sequences in a biological sample, wherein the genomic DNA sequences comprise CG loci in the genomic DNA selected from the group consisting of CG locus designation;

cg27553955, cg12799895, cg21296230, cg04084157, cg25148589, cg17861230, cg03734874, cg18236477, cg27320127, cg07621046, cg14456683, cg21801378, cg00107187, cg05508084, cg07533148, cg03975694, cg19945840, cg00399483, cg06291867, cg24826867, cg06092815, cg19885761, cg24199834, cg04528819, cg13434842, cg02008154, cg25044651, cg02994956, cg20366906, cg27389185, cg14826456, cg12111714, cg12457773, cg11981599, cg00059225, cg06572160, cg08668790, cg12782180, cg20134215, cg13921352, cg13614181, cg23563234, cg00201234, cg21992250, cg00911351, cg19594666, cg15425280, cg06156376, cg19831077, cg27409364, cg15747595, cg02154186, cg20616414, cg10235817, cg16232126, cg24646414, cg17241310, cg10031651, cg23290344, cg06908778, cg02844545, cg14614211, cg25511429, cg15201635, cg19246110, cg06760035, cg13603171, cg13282837, cg20792062, cg02228185, cg13547237, cg09809672, cg01293143, cg05822532, cg07408456, cg08468689, cg27210390, cg01820374, cg17589341, cg19761273, cg03440846, cg08909157, cg11136562, cg16464322, cg08872742, cg18328933, cg15784615 and cg23282949; and

a reagent used in;

a genomic DNA polymerization process;

a genomic DNA hybridization process;

or

a genomic DNA bisulfite conversion process.

17. The kit of claim 16, wherein the kit comprises a plurality of primer sets for amplifying at least two genomic DNA sequences.

18. The kit of claim 17, wherein the kit comprises primer sets for amplifying at least two genomic DNA sequences in the biological sample selected from the group consisting of Edaradd (SEQ ID NO:

1), TomL1 (SEQ ID NO;

     2), NPTX2 (SEQ ID NO;

     3) and ELN (SEQ ID NO;

     4).

19. The kit of claim 16, wherein the kit further comprises a probe or primer used to perform a DNA fingerprinting analysis.

20. The kit of claim 16, wherein the kit comprises a methylation microarray.