Method for determining severity and progression of periodontal disease
An improved method and kit of determining whether a patient is predisposed to having severe periodontal disease and/or having high risk of progression of periodontal disease, comprising the steps of (i) taking a biological sample from said patient; (ii) genotyping said biological sample for genetic polymorphism pattern comprising IL 1B (rs16944), IL 1B (rs1143623) and IL 1B (rs4848306); and (iii) comparing said genetic polymorphism patterns to a reference composite genotype pattern; wherein the similarity of said genetic polymorphism patterns to said reference pattern indicate said patient's predisposition to having severe periodontal disease and/or having high risk of progression of periodontal disease.
1. A method comprising the follow steps:
(i) obtaining a biological sample from a patient who does not have severe periodontal disease;
(ii) isolating a nucleic acid sample from said biological sample;
(iii) contacting said nucleic acid sample with oligonucleotide primers that hybridize 5′ and 3′ to each of the following single nucleotide polymorphisms (SNPs) in the IL1B gene: rs16944 C/T; rs1143623 G/C; and rs4848306 C/T;
(iv) amplifying nucleic acid in said nucleic acid sample with said oligonucleotide primers to produce one or more amplified fragments, wherein each of said SNPs is included in at least one of said one or more amplified fragments;
(v) detecting the number of copies of allele 1 and allele 2 of each of said SNPs in said one or more amplified fragments, wherein as a result of said detecting, the presence of one of the following composite genotypes is detected in said patient:
a) one copy rs16944 allele 1 (C), one copy rs1143623 allele 1 (G), and two copies of rs4848306 allele 1 (C);
b) two copies of rs16944 allele 2 (T), one copy of rs1143623 allele 1 (G), and two copies of rs4848306 allele 1 (C);
c) two copies of rs16944 allele 1 (C), two copies of rs1143623 allele 1 (G), and two copies of rs4848306 allele 1 (C);
d) one copy of rs16944 allele 1 (C), two copies of rs1143623 allele 1 (G), and two copies of rs4848306 allele 1 (C);
e) two copies of rs16944 allele 2 (T), two copies of rs1143623 allele 1 (G), and two copies of rs4848306 allele 1 (C); and
(vi) treating the patient of step (v), in whom one of the composite genotypes a)-e) has been detected, with a treatment regimen to slow down the progression of periodontal disease.
2. A method comprising the follow steps:
(i) obtaining a biological sample from a patient who does not have severe periodontal disease;
(ii) isolating a nucleic acid sample from said biological sample;
(iii) contacting said nucleic acid sample with oligonucleotide primers that hybridize 5′ and 3′ to each of the following single nucleotide polymorphisms (SNPs) in the IL 1B gene: rs16944 C/T; rs1143623 G/C; rs4848306 C/T, and rs1143633 G/A;
(iv) amplifying nucleic acid in said nucleic acid sample with said oligonucleotide primers to produce one or more amplified fragments, wherein each of said SNPs is included in at least one of said one or more amplified fragments;
(v) detecting the number of copies of allele 1 and allele 2 of each of said SNPs in said one or more amplified fragments, wherein as a result of said detecting, the presence of one of the following composite genotypes is detected in said patient:
f) two copies of ID B rs16944 allele 1 (C), two copies of rs1143623 allele 1 (G), two copies of rs4848306 allele 2 (T), and two copies of rs1143633 allele 1 (G);
g) one copy of rs16944 allele 1 (C), two copies of rs1143623 allele 1 (G), one copy of rs4848306 allele 2 (T), and two copies of rs1143633 allele 1 (G); and
(vi) treating the patient of step (v), in whom one of the composite genotypes f) or g) has been detected, with a treatment regimen to slow down the progression of periodontal disease.
3. The method of claim 1 or claim 2 , wherein said patient is a smoker.
4. The method of claim 1 or claim 2 , wherein said amplifying in step (iv) comprises a polymerase reaction.
5. The method of claim 4 , wherein the polymerase reaction is PCR.
6. The method of claim 1 or claim 2 , wherein at least one of said oligonucleotide primers of step (iii) is a labeled oligonucleotide primer.
7. The method of claim 6 , wherein said labeled oligonucleotide primer comprises a radiolabel, an enzyme label, a fluorescent compound, a streptavidin, an avidin, a biotin, a magnetic moiety, an antigen, or an antibody moiety.
8. The method of claim 1 or claim 2 , wherein the detecting in step (v) comprises use of at least one allele-specific oligonucleotide.
9. The method of claim 8 , wherein said allele-specific oligonucleotide comprises a radiolabel, an enzyme label, a fluorescent compound, a streptavidin, an avidin, a biotin, a magnetic moiety, an antigen, or an antibody moiety.
10. The method of claim 1 or claim 2 , wherein the method comprises the use of a TaqMane® assay.