A method to identify recurrent immunodeficiency caries based on genetic variation in DMBT1 and two immunity genes

Abstract

It has been found that Copy Number Variation (CNV) in the gene DMBT1, specifically at two sites called CNV1 and CNV2 within its SRCR-SID repeat region, is meaningfully associated with Genetic Susceptibility (GS) and Genetic Resistance (GR) in dental caries. Further it has been found that DMBT1 CNV cooperates with PRH1 / PRH2 genetic variation, and that combining these two genetic dimensions produces a much more powerful and precise risk stratification than either of them alone.

Description

[0001] A method to identify recurrent immunodeficiency caries based on genetic variation in DMBT1 and two immunity genes.

[0002] Filed of Invention

[0003] The present invention relates to fingerprints such as genetic origin, phenotype origin fingerprints and combined genetic origin and phenotype origin fingerprints, a method for assessing the predisposition of a person to / for dental caries based said biomarkers, and an analytical kit for determining the risk of a person developing dental caries. It appears that DMBT1 co-operates with allelic PRH1 / PRH2 variation in terms of dental caries and genetic interactions.

[0004] Introduction

[0005] Dental caries is the most prevalent and costly disease worldwide (1, 2, 5, 6, 33). It changed from a caries-free condition in neanderthals due to hunter-to-farmer transition (domestication of starch) and industrialization in modem time (availability of sucrose) into caries-sick populations (90-100%) in Swedish and other Western populations in the 1950's (3). The caries-sick populations were, however, transformed by oral hygiene, diet routines and fluoride prevention to a smaller group of people (15 %) with severe, recurrent caries and a larger group (85 %) more or less free of caries (3, 5, 6). In these high-income low prevalence populations with physiological homogeneity, genetic diversity remains large and constitutes a primary cause for severe, recurrent caries (8, 9-11).

[0006] Agricultural transition coincides with increased copy numbers of salivary amylase AMY 1 genes (14) and repeat sequence motifs in salivary pattern recognition DMBT1 (13) in high-starch populations. Copy number variation (CNV) and SNPs are two major genetic polymorphisms where SNPs influence one gene and CNV may influence multiple genes through enhancer mechanisms (26). Agricultural transition also impacted both expansion of Streptococcus mutans (15), a caries-associated bacterium with 15 % of its genome for carbohydrate utilization (34), and CNV in the S. mutans primary DMBT1 receptor to reduce its cariogenicity (13). The saliva PRH1-2, PRB1-4 acidic, basic and glycosylated proline-rich proteins (PRPs), which are duplications from an ancestral gene, are primary receptors on teethfor oral pioneer streptococci and actinomycetes and co-receptors for S. mutans and modulators of taste perception (19, 20, 36).

[0007] Allelic variation in salivary PRH1, PRH2 acidic PRPs have identified immunodeficiency (P4a) and traditional lifestyle (Pl) causal caries subtypes in a prospective case-control study in 452 adolescents (9-11). The immunodeficiency (P4a) caries phenotype differed from the moderate (P6) and low lifestyle (Pl) caries phenotypes by a high caries progression, a broader microbiota profile in caries and a lifestyle- and S. mutans-independency in caries. Moreover, adolescents with immunodeficiency caries were independently identified at high risk and thus given extra fluoride at the clinics (9). Besides the role of acidic PRPs as receptors for bacteria on teeth and barriers against their short chain fatty acid end products, the PRP family neutralizes pathogens and dietary polyphenols (37). Acidic PRPs harbor allelic variants Db, PIF, Pa (PRH1) and PRP-1, PRP-2 (PRH2) that are secreted as large 150-171 and small, truncated 106 amino acid polypeptides and form up to 18 PRP phenotypes. Bacterial proteolysis of PRPs generates bioactive and prebiotic peptides, such as RGRPQ (22, 39). So far, however, only the predominant P4a, P6 and Pl PRP phenotypes have been explored in more detail (9-11).

[0008] The pattern recognition protein DMBT1 is a mucin hybrid glycoprotein composed of 13 SRCR repeats, which bind endogenous immunity proteins, and interspersed O-glycosylated repeats, which bind various microbial ligands and CUB and ZP domains (17, 18). DMBT1 is subject to balancing selection and to CNV at two sites in the SRCR-SID region, CNV1 and CNV2, that coincide differently with starch-rich populations (13, 40). DMBT1 size isoforms have been implicated in dental caries (12, 41) and DMBT1 CNV and SNPs (e.g. rs2981745, rs 11523871 and rs2981804) have been implicated in cancer (42, 43), inflammatory bowel diseases (16, 44) infections and other conditions (46, 47, 48 reviewed in 17, 18). A SRCR-SID3-6 deletion variant coincided with inflammatory bowel disease in one (44) but not in another (16) study, and a SRCR-SID 9-11 deletion variant with malignant glioma. It is generally assumed that DMBT1 CNV and isoforms coincide in terms of size and function, while nothing is known about how DMBT1 CNV, size isoforms and SNPs interacts with PRH1, PRH2 in immunodeficiency and other caries subtypes and health.

[0009] AN mz / tan -dependent caries type was identified in the 452-adolescents where infection with the organism influence caries progression in high (Pl) to moderately resistant (P6) phenotypes (10, 11). Immunodeficiency caries developed from another less cariogenic butabundant part of the oral microbiota (49). The S. mutans biotypes SpaP A, B and C with primary DMBT1 -receptors and acidic PRP co-receptors showed tropism for individual human hosts and ranged from low SpaP A- 1 to high virulence B-l and Cnm adhesion types in caries and systemic infections. High virulence seemed to coincide with inactivation of DMBT1 pattern recognition by tight binding (9) and immunodeficiency caries while loss of saliva (DMBT1) pattern recognition of S. mutans (10). Pattern recognition of S. mutans and other microorganisms by DMBT1 involve multiple epitopes and surface versus solution modes (SO-57). However, the key modulators of adhesion and biofilm formation in caries and health remain to be elucidated.

[0010] Objects of the invention

[0011] One objective is the enhancement of the precision of the susceptibility of dental caries.

[0012] An additional objective is to further improve a diagnostic methodology related to the susceptibility of dental caries based on acidic PRPs.

[0013] A further objective is the identification and characterization of distinct genetically susceptible (GS) and genetically resistant (GR) caries subtypes, defined by the cross-stratification of DMBT1 CNV groups with PRH1, PRH2 allelic variation, and the elucidation of salivary inflammatory and metabolic biomarkers that show near-linear penetrance of caries progression in each GS subtype.

[0014] Further objectives are apparent from the following disclosure of the invention.

[0015] Summary of the invention

[0016] It has been discovered that Copy Number Variation (CNV) in the gene DMBT1, specifically at two sites called CNV1 and CNV2 within its SRCR-SID repeat region, is meaningfully associated with Genetic Susceptibility (GS) and Genetic Resistance (GR) in dental caries. Further, it has been found that DMBT1 CNV cooperates with PRH1 / PRH2 genetic variation, and that combining these two genetic dimensions produces a much more powerful and precise risk stratification than either of them alone.Key biological concepts

[0017] DMBT1 (Deleted in Malignant Brain Tumors 1): A pattern recognition glycoprotein in saliva composed of SRCR (Scavenger Receptor Cysteine-Rich) repeats. It binds bacteria (including Streptococcus mutans) and plays a key role in innate oral immunity. It is subject to Copy Number Variation at two regions, CNV1 and CNV2, which affect how many SRCR-SID repeat units are present.

[0018] CNV (Copy Number Variation): Atype of genetic polymorphism where segments of DNA are deleted or duplicated, resulting in individuals carrying different numbers of copies of that segment. Unlike SNPs (which affect a single nucleotide), CNVs can influence multiple genes. CNV1 and CNV2 refer to two specific deletion-prone sites within DMBT1.

[0019] PRH1 / PRH2 (Proline-Rich Histatin genes 1 & 2): Genes encoding acidic Proline-Rich Proteins (PRPs) in saliva. Their allelic variants, designated Db, PIF, Pa (from PRH1) and PRP-1, PRP-2 (from PRH2), combine into phenotype patterns. These PRPs act as receptors on teeth for oral bacteria and as modulators of immunity.

[0020] PRP Phenotype Groups: The combination of PRH1 / PRH2 alleles produces distinct salivary protein phenotypes. Important groups are:

[0021] • P4a (Db, PIF, PRP1, PRP1) — immunodeficiency, high caries

[0022] • P7 (Db, Pa, PRP1, PRP2) — immunodeficiency, high caries

[0023] • P8 (Db, PIF, PRP1, PRP2) — immunodeficiency, high caries

[0024] • P6 (Pa, PIF, PRP1, PRP2) — low-moderate caries

[0025] • Pl (PIF, PIF, PRP1, PRP1) — lifestyle-driven, low caries.

[0026] DeFS Score: The clinical outcome measure used: Decayed (including enamel), Filled Surfaces in permanent dentition — a standard index of caries burden and progression.

[0027] Basis for the current invention is the body of work related to the involvement of PRH1 and PRH2 in dental caries. As alluded to in the introduction, isoforms of DMBT1 have been suggested to be involved in dental caries. The extensive research on DMBT1 and specifically in the context of PRH1 and PRH2 has led to the discovery that variation in CNV1 and CNV2of DMBT1 is involved in dental caries. Additionally, DMBT1 has been found to collaborate with PRH1 and PRH2 in the context of dental caries. Further knowledge of DMBT1 as to dental caries has enabled a further stratification of the groups related to genetic susceptibility for dental caries hinged on PRH1 and PRH2 alone further sharpening diagnostic resolution. In addition, and within specific immunodeficiency caries phenotypes defined by DMBT1 CNV / groups combined / scrambled with PRH1 and PRH2, linear penetrance of salivary biomarkers has been found even further enhancing diagnostic precision of the susceptibility of dental caries.

[0028] The knowledge of DMBT1 cooperating with PRH1 and PRH2 with regard to dental caries, has enabled extracting statistically relevant stratification of the genetic subgroupings of PRH1, PRH2, e.g. the discovery of new immunodeficiency groups, e.g. GS1, GS2, GS3 (GS: Genetically Susceptible), within known genetic subgroupings of PRH1, PRH2 clearly enhancing the diagnostic value proposition.

[0029] The present invention encompassed fingerprints of genetic and / or phenotype origin predisposing caries, a method for assessing susceptibility to dental caries, a kit for determining the risk for a person developing dental caries.

[0030] More specifically, the invention relates genetic origin fingerprint for predisposition to dental caries, the fingerprint comprising a copy number variation pattern at CNV1 and CNV2 of the DMBT1 gene, wherein said copy number variation pattern is characterized by a diploid copy number at CNV1 and a diploid copy number at CNV2 assigned to one of the following CNV groups: CNV group 1: CNV1 = 0 and CNV2 < 4; CNV group 2: CNV1 = 1 and CNV2 < 4; CNV group 3: CNV1 = 1 and CNV2 > 4; CNV group 4: CNV1 > 2 and CNV2 < 4; CNV group 5: CNV1 > 2 and CNV2 > 4; wherein group 1 and 5 are indicative of low incidence of dental caries; group 2 is indicative of moderate incidence of dental caries; and group 3 and 4 are indicative to high incidence of dental caries.

[0031] A further embodiment as to fingerprints relates to a phenotype origin fingerprint for predisposition to dental caries, the phenotype fingerprint being an allelic phenotype of acidic proline-rich proteins (PRPs) encoded by PRH1 and PRH2, wherein said allelic phenotype is selected from any one of the following PRP groups: P4a: heterozygous at PRH1 (Db-PIF) combined with homozygous at PRH2 (PRP 1 -PRP 1) [Db, PIF, PRP1, PRP1]; P7: heterozygous at PRH1 (Db-Pa) combined with heterozygous at PRH2 (PRP1-PRP2) [Db-Pa-PRP1-PRP2]; P8: heterozygous at PRH1 (Db-PIF) combined with heterozygous at PRH2 (PRP-l-PRP-2)[Db-PIF-PRP1-PRP2]; P6: heterozygous atPRHl (Pa, PIF) combined with heterozygous at PRH2 (PRP1, PRP2) [Pa, PIF, PRP1, PRP2]; P1: homozygous at PRH1 (PIF, PIF) combined with homozygous at PRH2 (PRP1-PRP1) [PIF, PIF, PRP1, PRP1]; P4b: homozygous at PRH1 (Db, Db) combined with homozygous at PRH2 (PRP1-PRP1) [Db, Db, PRP1, PRP1]; P5: homozygous at PRH1 (PIF, PIF) combined with heterozygous at PRH2 (PRP1, PRP2) [PIF, PIF, PRP1, PRP2]; P10: homozygous at PRH1 (Pa, Pa) combined with homozygous at PRH2 (PRP2-PRP2) [Pa, Pa, PRP2-PRP2]; wherein groups P4a, P8 and P7 are attributed to immunodeficiency and high incidence of dental caries; groups P5 and P6 are attributed to low to moderate incidence of dental caries; and groups P1, P4b, P1, P10 attributed to lifestyle and low incidence of dental caries.

[0032] Preferably, the allelic phenotype is selected from any one of the following PRP groups: P4a: heterozygous at PRH1 (Db-PIF) combined with homozygous at PRH2 (PRP1-PRP1) [Db, PIF, PRP1, PRP1]; P7: heterozygous at PRH1 (Db-Pa) combined with heterozygous at PRH2 (PRP1-PRP2) [Db-Pa-PRP1-PRP2]; P8: heterozygous atPRHl (Db-PIF) combined with heterozygous atPRH2 (PRP-l-PRP-2) [Db-PIF-PRP1-PRP2]; P6: heterozygous atPRHl (Pa, PIF) combined with heterozygous at PRH2 (PRP1, PRP2) [Pa, PIF, PRP1, PRP2];

[0033] Pl:homozygous atPRHl (PIF, PIF) combined with homozygous atPRH2 (PRP1-PRP1) [PIF, PIF, PRP1, PRP1]; wherein groups P4a, P8 and P7 are attributed to immunodeficiency and high incidence of dental caries; group P6 is attributed to low to moderate incidence of dental caries; and group Pl attributed to lifestyle and low incidence of dental caries.

[0034] An additional embodiment relates to phenotype origin fingerprint for predisposition to dental caries, the phenotype fingerprint being an allelic phenotype of acidic proline-rich proteins (PRPs) encoded by PRH1 and PRH2, wherein said allelic phenotype is selected from any one of the following PRP groups: P4a: heterozygous at PRH1 (Db-PIF) combined with homozygous at PRH2 (PRPl-PRPl) [Db, PIF, PRP1, PRP1]; P7: heterozygous at PRH1 (Db-Pa) combined with heterozygous at PRH2 (PRP1-PRP2) [Db-Pa-PRP1-PRP2]; P8: heterozygous at PRH1 (Db-PIF) combined with heterozygous at PRH2 (PRP-l-PRP-2) [Db-PIF -PRP 1-PRP2]; wherein groups P4a, P8 and P7 are attributed to immunodeficiency and high incidence of dental caries that is independent of Streptococcus mutans infection status.

[0035] A still further embodiment related to fingerprints relates to a fingerprint from genetic and phenotype origin from claim 1 and claim 2 for predisposition to dental caries, the fingerprint comprising the following CNV stratified RPR groups: CNV-PRP group 1: [P4a-CNV group2], CNV-PRP group 2: [P4a-CNV group 3], CNV-PRP group 3: [P4a-CNV group 2-CNV group 3], CNV-PRP group 4: [[P4a-CNV group 4-CNV group 5], CNV-PRP group 5: [P7-CNV group 2], CNV-PRP group 6: [P7-CNV group 4], CNV-PRP group 7: [P7-CNV group 2-CNV group 4], CNV-PRP group 8: [P7-CNV group 3-CNV group 5], CNV-PRP group 9:

[0036] [P8-CNV group 2], CNV-PRP group 10: [P8-CNV group 3], CNV-PRP group 11: [P8-CNV group 4], CNV-PRP group 12: [P8-CNV group 2-CNV group- 3 - CNV group 4], CNV-PRP group 13: [P8-CNV group 5], CNV-PRP group 14: [P4b- CNV groups 1-5], CNV-PRP group 15: [Pl- CNV groups 1-5], CNV-PRP group 16: [P5- CNV groups 1-5], CNV-PRP group 17:

[0037] [P6- CNV groups 1-5], CNV-PRP group 18: [PIO- CNV groups 1-5],

[0038] According to an embodiment, CNV stratified RPR groups are selected from: CNV-PRP group 1: [P4a-CNV group 2], CNV-PRP group 2: [P4a-CNV group 3], CNV-PRP group 3: [P4a-CNV group 2-CNV group 3], CNV-PRP group 4: [[P4a-CNV group 4-CNV group 5], CNV-PRP group 5: [P7-CNV group 2], CNV-PRP group 6: [P7-CNV group 4], CNV-PRP group 7:

[0039] [P7-CNV group 2-CNV group 4], CNV-PRP group 8: [P7-CNV group 3-CNV group 5], CNV-PRP group 9: [P8-CNV group 2], CNV-PRP group 10: [P8-CNV group 3], CNV-PRP group 11: [P8-CNV group 4], CNV-PRP group 12: [P8-CNV group 2-CNV group- 3 - CNV group 4], CNV-PRP group 13: [P8-CNV group 5],

[0040] According to a further embodiment, CNV stratified RPR groups are selected from: CNV-PRP group 3: [P4a-CNV group 2-CNV group 3], CNV-PRP group 7: [P7-CNV group 2-CNV group 4], and CNV-PRP group 12: [P8-CNV group 2-CNV group- 3 - CNV group 4],

[0041] The CNV-stratified PRP groups CNV-PRP group 3: [P4a-CNV group 2-CNV group 3], CNV-PRP group 7: [P7-CNV group 2-CNV group 4], and CNV-PRP group 12: [P8-CNV group 2-CNV group- 3 - CNV group 4] represent the genetically susceptible dental caries groups (GS): GS1, GS2, and GS3, respectively.

[0042] A further significant fingerprint embodiment relates to a fingerprint from genetic and phenotype origin for predisposition to dental caries, by the provision of the following two groups / entities: a genetically susceptible dental caries (GS) group and a genetically resistant dental caries (GR) group, the genetic fingerprint comprising: (i) a copy number variation pattern at CNV1 and CNV2 of the DMBT1 gene assigned to a CNV group based on a copy number variation pattern at CNV1 and CNV2 of the DMBT1 gene, wherein said copy number variation pattern is characterized by a diploid copy number at CNV1 and a diploid copy number at CNV2 assigned to one of the following CNV groups: CNV group 1: CNV1 = 0 andCNV2 < 4; CNV group 2: CNV1 = 1 and CNV2 < 4; CNV group 3: CNV1 = 1 and CNV2 > 4; CNV group 4: CNV1 > 2 and CNV2 < 4; CNV group 5: CNV1 > 2 and CNV2 > 4; wherein group 1 and 5 are indicative of low incidence of dental caries; group 2 is indicative of moderate incidence of dental caries; and group 3 and 4 are indicative to high incidence of dental caries; and

[0043] (ii) an allelic phenotype of acid PRPs encoded by PRH1 and PRH2 assigned to a PRP group based on the phenotype fingerprint being an allelic phenotype of acidic proline-rich proteins (PRPs) encoded by PRH1 and PRH2, wherein said allelic phenotype is selected from any one of the following PRP groups:: P4a: heterozygous at PRH1 (Db-PIF) combined with homozygous at PRH2 (PRPl-PRPl) [Db, PIF, PRP1, PRP1]; P7: heterozygous at PRH1 (Db-Pa) combined with heterozygous at PRH2 (PRP1-PRP2) [Db-Pa-PRP1-PRP2]; P8: heterozygous at PRH1 (Db-PIF) combined with heterozygous at PRH2 (PRP- 1 -PRP -2) [Db-PIF -PRP 1-PRP2]; P6: heterozygous at PRH1 (Pa, PIF) combined with heterozygous at PRH2 (PRP1, PRP2) [Pa, PIF, PRP1, PRP2]; Pl: homozygous at PRH1 (PIF, PIF) combined with homozygous at PRH2 (PRPl-PRPl) [PIF, PIF, PRP1, PRP1]; P4b: homozygous at PRH1 (Db, Db) combined with homozygous at PRH2 (PRPl-PRPl) [Db, Db, PRP1, PRP1]; P5: homozygous at PRH1 (PIF, PIF) combined with heterozygous at PRH2 (PRP1, PRP2) [PIF, PIF, PRP1, PRP2]; P10: homozygous at PRH1 (Pa, Pa) combined with homozygous at PRH2 (PRP2-PRP2) [Pa, Pa, PRP2-PRP2]; wherein the fingerprint is a GS fingerprint when the combination of CNV group and PRP group is any one of the following GS or GR groups: GS1: P4a combined with CNV group 2 or CNV group 3; GS2: P7 combined with CNV group 2 or CNV group 4; GS3: P8 combined with any one of CNV groups 2, 3 or 4;

[0044] and wherein the genetic fingerprint is a GR fingerprint when the combination is: GR1: P4a combined with CNV group 4 or CNV group 5; GR2: P7 combined with CNV group 3 or CNV group 5; GR3: P8 combined with CNV group 5; GR-P4b: P4b combined with CNV groups 1-5; GR-P1: P1 combined with CNV groups 1-5; GR-P5: P5 combined with CNV groups 1-5; GR-P6: P6 combined with CNV groups 1-5; and GR-P10: P10 combined with CNV groups 1-5.

[0045] The allelic phenotype of acid PRPs encoded by PRH1 and PRH2 under (ii) above may be selected from: P4a: Db heterozygous at PRH1 (Db-PIF) combined with PRP1 homozygous at PRH2 (PRPl-PRPl) [Db, PIF, PRP1, PRP1]; P7: Db heterozygous at PRH1 (Db-Pa) combined with PRP1 / PRP2 heterozygous at PRH2 (PRP1-PRP2) [Db-Pa-PRP1-PRP2]; P8:Db heterozygous at PRH1 (Db-PIF) combined with PRP1 / PRP2 heterozygous at PRH2 (PRP-l-PRP-2) [Db-PIF-PRP1-PRP2]; wherein the fingerprint is a GS fingerprint when the combination of CNV group and PRP group is any one of the following GS or GR groups: GS1: P4a combined with CNV group 2 or CNV group 3; GS2: P7 combined with CNV group 2 or CNV group 4; GS3: P8 combined with any one of CNV groups 2, 3 or 4; and wherein the fingerprint is a GS fingerprint when the combination of CNV group and PRP group is any one of the following GS or GR groups: GS1: P4a combined with CNV group 2 or CNV group 3; GS2: P7 combined with CNV group 2 or CNV group 4; GS3: P8 combined with any one of CNV groups 2, 3 or 4; and wherein the genetic fingerprint is a GR fingerprint when the combination is: GR1: P4a combined with CNV group 4 or CNV group 5; GR2: P7 combined with CNV group 3 or CNV group 5; GR3: P8 combined with CNV group 5

[0046] Or alternatively allelic phenotype of acid PRPs encoded by PRH1 and PRH2 under (ii) above may be selected from: P4a: heterozygous at PRH1 (Db-PIF) combined with homozygous at PRH2 (PRP1-PRP1) [Db, PIF, PRP1, PRP1]; P7: heterozygous atPRHl (Db-Pa) combined with heterozygous at PRH2 (PRP1-PRP2) [Db-Pa-PRP1-PRP2]; P8: heterozygous at PRH1 (Db-PIF) combined with heterozygous at PRH2 (PRP-l-PRP-2) [Db-PIF-PRP1-PRP2]; wherein groups P4a, P8 and P7 are attributed to immunodeficiency and high incidence of dental caries that is independent of Streptococcus mutans infection status; and wherein the fingerprint is a GS fingerprint when the combination of CNV group and PRP group is any one of the following GS or GR groups: GS1: P4a combined with CNV group 2 or CNV group 3; GS2: P7 combined with CNV group 2 or CNV group 4; GS3: P8 combined with any one of CNV groups 2, 3 or 4; and wherein the genetic fingerprint is a GR fingerprint when the combination is: GR1: P4a combined with CNV group 4 or CNV group 5; GR2: P7 combined with CNV group 3 or CNV group 5; GR3: P8 combined with CNV group 5.

[0047] According to an embodiment, a fingerprint as defined by any one of claims 1 to 7 shows penetrance, such as linear penetrance, as to biomarkers selected from the group of proteins, salivary short-chain fatty acids (SCFAs), inflammatory biomarkers in parotid saliva, and biofilm (fig. 2, variable blocks; fig 3).

[0048] According to an embodiment, a fingerprint derived from the CNV groups; PRP groups, CNV-PRP group and / or GS,, in particular GS groups GS1, GS2, and GS3, shows penetrance, such as linear penetrance, as to biomarkers selected from salivary short-chain fatty acids (SCFAs) such as butyric acid, lactic acid and 2-hydroxybutyric acid.According to an embodiment, fingerprint derived from GS, GR groups i.e. GSl, GS2 or GS3 or GR1, GR2 or GR3, and specifically GS1, GS2 or GS3, shows a penetrance, such as linear penetrance, as to biomarkers, such as biomarkers selected from of proteins, salivary shortchain fatty acids (SCFAs), inflammatory biomarkers in parotid saliva, and biofilm, in particular, salivary short-chain fatty acids (SCFAs) such as butyric acid, lactic acid and 2-hydroxybutyric acid. Specifically, the GS groups, GS1, GS2 and GS3 show linear penetrance as to all biomarkers (collectively) presented in table 6 (fig. 2 and 3). According to an embodiment, groups GS1, GS2 and GS3 show penetrance, such as linear penetrance, as to biomarkers such as proteins, salivary short-chain fatty acids (SCFAs), inflammatory biomarkers in parotid saliva, and biofilm.

[0049] According to an embodiment, groups GS1, GS2 and GS3 show penetrance, such as linear penetrance, as to biomarkers represented by salivary short-chain fatty acids (SCFAs), in particular butyric acid, lactic acid and 2-hydroxybutyric acid.

[0050] An aspect of the invention relates to a method assessing the susceptibility (predisposition) of a person for the development of dental caries, the, the method comprising: a) providing a biological sample obtained from the person; b) from the biological sample extracting one or more fingerprints as defined by any one of claims 1 to 7, and c) attributing the person to any of the CNV groups; PRP groups, CNV-PRP group and / or GS, GR groups.

[0051] Thus, the method can attribute the person to one of CNV groups 1 to 5 (claim 1), or one of the PRP groups (claim 2 and 3), or one of the CNV-PRP groups 1 to 10 (claim 4), or one of the GS or GR groups, i.e. GSl, GS2 or GS3 or GR1, GR2, GR3, GR-P4b, GR-P1, GR-P5, GR-P6, GR-P10.

[0052] The method may also be complemented by extracting information from biomarkers selected from the group of proteins, salivary short-chain fatty acids (SCFAs), inflammatory biomarkers in parotid saliva, and biofilm.

[0053] Other embodiments of the method are:

[0054] A method (A) for assessing the susceptibility (predisposition) of a person for the development of dental caries, the method comprising: a) providing a biological sample obtained from the person; b) from the biological sample extracting the genetic origin fingerprint of claim 1; and c) attributing the person to one of the CNV groups. Preferably, this method comprises the stepof stratifying the PRP group by the CNV groups; and assigning the person to a CNV stratified PRP group. The PRP groups may be selected from P4a (Db, PIF, PRP-1, PRP-1), P6 (Pa, PIF, PRP- II, PRP-2), Pl (PIF, PIF, PRP-1, PRP-1), P8 (Db-PIF-PRP-l-PRP-2), and P7 (Db-Pa-PRP-l-PRP-2), wherein groups P4a, P8 and P7 are attributed to immunodeficiency and high incidence of dental caries; group P6 is attributed to low to moderate incidence of dental caries; and group Pl attributed to lifestyle and low incidence of dental caries. Method (A) may comprise assigning the person to a genetically susceptible (GS) caries subtype based on the stratification of PRH1, PRH2 allelic phenotype (PRP groups) with DMBT1 CNV group(s) and, thereby providing the GS subtypes: GS1: P4a and CNV groups 2 and 3; GS2: P7 and CNV groups 2 and 4; and GS3: P8 and CNV groups 2, 3 and 4 and optionally genetically resistant (GR) caries subtype based on the stratification of PRH1, PRH2 allelic phenotype (PRP groups) with DMBT1 CNV group(s) and, thereby providing the GR subtypes: GR-P4b: P4b combined with CNV groups 1-5; GR-P1: P1 combined with CNV groups 1-5; GR-P5: P5 combined with CNV groups 1-5; GR-P6: P6 combined with CNV groups 1-5; and GR-P10: P10 combined with CNV groups 1-5.

[0055] A method for assessing the susceptibility (predisposition) of a person for the development of dental caries, the method comprising: a) providing a biological sample obtained from the person; b) from the biological sample extracting the phenotype origin fingerprint of any one of claims 2 to 4; and c) attributing the person to one of the PRP groups.

[0056] A method for assessing the susceptibility (predisposition) of a person for the development of dental caries, the method comprising: a) providing a biological sample obtained from the person; b) from the biological sample extracting the fingerprint from genetic and phenotype origin of claim 5 or 6; and c) attributing the person to one of the CNV-PRP groups; or GS or GR groups.

[0057] A further embodiment relates to a method for assessing the susceptibility of a person for the development of dental caries, having established the following stratifications on the genetic level and the phenotype level:

[0058] i) Stratification at the genetic level based on copy number variation pattern at CNV1 and CNV2 of the DMBT1 gene, wherein said copy number variation pattern is characterized by a diploid copy number at CNV1 and a diploid copy number at CNV2 assigned to one of the following CNV groups:

[0059] • CNV group 1: CNV1 = 0 and CNV2 < 4• CNV group 2: CNV1 = 1 and CNV2 < 4

[0060] • CNV group 3: CNV1 = 1 and CNV2 > 4

[0061] • CNV group 4: CNV1 > 2 and CNV2 < 4

[0062] • CNV group 5: CNV1 > 2 and CNV2 > 4

[0063] wherein group 1 and 5 are indicative of low incidence of dental caries; group 2 is indicative of moderate incidence of dental caries; and group 3 and 4 are indicative to high incidence of dental caries;

[0064] ii) Stratification at the phenotype level based on an allelic phenotype of acidic proline-rich proteins (PRPs) encoded by PRH1 and PRH2, selected from any one of the following PRP groups:

[0065] • P4a: Db heterozygous at PRH1 (Db-PIF) combined with PRP1 homozygous at PRH2 (PRP 1 -PRP 1) [Db, PIF, PRP1, PRP1];

[0066] • P7: Db heterozygous at PRH1 (Db-Pa) combined with PRP1 / PRP2 heterozygous atPRH2 (PRP1-PRP2) [Db-Pa-PRP1-PRP2];

[0067] • P8: Db heterozygous at PRH1 (Db-PIF) combined with PRP1 / PRP2 heterozygous atPRH2 (PRP-l-PRP-2) [Db-PIF-PRP1-PRP2];

[0068] • P4b: homozygous at PRH1 (Db, Db) combined with homozygous at PRH2 (PRP1-PRP1) [Db, Db, PRP1, PRP1];

[0069] • P1: homozygous at PRH1 (PIF, PIF) combined with homozygous at PRH2 (PRP1-PRP1) [PIF, PIF, PRP1, PRP1];

[0070] • P5: homozygous at PRH1 (PIF, PIF) combined with heterozygous at PRH2 (PRP1, PRP2) [PIF, PIF, PRP1, PRP2];

[0071] • P6: heterozygous at PRH1 (Pa, PIF) combined with heterozygous at PRH2 (PRP1, PRP2) [Pa, PIF, PRP1, PRP2];

[0072] • P10: homozygous at PRH1 (Pa, Pa) combined with homozygous at PRH2 (PRP2-PRP2) [Pa, Pa, PRP2-PRP2];

[0073] iii) Combining the stratification based on at CNV1 and CNV2 of the DMBT1 gene and the phenotype level based on an allelic phenotype of acidic proline-rich proteins (PRPs) encoded by PRH1 and PRH2, thereby forming the following genetically susceptible dental caries groups:

[0074] • GS1: P4a combined with CNV group 2 or CNV group 3;

[0075] • GS2: P7 combined with CNV group 2 or CNV group 4;• GS3: P8 combined with CNV groups 2, 3 or 4;

[0076] • GR1: P4a combined with CNV groups 4 and 5;

[0077] • GR2: P7 combined with CNV groups 3 and 5;

[0078] • GR3: P8 combined with CNV group 5;

[0079] • GR-P4b: P4b combined with CNV groups 1 to 5;

[0080] • GR-P1: Pl combined with CNV groups 1 to 5;

[0081] • GR-P5: P5 combined with CNV groups 1 to 5;

[0082] • GR-P6: P6 combined with CNV groups 1 to 5;

[0083] • GR-P10: PIO combined with CNV groups 1 to 5;

[0084] the method comprising;

[0085] a) providing a biological sample obtained from the person;

[0086] b) extracting from the sample of said person information on CNV1 and CNV2 copy number variation patterns of DMBT1 and on allelic phenotypes of acid PRPs and optionally genotypes corresponding to the allelic acid PRPs; and

[0087] c) assigning the person to one group selected from GS1, GS2, GS3, GR1, GR2, GR3,, GR-P4b, GR-P1, GR-P5, GR-P6, GR-P10.

[0088] The method may be complemented by further from a saliva sample obtained from the person extracting information selected from the group of salivary proteins, salivary short-chain fatty acids (SCFAs), inflammatory markers and microbiota and lifestyle biomarkers, specifically selected from salivary short-chain fatty acids (SCFAs), preferably from butyric acid, lactic acid and 2-hydroxybutyric acid.

[0089] According to an embodiment, a fingerprint is extracted (obtained) by Paralogue Ratio Test (PRT), next generation sequencing (NGS), PCR such as Digital Droplet PCR (ddPCR), Array Comparative Genomic Hybridization (aCGH), Multiplex Ligation-dependent Probe Amplification (MLPA), and SNP genotyping arrays, Native alkaline polyacrylamide gel electrophoresis (PAGE), High-Performance Liquid Chromatography (HPLC), Mass Spectrometry (MS) - proteomics, Immunoassay - Western blot / ELISA, TaqMan SNP genotyping, Illumina SNP array. More specifically, a genetic fingerprint is extracted by Paralogue Ratio Test (PRT), next generation sequencing (NGS), PCR such as Digital Droplet PCR (ddPCR), Array Comparative Genomic Hybridization (aCGH), MultiplexLigation-dependent Probe Amplification (MLPA), and SNP genotyping arrays; a phenotype fingerprint is extracted by Native alkaline polyacrylamide gel electrophoresis (PAGE), High-Performance Liquid Chromatography (HPLC), Mass Spectrometry (MS) - proteomics, Immunoassay - Western blot / ELISA, TaqMan SNP genotyping, Illumina SNP array. These means of extracting fingerprint information may also be incorporated in any method of the present invention.

[0090] A further aspect relates to an analytical kit for determining the predisposition of a person developing dental caries, comprising means for extracting fingerprint information defined by any one of claims 1 to 8 and attributing the person to any one of the groups defined in any one of claims 1 to 8.

[0091] The means for extracting genetic fingerprint information may be selected from Paralogue Ratio Test (PRT), generation sequencing (NGS), PCR such as Digital Droplet PCR (ddPCR), Array Comparative Genomic Hybridization (aCGH), Multiplex Ligation-dependent Probe Amplification (MLPA), SNP genotyping arrays.

[0092] Means for extracting phenotype genetic fingerprint information can be selected from Native alkaline polyacrylamide gel electrophoresis (PAGE), High-Performance Liquid Chromatography (HPLC), Mass Spectrometry (MS) - proteomics, Immunoassay - Western blot / ELISA, TaqMan SNP genotyping, Illumina SNP array.

[0093] Means for extracting protein concentration may be selected from Slot-blot immunoassay, ELISA, and Proximity Extension Assay (PEA, Olink).

[0094] A further aspect of the invention relates to assigning the person to a genetically susceptible (GS) or genetically resistant (GR) caries subtype based on the combined DMBT1 CNV group and PRH1, PRH2 allelic phenotype, wherein the GS subtypes are: GS1 = P4a combined with CNV group 2 or 3 (or both); GS2 = P7 combined with CNV group 2 or 4 (or both); GS3 = P8 combined with any one of CNV groups 2, 3 or 4 (or combinations thereof); and wherein persons assigned to a GS subtype are further assessed using salivary biomarkers showing near-linear penetrance of 5-year caries progression, said biomarkers comprising one or more of the PRP3 / 1 cleavage ratio; DMBT1 concentration; short-chain fatty acids selected from butyric acid, lactic acid and 2-hydroxybutyric acid; and inflammatory markers selected from SIRT2, GDNF and SCF.Further aspects / embodiments are apparent from the claims and are incorporated herein by reference.

[0095] Elaboration of some terms

[0096] Copy number variation pattern: CNV1 and CNV2 constitute two independent, geographically distinct clusters of tandemly repeated SRCR-SID units within the DMBT1 gene. CNV1 encompasses a repeat unit comprising four SRCR domains (SRCR3-SRCR6), and CNV2 encompasses a repeat unit comprising three SRCR domains (SRCR9-SRCR11). Importantly, each of these sites is subject to both deletion and duplication relative to the canonical reference sequence: the diploid copy number at CNV1 ranges from 0 to 5 across human populations, and at CNV2 from 0 to 11. Consequently, individuals may carry fewer or more copies of these SRCR domain blocks than the canonical sequence, and the term 'copy number variation pattern' is therefore used throughout the present description. Both deletions and duplications at CNV1 and CNV2 form part of the five-group CNV classification of the invention, and the diagnostic associations described herein encompass the full spectrum of copy number variation at both sites.

[0097] SRCR, Scavenger Receptor Cysteine-Rich: An SRCR domain is a small, structurally stable, cysteine-locked protein module of the DMBT1 gene that grabs onto a wide range of microbial and host targets. DMBT1 has a long tandem array of these modules — 13 in the canonical sequence, more or fewer depending on CNV1 and CNV2 copy numbers — which gives the protein its broad-spectrum pattern recognition capacity. More SRCR domains generally means more binding sites and greater avidity for microbial targets, which is the basis of Dl's framework. The invention then shows that this simple "more is better" model breaks down entirely once you account for which specific domains are present or absent and which PRH1 / PRH2 background they operate in.

[0098] Biological sample: As used herein, the term "biological sample" refers to any material of biological origin obtained from a person from which genetic information, protein information, metabolic information or microbiome information can be extracted. A biological sample includes without limitation: saliva, parotid saliva, whole saliva, buccal scraping or swab, blood, serum, plasma, urine, faeces, cerebrospinal fluid, tissue biopsy, and any other tissue orfluid containing nucleated human cells. The biological sample may be used directly or after processing, fractionation, concentration or storage.

[0099] Salivary Biomarkers: Salivary biomarkers is the umbrella term for anything measurable in saliva that correlates with and predicts caries progression. Salivary biomarkers can be salivary proteins, Short Chain Fatty Acids (SCFAs), inflammatory markers and microbiota and lifestyle markers.

[0100] Salivary proteins are immunity proteins encoded by the genes of the present invention such as PRP3 / 1 cleavage ratio: the ration of small to large acidic PRPs, reflecting proteolytic activity in saliva.

[0101] SCFAs are metabolic end-products of the oral microbiome — produced by bacteria fermenting carbohydrates and amino acids. They are proxies for microbial community composition and metabolic activity. Examples of SCFAs are butyric acid, lactic acid and 2-hydroxybutyric acid, which can be measured in pM in whole saliva by e.g. UPLC-MS.

[0102] Inflammatory biomarkers are proteins reflecting the immune and inflammatory state of the individual, measured by the Proximity Extension Assay (PEA, Olink) in parotid saliva.

[0103] Inflammatory biomarkers are e.g. SIRT2, GDNF and SCF.

[0104] Microbiota and lifestyle biomarkers include plaque mass (PLI), toothbrushing frequency, and S. mutans counts.

[0105] Penetrance: penetrance describes the proportion of individuals carrying a particular genotype who show the expected phenotype. A gene variant with high penetrance means that almost everyone who carries it will develop the associated condition. A variant with low penetrance means that many carriers will never show symptoms despite having the genotype. Linear penetrance, or near linear penetrance, means that within a defined GS subtype, the salivary biomarker level predicts individual caries outcome in a graded, nearly proportional way. A linear penetrant is a biomarker that: works reliably at the individual level, shows a near-linear dose-response - small differences in the biomarker translate into predictable differences in caries outcome, and has high predictive power - the R2and Q2values from Partial Least Square (PLS) models confirm this statistically.Disclosure of the Invention

[0106] Information from DMBT1 and PRH1 / PRH2 can in principle be extracted from a variety of biological macro molecules using a variety of protocols and / or devices. Information may stem from nucleic acid such an DNA and various classes of RNA including mRNA, tRNA, rRNA; proteins and peptides including post-translational modifications of proteins and proteolytic derivatives thereof; and microbiome exemplified by cariogenic flora and commensal pathogens.

[0107] Useful protocols and / or devices / apparatus include nucleic acid sequencing, mass spectrometry, proteomic's, metabolomic's, transcriptomic's and microbiomic's.

[0108] Proteomics can include protein extraction, protein precipitation, protein separation, protein identification by e.g. mass spectrometry, western blotting, quantification and post-translational modification analysis such as phosphoproteomics and glycoproteomics.

[0109] The type of tissue or fluid to be collected from a person is partly dependent on the class of macro molecules used for deriving / extracting the relevant information and / or dependent on protocol. Where information is derived from nucleic acid and / or proteins / peptides any tissue and / or fluid can be used provided cells are comprised therein. If information is derived from microbiome it is preferred to collect tissue of fluid with extensive microbiome, such as saliva and / or buccal scraping.

[0110] Samples can be any kind of tissue and tissue fluids such as blood, faces, skin, and any tissue with human cells with a nucleus.

[0111] Samples are preferably selected from the buccal cavity such as saliva and buccal scraping. The method for assessing susceptibility (predisposition) for developing dental caries comprises extracting information on CNV1 and CNV2 copy number variation patterns of DMBT1 and preferably in conjunction with extracting information from PRH1 and PRH2 and assigning / attributing the extracted information to genetic caries types. Information related to genetic caries types are typically already available. Thus, the only data acquisition necessary in the method is usually only the extraction of the data (information) as to DMBT1, PRH1 and PRH2 for the person to be examined (diagnosed).

[0112] As stated in the introduction, there is some evidence that DMBT1 size isoforms may implicate dental caries.The present invention is based on the discovery that non-monotonic pattern of copy number variations at two distinct sites (CNV1 and CNV2) in the DMBT1 gene can be attributed to different susceptibilities of dental caries.

[0113] Further, it has been discovered that a specific, non-monotonic pattern of copy number variations at two distinct sites (CNV1 and CNV2) in the DMBT1 gene interacts with PRH1 / PRH2 allelic variation to produce a clinically actionable stratification of dental caries susceptibility — including the identification of a previously unrecognised, Streptococcus mutans-independent immunodeficiency caries subtype

[0114] Also, the data underlying the present invention, conveys that it is the CNV of DMBT1 (CNV1 and CNV2) which interacts with PRH1 and PRH2 in the immunodeficient caries P4a and P7 phenotypes (tables 2 and 4).

[0115] Based on a cohort of more than 400 adolescents the progression of total numbers of Decayed, enamel included, Filled Surfaces (DeFS) was analyzed with reference to CNV2 and CNV1 (fig.l). The qualitative pattern of deletions at CNV1 and CNV2 coincides with different levels of caries progression.

[0116] Additional and previously unknown enhanced diagnostic resolution is generated based on the discovery that CNV1 and CNV2 of DMBT1 and PRH1 / PRH2 obviously cooperate in respect of susceptibility of dental caries. The knowledge of CNV1 and CNV2 of DMBT1 in relation to PRH1 and PRH2 further enables stratification of PRH1, PRH2 genetic subgroupings, also referred to herein as PRP groups, such as any one of P4a (Db-PIF-PRP-l-PRP-2), P7 (Db-Pa-PRP-l-PRP-2), P8 (Db-PIF-PRP-l-PRP-2), P6 (Pa-PIF-PRP-l-PRP-2), and Pl (PIF PIF-PRP-l-PRP-1) with respect to the CNV groups. P4a, P7 and P8 have high caries immunodeficiency (table 2 and 4), Pl is traditional lifestyle causal caries subtype and P6 low-moderate. The CNV stratified PRP groups are set out in table 2.

[0117] CNV1 and CNV2 constitute two independent, geographically distinct clusters of tandemly repeated SRCR-SID units within the DMBT1 gene. CNV1 encompasses a repeat unit comprising four SRCR domains (SRCR3-SRCR6), and CNV2 encompasses a repeat unit comprising three SRCR domains (SRCR9-SRCR11). Importantly, each of these sites is subject to both deletion and duplication relative to the canonical reference sequence: the diploid copy number at CNV1 ranges from 0 to 5 across human populations, and at CNV2 from 0 to 11. Consequently, individuals may carry fewer or more copies of these SRCR domain blocks than the canonical sequence, which is characterized by the term 'copy numbervariation pattern'. Both deletions and duplications at CNV1 and CNV2 form part of the five-group CNV classification of the invention.

[0118] Stratification of DMBT1 CNV groups against PRH1, PRH2 allelic variation has identified three distinct genetically susceptible (GS) caries subtypes with markedly elevated 5-year caries progression: GS1 (P4a combined with CNV groups 2 and 3, influential site CNV1), GS2 (P7 combined with CNV groups 2 and 4, influential site CNV2), and GS3 (P8 combined with CNV groups 2, 3 and 4, influential sites CNV1 and CNV2). Each GS subtype shows a distinct profile of salivary protein, short-chain fatty acid (SCFA) and inflammatory biomarkers with near-linear penetrance of 5-year caries progression. Collectively, the GS1-3 subtypes constitute approximately 10% of a prospective cohort of 452 Swedish adolescents while contributing to 28% of the most severe incremental caries cases. Genetically resistant (GR) counterparts - GR1 (P4a-CNV groups 4,5), GR2 (P7-CNV groups 3,5) and GR3 (P8-CNV group 5) - within the same PRH1, PRH2 backgrounds do not show elevated caries progression, confirming that the CNV stratification is the decisive diagnostic variable within each PRH1, PRH2 phenotype. Evidence also indicates that distinct genetic forms of dental caries of inflammatory or immunodeficiency nature contribute significantly to recurrent caries cases that respond poorly to standard prevention in high-income, low-prevalence populations. Salivary short-chain fatty acids (SCFAs) - including butyric acid, lactic acid and 2-hydroxybutyric acid - as proxies for oral microbial community composition and metabolic activity, and inflammatory protein biomarkers, including sirtuin 2 (SIRT2), glial cell line-derived neurotrophic factor (GDNF) and stem cell factor (SCF), have been identified as near-linearly penetrant predictors of 5-year caries progression in genetically susceptible (GS) caries subtypes. These findings argue that the GS caries phenotypes reflect a primary inflammatory or immunodeficiency disease process rather than lifestyle-microbial dysbiosis alone.

[0119] Stratification of the four predominant CNV groups 2-5 against the GS (immunodeficiency) and GR (lifestyle) PRH1, PRH2 phenotypes reveals three distinct genetically susceptible caries subtypes with markedly increased 5-year caries progression and three genetically resistant counterparts within the same PRH1, PRH2 backgrounds:

[0120] GS1 (P4a-CNV groups 2 and 3; influential CNV site: CNV1): mean 5-year ADeFS = 8.3 ± 8.6, p = 0.001 versus GR-P1 reference; n = 27 (6% of cohort). The GS1 subtype shows a high-power caries prediction model (R2= 0.84, Q2= 0.25) based on salivary DMBT1 and PRP proteins, SCFAs and inflammatory biomarkers. Caries progression in GS1 is negatively correlated withthe PRP3 / 1 cleavage ratio (r = -0.692, p = 0.013) and with 2-hydroxybutyric acid (r = -0.428, p = 0.047), and negatively correlated with the inflammatory marker SIRT2 (r = -0.72, p < 0.001). DMBT1 concentration correlates positively with caries progression in GS1 (r = +0.510). GS2 (P7-CNV groups 2 and 4; influential CNV site: CNV2): mean 5-year ADeFS = 6.7 ± 5.0, p = 0.008 versus GR-P1 reference; n = 13 (3% of cohort). Caries progression in GS2 is negatively correlated with PRP3 / 1 ratio (r = -0.821, p = 0.023), DMBT1 concentration (r = -0.679), butyric acid (r = -0.797, p = 0.002), lactic acid (r = -0.741, p = 0.006), and the inflammatory marker GDNF (r = -0.88, p = 0.004). The inverse association of SCFAs with caries progression in GS2 differs markedly from the GR2 counterpart, emphasising the distinct genetic influence.

[0121] GS3 (P8-CNV groups 2, 3 and 4; influential CNV sites: CNV1 and CNV2): mean 5-year ADeFS = 10.3 ± 10.0, p = 0.005 versus GR-P1 reference; n = 6 (1% of cohort). GS3 shows the highest caries progression and the strongest prediction model (R2= 0.98, Q2= 0.76). Caries progression is negatively correlated with lactic acid (r = -0.943, p = 0.005) and 2-hydroxybutyric acid (r = -0.886, p = 0.019), and positively correlated with the inflammatory marker SCF (r = +0.83, p = 0.042). Toothbrushing frequency is also a significant predictor (r = -0.926).

[0122] The genetically resistant counterparts GR1 (P4a-CNV groups 4 and 5), GR2 (P7-CNV groups 3 and 5) and GR3 (P8-CNV group 5) show no significant difference in 5-year caries progression compared to the GR-P1 reference phenotype (p > 0.44 in all cases), confirming that within each immunodeficiency PRH1, PRH2 background it is the specific CNV group that determines susceptibility or resistance.

[0123] The area under the ROC curve (AUC) for single salivary biomarkers in each GS subtype demonstrates good-to-excellent diagnostic discrimination: AUC = 0.838 for GS1, 0.798 for GS2, and 0.929 for GS3, compared to GR counterparts. These values substantially exceed the diagnostic performance achievable from baseline clinical caries symptoms alone (the current standard of care), particularly in the GS1 and GS3 subtypes where salivary biomarkers are the dominant predictors.

[0124] In GR phenotypes, including GR-P1, long DMBT1 protein isoform III is caries-protective even in the presence of S. mutans infection or high plaque accumulation, while short isoforms I and II associate with increased caries progression. By contrast, in each GS1-3 subtype, long isoform III is rare and a unique DMBT1 isoform pattern consistent with the specific CNV deletionpattern is present. DMBT1 CNV per se does not correlate with caries progression and explains isoform size only marginally, reinforcing that the qualitative CNV pattern — not total copy number — is the operative diagnostic variable.

[0125] The following CNV stratified PRP groups have a particular susceptibility to dental caries: In PRP group P4: CNV group 2, CNV group 3 and combination of CNV groups 2 and 3. In PRP group P7: CNV group 2, CNV group 4 and combinations of CNV groups 2 and 4. In PRP group P8: CNV group 2, CNV group 3, CNV group 4 and combinations of CNV groups 2, 3 and 4.

[0126] The CNV stratified PRP groups particularly susceptibility to dental caries are also identified as follows:

[0127] [P4a-CNV group 2], [P4a-CNV group 3], [P4a-CNV group 2-CNV group 3],

[0128] [P7-CNV group 2], [P7-CNV group 4], [P7-CNV group 2-CNV group 4],

[0129] [P8-CNV group 2], [P8-CNV group 3], [P8-CNV group 4], [P8-CNV group 2-CNV group- 3 - CNV group 4],

[0130] Stratification on the genetic level and phenotype level

[0131] Information related to CNV1 and CNV2 of the SRCR-SID domains of the DMBT1 gene are stratified in the CNV groups 1 to 5. It is important to note that CNV groups 1 to 5 refer to five CNV groups not to CNV1 and CNV2. CNV1 and CNV2 are the two sites in the DMBT1 gene where copy number variation occurs. CNV1 is the SRCR3-6 repeat cluster, CNV2 is the SRCR9-11 repeat cluster. These are genomic locations.

[0132] The CNV groups 1 to 5 are diagnostic classification categories defined by the specific combination of diploid copy numbers observed at CNV1 and CNV2 in a given individual.

[0133] CNV1 and CNV 2 may also be referred to as CNV-site 1 and CNV site 2 for clarity reasons.

[0134] The number of CNV1 and CNV2 is table 3 represents diploid copies.Stratification is also provided by allelic phenotype information of acidic proline-rich proteins (PRPs) encoded by PRH1 and PRH2. Stratification based on PRPs is exemplified by the following groups:

[0135] P4a: heterozygous at PRH1 (Db-PIF) combined with PRP1 homozygous at PRH2 (PRP1-PRP1) [Db, PIF, PRP1, PRP1];

[0136] P7: heterozygous at PRH1 (Db-Pa) combined with heterozygous at PRH2 (PRP1-PRP2) [Db-Pa-PRP1-PRP2];

[0137] P8: heterozygous at PRH1 (Db-PIF) combined with heterozygous at PRH2 (PRP-l-PRP-2) [Db-PIF-PRP1-PRP2];

[0138] P6: heterozygous at PRH1 (Pa, PIF) combined with heterozygous at PRH2 (PRP1, PRP2) [Pa, PIF, PRP1, PRP2];

[0139] P1: homozygous at PRH1 (PIF, PIF) combined with homozygous at PRH2 (PRP1-PRP1) [PIF, PIF, PRP1, PRP1];

[0140] P4b: homozygous at PRH1 (Db, Db) combined with homozygous at PRH2 (PRP1-PRP1) [Db, Db, PRP1, PRP1];

[0141] P5: homozygous at PRH1 (PIF, PIF) combined with heterozygous at PRH2 (PRP1, PRP2) [PIF, PIF, PRP1, PRP2];

[0142] P10: homozygous at PRH1 (Pa, Pa) combined with homozygous at PRH2 (PRP2-PRP2) [Pa, Pa, PRP2-PRP2];

[0143] Groups P4a, P8 and P7 are attributed to immunodeficiency and high incidence of dental caries; groups P5 and P6 are attributed to low to moderate incidence of dental caries; and groups P1, P4b, P1, P10 attributed to lifestyle and low incidence of dental caries.

[0144] Further stratification is provided by the groups: genetically susceptible dental caries (GS) group and a genetically resistant dental caries (GR) group. The GS groups are: GS1, GS2 and GS3. The GR groups are:

[0145] GR1: P4a and CNV groups 4 and 5;

[0146] GR2: P7 and CNV groups 3 and 5;

[0147] GR3: P8 and CNV group 5;

[0148] GR-P4b: P4b combined with CNV groups 1-5;

[0149] GR-P1: P1 combined with CNV groups 1-5;

[0150] GR-P5: P5 combined with CNV groups 1-5;

[0151] GR-P6: P6 combined with CNV groups 1-5; andGR-P10: P10 combined with CNV groups 1-5. Further stratification / groups may be extracted from the information in this disclosure and in particular from the tables and figures, to the extent it is possible got the person skilled in this technical field.

[0152] It should be noted that the stratification underlying the present invention is based on a cohort of a total of 452 adolescents. Extending the number of adolescents may provide added granularity.

[0153] Analytical Kit

[0154] Genetic fingerprint, information on the genetic level, such as the determination of the diploid copy number at CNV1 and CNV2, is preferably provided by the Paralogue Ratio Test (PRT) This is the method used in the 452-adolescent cohort. It uses PCR with a single primer pair that amplifies both a copy-number variable region (test amplicon, inside the CNV) and a nonvariable reference region. The ratio of the two amplicon peak areas on a fragment analyzer gives the copy number. Four assays are run per sample — PRT1 / PRT2 for CNV1, PRT3 / PRT4 for CNV2. The software Fraggler (59) calls the peak areas automatically.

[0155] Advantages: robust, inexpensive, requires only standard PCR and fragment analysis equipment. Disadvantage: requires careful normalization against reference samples of known copy number.

[0156] Other measures for extracting genetic fingerprint information is sequencing such as next generation sequencing (NGS), PCR such as Digital Droplet PCR (ddPCR), Array Comparative Genomic Hybridization (aCGH), Multiplex Ligation-dependent Probe Amplification (MLPA), and SNP genotyping arrays.

[0157] Next generation sequencing (NGS): Whole genome sequencing or targeted panel sequencing of the DMBT1 locus allows copy number determination by counting sequencing reads mapping to CNV1 and CNV2 relative to flanking non-variable regions. With sufficient sequencing depth this is highly accurate and can resolve individual alleles. Advantages: can simultaneously genotype CNV1, CNV2 and flanking SNPs; amenable to high-throughput clinical platforms. Disadvantage: the highly repetitive nature of the SRCR-SID array makes read alignment challenging with short-read sequencing; long-read platforms (Oxford Nanopore, PacBio) handle this better.Digital Droplet PCR (ddPCR): Partitions the PCR reaction into thousands of individual droplets, allowing absolute copy number quantification without reliance on a standard curve. Highly accurate and reproducible. Increasingly available in clinical molecular diagnostics laboratories.

[0158] Array Comparative Genomic Hybridization (aCGH): Hybridization of labelled genomic DNA to a microarray carrying DMBT1 probes. Detects copy number changes as fluorescence intensity ratios. Used in the original CNV characterization studies by Polley et al. Less suitable for routine clinical use due to cost and complexity.

[0159] Multiplex Ligation-dependent Probe Amplification (MLPA): Probes specific to CNV1 and CNV2 regions are ligated and amplified; copy number is inferred from relative peak heights. Widely used in clinical diagnostics for copy number determination. Could be adapted for DMBT1 CNV1 and CNV2 genotyping.

[0160] SNP genotyping arrays: Flanking SNPs (e.g. rs11523871, rs2981745) are in partial linkage disequilibrium with CNV1 / CNV2 alleles and can provide indirect imputation of copy number haplotype. Used in large GWAS cohorts where direct CNV measurement is impractical. Less accurate than direct measurement but useful for population screening.

[0161] Allelic phenotype fingerprint information, at the protein level, can be obtained by Native alkaline polyacrylamide gel electrophoresis (PAGE), High-Performance Liquid Chromatography (HPLC), Mass Spectrometry (MS) - proteomics, Immunoassay — Western blot / ELISA, TaqMan SNP genotyping, Illumina SNP array.

[0162] Native alkaline polyacrylamide gel electrophoresis (PAGE): The method used in the invention. Parotid saliva is collected (by placing a collector over the parotid duct opening), lyophilized, reconstituted, and run on a 7% polyacrylamide gel under native (non-denaturing) alkaline conditions. The acidic PRP variants separate by charge and size into characteristic banding patterns. Gels are stained with Coomassie Brilliant Blue and typed visually or by densitometry. Advantages: direct protein-level readout, inexpensive, well-validated in the literature. Disadvantage: requires fresh or well-preserved parotid saliva; technical skill required for gel interpretation.

[0163] High-Performance Liquid Chromatography (HPLC): Reverse-phase or ion-exchange HPLC separates PRP variants by hydrophobicity or charge. Used as a validation method in theinvention alongside electrophoresis. Provides quantitative data on each variant. Can be coupled to mass spectrometry for positive identification of each PRP allelic form.

[0164] Mass Spectrometry (MS) - proteomics: MALDI-TOF or LC-MS / MS can identify and quantify individual PRP variants based on their molecular mass and fragmentation patterns. Particularly powerful for distinguishing variants with subtle differences such as the 21 -amino acid Db insert versus PIF. Advantages: highly accurate, multiplexable, no antibody required. Can simultaneously measure PRP variants and DMBT1. Disadvantage: requires specialized equipment and bioinformatics pipeline.

[0165] Immunoassay - Western blot / ELISA: Antibodies specific to the Db, PIF, Pa (PRH1) or PRP-1, PRP-2 (PRH2) variants can in principle be used for phenotyping. Western blot under denaturing conditions separates variants by molecular weight. ELISA could provide quantitative measurement. Advantage: familiar technology in clinical settings. Disadvantage: allele-specific antibodies are not yet commercially standardized for the full PRP variant set. TaqMan SNP genotyping: Protein-coding SNPs rs2923234, rs1049117 and rs1049112 have been validated as proxy markers for the Db, PIF, Pa and PRP-1, PRP-2 protein variants, yielding 98-100% congruence with protein phenotyping in the invention's cohort. This allows DNA-level genotyping from any nucleated cell (buccal swab, blood) rather than requiring parotid saliva. Advantages: robust, high-throughput, compatible with standard clinical molecular diagnostics platforms. This is arguably the most practical route for clinical implementation.

[0166] Illumina SNP array: The Golden Gate array used in the original cohort genotyped 45 SNPs in the PRH1 / PRH2 region, enabling full allelic haplotype reconstruction by principal component analysis. Suitable for research and large-scale population screening. Clinical adaptation would use a targeted panel of the key protein-coding SNPs.

[0167] Additional protein concentration such as DMBT1 protein concentration can be provided by Slot-blot immunoassay, ELISA, and Proximity Extension Assay (PEA, Olink).

[0168] Slot-blot immunoassay: The method used in the invention. Parotid saliva is diluted and applied directly to a nitrocellulose membrane in a slot-blot apparatus. The membrane is probed with anti-DMBT1 antibody (mAb-143 or equivalent polyclonal) and quantified by densitometry. Gives a measure of DMBT1 concentration normalized by saliva volume.ELISA: A standardized sandwich ELISA using paired anti-DMBT1 antibodies would provide a quantitative, high-throughput alternative to the slot-blot. Commercially available anti-DMBT1 antibodies (e.g. Invitrogen PA5-107112) are suitable for this purpose.

[0169] Proximity Extension Assay (PEA, Olink): Used for the 92 inflammatory markers in the manuscript. Two antibodies each carrying a DNA tag bind the target protein; when in proximity the DNA strands hybridize and are amplified, giving a highly sensitive digital readout. Provides simultaneous measurement of SIRT2, GDNF, SCF and many other inflammatory proteins from a small saliva volume.

[0170] Information related to Short-Chain Fatty Acids (SCFAs) can be derived through Ultraperformance Liquid Chromatography - Mass Spectrometry (UPLC-MS), Gas Chromatography - Mass Spectrometry (GC-MS), Nuclear Magnetic Resonance (NMR) spectroscopy, Enzymatic colorimetric assays and Lateral flow immunoassay.

[0171] Ultraperformance Liquid Chromatography - Mass Spectrometry (UPLC-MS): The method used in the manuscript. Whole saliva is collected, derivatized if necessary, and separated by reversed-phase UPLC before detection by triple quadrupole mass spectrometry. Provides accurate quantification of butyric acid, lactic acid, 2-hydroxybutyric acid and nine other SCFAs in pM concentrations from a 10 pL saliva volume. This is currently the gold standard. Gas Chromatography - Mass Spectrometry (GC-MS): Traditional method for SCFA analysis. SCFAs are volatile and separate well on GC columns. Widely available in clinical and research laboratories. Slightly lower throughput than UPLC-MS but well-validated.

[0172] Nuclear Magnetic Resonance (NMR) spectroscopy: Can quantify multiple metabolites including SCFAs simultaneously from an untreated saliva sample. Advantages: nondestructive, no derivatization required, broad metabolite coverage. Disadvantage: lower sensitivity than MS for low-abundance SCFAs; requires specialized equipment.

[0173] Enzymatic colorimetric assays: Specific enzyme-coupled reactions can quantify individual SCFAs such as lactic acid and butyric acid using simple spectrophotometric readouts. Suitable for point-of-care or lower-resource settings. Less multiplexable than MS-based approaches but potentially the most practically deployable in a clinical kit format.

[0174] Lateral flow immunoassay: For clinical kit applications, antibody -based lateral flow strips specific to key SCFAs (particularly lactic acid, which is commercially measurable this way)could provide a rapid, low-cost qualitative or semi -quantitative readout. This is the format most compatible with a chairside dental diagnostic kit.

[0175] SHORT DESCRIPTION OF FIGURES

[0176] Figure 1. Genetically susceptibility (GS1-3) and genetically resistant (GR) causal types of caries based on DMBT1 CNV-PRH1, PRH2 variation.

[0177] A) Stratification of DMBT1 CNV at CNV1 and CNV2 (shown at the bottom) into five CNV1'5deletion groups 1-5 with high (CNV2,3), moderate (CNV4) and low (CNV1,5) 5-year caries progression. Stratification of CNV2'5groups against the GS and GR phenotypes identified GS1 (P4a-CNV2,3), GS2 (P7- CNV2,4) and GS3 (P8-CNV2'4) with markedly increased 5-year caries progression, in contrast to the GR counterparts

[0178] B) Major causal caries types (upper); with DMBT1 CNV-PRH1, PRH2 GS caries type of inflammatory or immunodeficiency nature and GR caries types caused by S. mutans high virulence types or by poor lifestyle behaviors. Middle: Violin plots showing caries progression at 17 years old for the GS1-3 and GR causal caries types. Bottom: Receiver operating characteristic (ROC) curves and area under the curve (AUC) for a single small / large protein-rich protein, lactic acid, and 2-hydroxybutyric acid in each GS phenotype (AUC = 0-838, 0-798, and 0-929 for GS1, GS2, and GS3, respectively) versus GR phenotypes.

[0179] C) Top: Schematic illustration of genetic-microbial dysbiosis or dysfunction in GS1-3 caries versus S. mutans high virulence- or lifestyle-microbial dysbiosis in GR caries. Bottom:

[0180] Schematic illustration of direct and indirect effector mechanisms underlying the genetic type of caries.

[0181] Figure 2. 5-year caries prediction models with near-linear individual caries penetrance from blocks of salivary biomarkers.

[0182] A) Multivariate caries prediction models (R2, Q2) of blocks of salivary proteins, short-chain fatty acids (SCFAs), inflammatory and microbiota biomarkers, and lifestyle markers against 5-year caries progression in genetically susceptible (GS) and genetically resistant (GR) phenotypes. The heatmap colors and numbers gives the influential values (VIP) foreach biomarker.

[0183] B) Partial least squares prediction plots for the blocks of salivary proteins, SCFAs, inflammatory and microbiota biomarkers, and lifestyle markers relative to baseline clinical symptoms and all salivary biomarkers.C) The inverse association of SCFA's with 5-year caries progression in GS2 and GR2 phenotypes.

[0184] Figure 3. Prediction of 5-year caries progression by individual salivary biomarkers. Linear regression models for the strongest salivary protein, short-chain (SCFA) and inflammatory biomarkers and for baseline (DeFS) caries in each GS1, GS2 and GR-P1, GRl(P4a) group. Regression lines, R2and p values, and 95 % confidence intervals (95% CI) are shown: red (p < 0.05), yellow (0.05 < p < 0.1) and black (not significant). Strong predictors, such as butyric acid in GS2 did not predict caries in GRl(P4a) and GR-P1, in which baseline caries was a comparably strong predictor. The x-axis represents 5-year caries increment / progression, and the y-axis represents the PRP3 / PRP1 ratio or concentrations of DMBT1 (amount standardised by saliva volume), SCFAs (pM), or inflammatory biomarkers (normalized protein expression; NPX).

[0185] Figure 4. Three-gene stratification of DMBT1 CNV-PRH1, PRH2 allelic variation against 5-year caries progression. Typing scheme shows matching of all PRH1, PRH2, and DMBT1 deletion groups with their associated caries level and t

[0186] Figure 5. Distribution of DeFS scores at 12 and 17 years of age, and the incremental increase (ADeFS 5-y). Gray boxes indicate the number of caries-free individuals within each genetic group: genetically susceptible groups (GS1-3) versus genetically resistant (GR).Disclosure of Embodiments

[0187] Materials, Methods and Experiments

[0188] Study Sample. A caries-referent sample of 452 adolescents were collected at two occasions in northern Sweden (9-11). The first sample (n=218 children), pre-selected in equal amounts as caries-free or with caries (> 1 DFS), was examined and collected 2008; the second sample (n=234 children), pre-selected as caries-free or with caries (> 2 DFS), was collected and examined 2010. Caries and lifestyle date and biological samples (e. g. parotid and whole salivas, buccal DNAand S. mutans isolates) were collected for all adolescents.

[0189] Clinical registrations. Caries was recorded by a dentist using the DeFS index (Decayed, enamel caries included, Filled Surfaces in the permanent dentition) (9-11). Lifestyle data on sex, ethnicity (Ethn), oral hygiene (Oh), intake frequency of sweets (Sweets), sweetened drinks (Drinks) or extra fluoride taken (F) were from the children by questionnaires as described (5). The numbers of mutans streptococci (ms), total streptococci (strept) or lactobacilli (lbc) were measured in whole saliva (ms, strept, lbc) and plaque (ms pl, strept pl) samples as previously described (9-11), and proportions of ms out of total streptococci in saliva (% ms) and plaque (% ms pl) calculated.

[0190] PRH1, PRH2 andPRBl-4 genotyping. Buccal epithelia were collected using swabs (Catch-A11TM Sample Collection Swab, Epicentre Biotechnologies) and genomic DNA isolated with QIAamp DNA Micro Kit (Qiagen) (9-11). The genomic DNA was whole genome amplified (Illustra Ready-To-GoTM GenomiPhi V3 DNA kit, GE Healthcare) and genotyped using 6 tag and 39 additional single nucleotide polymorphisms (SNPs) with an allele frequency generally >5% of PRH1 and PRH2 and 16 tag SNPs of PRB1-4 in an Illumina Golden Gate array at the SNP& SEQ Technology Platform in Uppsala (9-11). Five PRH1, PRH2 SNPs and one PRB3 SNP with no call frequencies were excluded. Mixed PRH1, PRH2 genotypes were resolved in the vast majority of subjects (n=441) by principal component analysis of the remaining PRH1, PRH2 SNPs (n=40). The 40 SNPs used to resolve the mixed PRH1, PRH2 genotypes were highly conserved in the Db, PIF, Pa (PRH1) and PRP1, and PRP2 (PRH2) alleles. Illumina and protein typing as well as TaqMan typing using protein coding SNPs rs2923234, rs1049117 and rs1049112 revealed 98-100 % typing congruence and generated essentially identical caries-related outcome results.Paralogue Ratio Test (PRT) for DMBT1 CNV. DNA was extracted from buccal swabs with QIAamp DNA Micro Kit (Qiagen) (9-11). Copy number variation (CNV) in the DMBT1 gene was detected in native DNA with the Paralogue Ratio Test (PRT) (13, 58, 59). Briefly, PRT uses PCR to amplify regions both inside and outside the target, utilizing the same set of primers (Fig.1, A). The resulting amplicons differ in size, allowing copy number determination by quantifying the relative amounts of the distinct amplicons, based on peak size measurement through fragment analysis. Four PCR assays (PRT1-4) were performed for each sample. Assays PRT1 and PRT2 targeted the CNV1 -region of the DMBT1 gene, while PRT3 and PRT4 CNV2-region of the DMBT1 gene PCR primers were purchased from ThermoFisher with forward primers labelled with FAM. All PCR reactions were carried out on an Applied Biosystems Veriti Thermal Cycler. PCR reaction mix composition, thermocycler programs and PCR primer sequences are essentially as described (13). PCR setup was performed using Myra pipetting robot (Bio Molecular Systems, Australia) and PCR reactions conducted in 96-well plates (ThermoFisher). For each sample, 5 pL from each PRT assay was pooled and 1 pL of the pool was diluted with a mix of Hi -Di formamide (ThermoFisher) and ladder GeneScan 600 LIZ Size Std v2.0 (ThermoFisher) (95:5 ratio) to a final volume of 11 pL. The mix was subsequently loaded and separated by electrophoresis on an Applied Biosystems 3500 XL Genetic Analyzer. Each PCR plate also included seven DNA control samples (NA07056, NA12044, NA12752, NA18507, NA18517, NA18555, NA18956) with predetermined copy numbers for regions CNV1 and CNV2, obtained from the Coriell Institute (Camden, NJ), to ensure accuracy. The software Fraggler (59) was used to call peak areas for fragments in each analysis. Calls are performed using a for all trace files using a config file where settings are provided in a comma-separated file format.

[0191] Native alkaline electrophoresis of acidic PRP saliva phenotypes. Acidic PRPs were typed in parotid saliva using native alkaline electrophoresis as described (9, 36). Saliva was lyophilized and re-dissolved to the same volume using distilled water containing 1% glycine, 10% glycerol and 0,025% bromphenol blue. Roughly 40 test and reference saliva samples (each 25 pL) were separated in a single run under native conditions on 7.0 % (w / w) polyacrylamide (27:1 bisacrylamide w / w) gels using a 1.5 mM TRIS, 38 mM glycine electrophoresis buffer (pH 8.4) and a PROTEAN Ilxi apparatus (BioRad). The gels were stained with 0.1% Commassie Brilliant Blue (CBB-R250) in 20% trichloroacetic acid for 1 h and destained overnight in 2% acetic acid. A total of 218 samples were analyzed and typed in a double-blind fashion, with the vast majority typable (n=213), and quantified viadensitometry (optical density x mm2) using Molecular Analyst 1.5 software (BioRad). Single representatives of each PRP phenotype were validated using high-performance liquid chromatography as described previously (9-11).

[0192] Western blot typing of DMBT1 size isoforms I-IV. Parotid saliva samples collected from the adolescents were denatured by heating in sample buffer (4 x LDS Sample Buffer, NP0007, Nupage) at 98°C for 10 min and separated by 3-8% Tris-Acetate gel (1.5 mm, Invitrogen Nupage EA03785BOX) at 160 V constantly for 160 minutes. The running buffer used was 20 x Tris-Acetate SDS Running Buffer (LA0041, Nupage). After separation, the saliva samples were transferred to a 0.2 pm PVDF membrane (Trans-Blot Turbo Mini 0.2 pm PVDF Transfer Packs #1704156) by running at 1.3 A and 15V per gel for 12 minutes using TransBlot Turbo. After transfer, the membrane was washed once with PBS-T (50 mM Tris, 150 mM NaCl and 0.05 % Tween 20, pH 7.4), followed by blocking in blocking buffer (5% non-fat dried milk in TBS-T) for 1 hour. The membrane was then incubated with an anti-DMBT1 antibody (Polyclonal Antibody, # PA5-107112, Invitrogen) diluted 1:10000 in blocking buffer overnight at 4°C. After three washes in PBS-T of 10 minutes each, the membrane was incubated with horseradish peroxidase-conjugated goat anti-rabbit IgG antibodies in blocking buffer (5% non-fat dried milk in TBS-T) for 2 hours. Finally, the membrane was washed four times x 10 minutes in PBS-T before detection using chemiluminescence Super Signal substrate (Pierce, Rockford, IL) in Chemidoc. Typing of samples into size isoforms I-IV used the Image Lab program and reference isoform I-IV saliva (41). The anti-DMBTl polyclonal antibodies generated identical typing results with antibody mAb-143 (41) when tested against 14 reference salivas.

[0193] Slot-blot measurements ofDMBTl in saliva. DMBT1 in parotid saliva was quantified using a slot-blot assay and densitometry. Briefly, parotid saliva diluted 1:50 was transferred to a 0.45 pm nitrocellulose membrane (Protran BA85-SB, Whatman) followed by blocking with 5% dry milk in buffer (50 mM Tris, 150 mM NaCl, 0.05% Tween-20, pH 7.4). The membrane was then incubated with anti-gp340 antibody (mAb-143, 1:60,000, kindly provided by Dr. Malamud, University of Pennsylvania, Philadelphia) for 1 hour, followed by two washes for lOmin each and incubation with secondary antibody SAB-100 (1:60,000, Nordic Biosite AB, Sweden) for another one hour. After two washes, binding was visualized using the Super Signal West Dura Detection kit (Pierce Protein Research Products, IL) and quantified by densitometry (INTxmm2) using Chemidoc (Bio-Rad).Short chain fatty acids (SCFAs). Short-chain fatty acids were determined in parotid saliva samples (10 pL) from 452 adolescents using ultraperformance liquid chromatography -mass spectrometry (UPLC-MS) at Chalmers Technical High School. The metabolites in saliva were derivatized with 3 -nitrophenylhydrazine in a methanol solution, separated on a Waters ACQUITY UPLC BEH Cl 8 column using an acetonitrile-water gradient, and detected using a 6500+ QTRAP triple-quadrupole mass spectrometer.

[0194] Proximity Extension Assay (PEA) by Olink® Proteomics. Undiluted samples (10 pL) of parotid saliva were analyzed by PEA. A panel of 92 immune-related proteins, primarily cytokines and chemokines, was determined using the technology provided by Olink® Proteomics (Uppsala, Sweden). The assay uses epitope-specific binding and hybridization with paired oligonucleotide antibody probes that are amplified by quantitative PCR to generate log base-2 normalized protein expression (NPX) values from quantitative PCR Ct values. Proteins with no call rate were excluded from further analysis, resulting in 92 proteins in saliva being included.

[0195] Statistics. Quantitative differences in numbers of DeFS caries lesions at ages 12 and 17 years and of 5-year increment ADeFS are given as means ± standard deviations (SDs) for comparability with previous relevant studies (9-11). The visualised quantitative data and data trends were interpreted in terms of fold and mean difference in mean / median values, combined with P-values and total partial least squares (PLS) models. Mann-Whitney U tests were used because of the large spread and skewed distribution of the caries and microbiota data. To analyse proportions, we use Fisher’s exact test except for the use of chi-square test for contingency tables exceeding 2x2 (9-11). Pearsson regression and Anova regression were used. All analyses used SPSS software (version 28). The statistical analyses used two-tailed tests, with p < 0.05 considered significant. PLS models, which relate two data matrices (X and Y) to each other, used Simca software (version 17) are used for explanatory and predictive caries models as described (9-11). The PLS models show the ability of the X variables to explain (R2) or predict (Q2) the variation in Y. The predictive ability (Q2) was estimated by cross-validation via PLS modelling in seven repeated blocks that excluded all participants once. Skewed data were log transformed by established norm and auto-scaled to unit variance before PLS models were generated.Results

[0196] Distinct DMBT1 CNV-PRH1, PRH2 caries subtypes GS1-3 with markedly high 5-year caries progression.

[0197] We previously identified PRHL PRH2 genetic susceptibility (GS-P4a) and genetic resistance (GR-P1) caries subtypes of immunodeficiency and lifestyle nature, respectively9'11. Here we show that Db heterozygosity a PRHl represent GS phenotypes (i.e. GS-P4a, -P7 and -P8) with increased 5-year caries progression compared to GR phenotypes (e.g. GR-P1) in the 452 Swedish case-control adolescents (Table 1).

[0198] We previously also associated caries with short size isoforms of DMBT1 in saliva12that may reflect deletions in DMBT1 due to copy number variation (CNV) of SRCR-SID repeats at sites CNV1 and CNV2. We therefore classified the 452 adolescents into five CNV1'5groups with high (CNV2,3), moderate (CNV4) and low (CNV1,5) 5-year caries progression according to CNV deletion patterns as measured by the paralogue ratio test (Figs. 1 and 4, Table 1 to 3). Stratification of the four predominant CNV2'5groups against the GS and GR phenotypes identified GS1 (P4a-CNV23), GS2 (P7- CNV2’4) and GS3 (P8-CNV2'4) with markedly increased 5-year caries progression and CNV1, CNV2 and CNV1 / 2 deletions, respectively, in contrast to GRl(P4a-CNV4’5), GR2 (P7- CNV3,5) and GR3 (P8-CNV5) and GR phenotypes (Fig. 1, Tables 1 to 3). The GS1-3 subtypes contributed to 30 % of the most severe 5-year incremental caries cases (Table 4, Fig. 5).

[0199] Inflammatory or immunodeficiency nature of the GS1-3 caries subtypes. We next explored the GS1-3 caries subtypes for caries PLS prediction models and penetrance of 5-year caries progression based on salivary DMBT1 and PRP, short chain fatty acid (SCFA), inflammation and bacteria biomarkers and lifestyle variables (Figs 2 and 3, Tables 1 and 2). The blocks of salivary biomarkers and lifestyle variables predicted 5-year caries progression strongly in the GS1 (R2= 0 84, Q2= 0 25), GS2 (R2= 0 53, Q2= -0- 1), and GS3 (R2= 0 98, Q2= 0-76) phenotypes (Fig 2, Table 6 and 7). All salivary and inflammatory biomarkers predicted 5-year caries progression near-linearly in GS1 and markedly better than baseline caries symptoms (Fig 2), the gold standard in caries prediction. While the block of SCFA's were comparably weak predictors in GS1, distinctly different sets of SCFA's coincided inversely with 5-year caries progression in GS2 and GR2 (Fig 2, Table 5), emphasizing the distinct genetic influence in each GS1-3 and GR phenotype on blocks of inflammatorymarkers. The traditional GR-P1 caries type, on the other hand, had a comparably weak caries prediction model (R2= 0-36, Q2= 0 006) with the two best predictors - baseline caries symptoms and all biomarkers - predicting 5-year caries progression poorly (Fig. 2).

[0200] Moreover, the GS1 and GS3 phenotypes were more sensitive to high biofilm mass and infrequent tooth brushing than GR phenotypes in terms of 5-year caries progression (Table 2). Salivary bacteria and adhesion of S. mutans and commensal Actinomyces to parotid saliva on artificial tooth surfaces influenced caries progression differently in the GS1-3 and GR phenotypes (Fig. 2).

[0201] Each GS1-3 phenotype shows distinct salivary protein, SCFA and inflammatory biomarkers. The concentration or ratio of influential salivary biomarkers either promoted or inhibited caries progression strongly and differently in each GS1-3 group (Fig. 3, Table 2 and 7). Penetrance of 5-year caries progression in GS1 negatively correlated with the ratio of small to large acidic PRPs and concentration of 2-hydroxybutyric acid and inflammatory biomarker SIRT2 and positively with concentration of DMBT1 (Fig. 3). Penetrance of caries in GS2 negatively correlated with the ratio of small to large acidic PRPs and concentration of DMBT1, lactic acid, butyric acid and inflammatory biomarker GDNF (Fig.3). Moreover, each GS1-3 subgroup differed in SCFA and inflammatory biomarker profiles in caries progression and from GR1 and GR-P1 caries types having baseline caries symptoms as the strongest predictor (Figs. 2 and 3).

[0202] Long salivary DMBT1 isoforms are caries-protective in GR phenotypes while each GS1-3 type shows a unique SRCR-SID deletion pattern. We next measured single (III > II > Iab) and double band (IVb > IVa) isoforms of DMBT1 by Western blot analyses of parotid salivas in the 452adolescents (Table 9). In GR and GR-P1 phenotypes, long DMBT1 isoform III coincided with low caries progression, even in case of S. mutans or plaque-accumulating (i.e. orthodontic treatment) risk factors, and shorter DMBT1 isoforms I and II with increased caries progression (Table 9). By contrast, in each GS1-3 type was only one adolescent with long isoform III and a unique DMBT1 isoform pattern, in consistency with their CNV deletion patterns. Moreover, CNV or size isoform variation per se failed to correlate with caries progression and CNV explained isoform size marginally (Table 8); and in each isoform group lab, II or III, adolescents with markedly high caries progression coincided with S. mutans-miQciAon and high copy numbers. Together, these findings and role of salivary factorsin penetrance of GS1-3 caries, suggests that the GS and GR phenotypes represents complex DNA mechanisms formed by co-evolution of DMBT1 CNV-PRH1, PRH2 and the S. mutans and oral commensal microbiota populations since origin of agriculture and caries13'15FURTHER EMBODIMENTS

[0203] 1. A genetic origin fingerprint (stratification at the genetic level) for predisposition to dental caries, the fingerprint comprising a copy number variation pattern at CNV1 and CNV2 of the DMBT1 gene, wherein said copy number variation pattern is characterized by a diploid copy number at CNV1 and a diploid copy number at CNV2 assigned to one of the following CNV groups: CNV group 1: CNV1 = 0 and CNV2 < 4; CNV group 2: CNV1 = 1 and CNV2 < 4; CNV group 3: CNV1 = 1 and CNV2 > 4; CNV group 4: CNV1 > 2 and CNV2 < 4; CNV group 5: CNV1 > 2 and CNV2 > 4; wherein group 1 and 5 are indicative of low incidence of dental caries; group 2 is indicative of moderate incidence of dental caries; and group 3 and 4 are indicative to high incidence of dental caries.

[0204] 2. A phenotype origin fingerprint for predisposition to dental caries, the phenotype fingerprint being an allelic phenotype of acidic proline-rich proteins (PRPs) encoded by PRH1 and PRH2, wherein said allelic phenotype is selected from any one of the following PRP groups: P4a: heterozygous at PRH1 (Db-PIF) combined with PRP1 homozygous at PRH2 (PRP1-PRP1) [Db, PIF, PRP1, PRP1]; P7: heterozygous atPRHl (Db-Pa) combined with heterozygous atPRH2 (PRP1-PRP2) [Db-Pa-PRP1-PRP2]; P8: heterozygous atPRHl (Db-PIF) combined with heterozygous at PRH2 (PRP-l-PRP-2) [Db-PIF-PRP1-PRP2];

[0205] P6: heterozygous at PRH1 (Pa, PIF) combined with heterozygous at PRH2 (PRP1, PRP2) [Pa, PIF, PRP1, PRP2]; P1: homozygous at PRH1 (PIF, PIF) combined with homozygous at PRH2 (PRP1-PRP1) [PIF, PIF, PRP1, PRP1]; P4b: homozygous at PRH1 (Db, Db) combined with homozygous at PRH2 (PRP1-PRP1) [Db, Db, PRP1, PRP1]; P5: homozygous at PRH1 (PIF, PIF) combined with heterozygous at PRH2 (PRP1, PRP2) [PIF, PIF, PRP1, PRP2];

[0206] P10: homozygous at PRH1 (Pa, Pa) combined with homozygous at PRH2 (PRP2-PRP2) [Pa, Pa, PRP2-PRP2]; wherein groups P4a, P8 and P7 are attributed to immunodeficiency and high incidence of dental caries; groups P5 and P6 are attributed to low to moderate incidence of dental caries; and groups P1, P4b, P1, P10 attributed to lifestyle and low incidence of dental caries.

[0207] 3. The phenotype origin fingerprint according to claim 2, wherein the allelic phenotype is selected from any one of the following PRP groups:

[0208] P4a: heterozygous at PRH1 (Db-PIF) combined with homozygous at PRH2 (PRP1-PRP1) [Db, PIF, PRP1, PRP1]; P7: heterozygous at PRH1 (Db-Pa) combined with heterozygous at PRH2 (PRP1-PRP2) [Db-Pa-PRP1-PRP2]; P8: heterozygous atPRHl (Db-PIF) combinedwith heterozygous at PRH2 (PRP-l-PRP-2) [Db-PIF-PRP1-PRP2]; P6: heterozygous at PRH1 (Pa, PIF) combined with heterozygous at PRH2 (PRP1, PRP2) [Pa, PIF, PRP1, PRP2];

[0209] P1: homozygous at PRH1 (PIF, PIF) combined with homozygous at PRH2 (PRP1-PRP1) [PIF, PIF, PRP1, PRP1]; wherein groups P4a, P8 and P7 are attributed to immunodeficiency and high incidence of dental caries; group P6 is attributed to low to moderate incidence of dental caries; and group Pl attributed to lifestyle and low incidence of dental caries.

[0210] 4. A phenotype origin fingerprint according to claim 2, wherein the allelic phenotype of acidic proline-rich proteins (PRPs) encoded by PRH1 and PRH2, wherein said allelic phenotype is selected from any one of the following PRP groups: P4a: heterozygous at PRH1 (Db-PIF) combined with homozygous at PRH2 (PRP 1 -PRP 1) [Db, PIF, PRP1, PRP1]; P7: heterozygous at PRH1 (Db-Pa) combined with heterozygous at PRH2 (PRP1-PRP2) [Db-Pa-PRP1-PRP2]; P8: heterozygous at PRH1 (Db-PIF) combined with heterozygous at PRH2 (PRP-l-PRP-2) [Db-PIF-PRP1-PRP2]; wherein groups P4a, P8 and P7 are attributed to immunodeficiency and preferably high incidence of dental caries that is independent of Streptococcus mutans infection status.

[0211] 5. A fingerprint from genetic and phenotype origin according to claim 1, and 2 for predisposition to dental caries, the fingerprint comprising the following CNV stratified RPR groups, CNV-PRP groups: CNV-PRP group 1: [P4a-CNV group 2], CNV-PRP group 2: [P4a-CNV group 3], CNV-PRP group 3: [P4a-CNV group 2-CNV group 3], CNV-PRP group 4: [P4a-CNV group 4-CNV group 5], CNV-PRP group 5: [P7-CNV group 2], CNV-PRP group 6: [P7-CNV group 4], CNV-PRP group 7: [P7-CNV group 2-CNV group 4], CNV-PRP group 8: [P7-CNV group 3-CNV group 5], CNV-PRP group 9: [P8-CNV group 2], CNV-PRP group 10: [P8-CNV group 3], CNV-PRP group 11: [P8-CNV group 4], CNV-PRP group 12: [P8-CNV group 2-CNV group- 3 - CNV group 4], CNV-PRP group 13: [P8-CNV group 5], CNV-PRP group 14: [P4b- CNV groups 1-5], CNV-PRP group 15: [Pl- CNV groups 1-5], CNV-PRP group 16: [P5- CNV groups 1-5], CNV-PRP group 17: [P6- CNV groups 1-5], CNV-PRP group 18: [PIO- CNV groups 1-5],

[0212] 6. A fingerprint from genetic and phenotype origin according to claim 1, and 4 for predisposition to dental caries, the fingerprint comprising the following CNV stratified RPR groups, CNV-PRP groups: CNV-PRP group 1: [P4a-CNV group 2], CNV-PRP group 2: [P4a-CNV group 3], CNV-PRP group 3: [P4a-CNV group 2-CNV group 3], CNV-PRP group 4: [P4a-CNV group 4-CNV group 5], CNV-PRP group 5: [P7-CNV group 2], CNV-PRP group6: [P7-CNV group 4], CNV-PRP group 7: [P7-CNV group 2-CNV group 4], CNV-PRP group 8: [P7-CNV group 3-CNV group 5], CNV-PRP group 9: [P8-CNV group 2], CNV-PRP group 10: [P8-CNV group 3], CNV-PRP group 11: [P8-CNV group 4], CNV-PRP group 12: [P8-CNV group 2-CNV group- 3 - CNV group 4], CNV-PRP group 13: [P8-CNV group 5],

[0213] 7. A fingerprint from genetic and phenotype origin for predisposition to dental caries, by the provision of the following two groups / entities: a genetically susceptible dental caries (GS) group and a genetically resistant dental caries (GR) group, the genetic fingerprint comprising:

[0214] (i) a copy number variation pattern at CNV1 and CNV2 of the DMBT1 gene assigned to a CNV group as defined in claim 1; and

[0215] (ii) an allelic phenotype of acid PRPs encoded by PRH1 and PRH2 assigned to a PRP group as defined in any one of claim 2 to 4;

[0216] wherein the fingerprint is a GS fingerprint when the combination of CNV group and PRP group is any one of GS or GR groups:

[0217] GS1: P4a combined with CNV group 2 or CNV group 3; GS2: P7 combined with CNV group 2 or CNV group 4; GS3: P8 combined with CNV groups 2, 3 and 4;

[0218] and wherein the genetic fingerprint is a GR fingerprint when the combination is:

[0219] GR1: P4a combined with CNV group 4 or CNV group 5; GR2: P7 combined with CNV group 3 or CNV group 5; GR3: P8 combined with CNV group 5; GR-P4b: P4b combined with CNV groups 1-5; GR-P1: P1 combined with CNV groups 1-5; GR-P5: P5 combined with CNV groups 1-5; GR-P6: P6 combined with CNV groups 1-5; and GR-P10: P10 combined with CNV groups 1-5.

[0220] 8. A fingerprint as defined by any one of claims 1 to 7 showing penetrance such as linear penetrance, as to biomarkers such as proteins, salivary short-chain fatty acids (SCFAs), inflammatory biomarkers in parotid saliva, and biofilm.

[0221] 9. A method for assessing the susceptibility (predisposition) of a person for the development of dental caries, the method comprising:a) providing a biological sample obtained from the person; b) from the biological sample extracting one or more fingerprints as defined by any one of claims 1 to 7; and c) attributing the person to any one of the CNV groups; PRP groups, CNV-PRP group and GS, GR groups.

[0222] 10. A method for assessing the susceptibility (predisposition) of a person for the development of dental caries, the method comprising:

[0223] a) providing a biological sample obtained from the person; b) from the biological sample extracting the genetic origin fingerprint of claim 1; and c) attributing the person to one of the CNV groups.

[0224] 11. A method for assessing the susceptibility (predisposition) of a person for the development of dental caries, the method comprising: a) providing a biological sample obtained from the person; b) from the biological sample extracting the phenotype origin fingerprint of any one of claims 2 to 4; and c) attributing the person to one of the PRP groups.

[0225] 12. A method for assessing the susceptibility (predisposition) of a person for the development of dental caries, the method comprising: a) providing a biological sample obtained from the person; b) from the biological sample extracting the fingerprint from genetic and phenotype origin of claim 5 or 6; and c) attributing the person to one of the CNV-PRP groups; or GS or GR groups.

[0226] 13. The method according to claim 10, further comprising from the sample extracting information on allelic phenotypes of acid PRPs; attributing the allelic phenotypes of acid PRPs from the person to one of several allelic phenotype acid PRP groups (PRP groups); stratifying the PRP group by the CNV groups; and assigning the person to a CNV stratified PRP group.

[0227] 14. The method according to claim 10, wherein the PRP groups are one or more of the following: P4a (Db, PIF, PRP-1, PRP-1), P6 (Pa, PIF, PRP-1I, PRP-2), Pl (PIF, PIF, PRP-1, PRP-1), P8 (Db-PIF -PRP-1 -PRP-2), and P7 (Db-Pa-PRP-1 -PRP-2), wherein groups P4a, P8 and P7 are attributed to immunodeficiency and high incidence of dental caries; group P6 is attributed to low to moderate incidence of dental caries; and group Pl attributed to lifestyle and low incidence of dental caries.

[0228] 15. The method according to claim 13 or 14, further comprising assigning the person to a genetically susceptible (GS) caries subtype based on the stratification of PRH1, PRH2 allelic phenotype (PRP groups) with DMBT1 CNV group(s) and, thereby providing the GSsubtypes: GS1: P4a and CNV groups 2 and 3; GS2: P7 and CNV groups 2 and 4; and GS3: P8 and CNV groups 2, 3 and 4.

[0229] 16. The method according to claim 15, further comprising assigning the person to a genetically resistant (GR) caries subtype based on the stratification of PRH1, PRH2 allelic phenotype (PRP groups) with DMBT1 CNV group(s) and, thereby providing the GR subtypes: GR1: P4a and CNV groups 4 and 5; GR2: P7 and CNV groups 3 and 5;

[0230] GR3: P8 and CNV group 5; GR-P4b: P4b combined with CNV groups 1-5; GR-P1: P1 combined with CNV groups 1-5; GR-P5: P5 combined with CNV groups 1-5; GR-P6: P6 combined with CNV groups 1-5; and GR-P10: P10 combined with CNV groups 1-5.

[0231] 17. The method according to claim 15 or 16, further from a saliva sample obtained from the person extracting information selected from the group of salivary proteins, salivary shortchain fatty acids (SCFAs) and inflammatory markers.

[0232] 18. The method according to any one of claims 15 to 17, wherein further from a saliva sample obtained from the person extracting information selected from salivary short-chain fatty acids (SCFAs), preferably from butyric acid, lactic acid and 2-hydroxybutyric acid.

[0233] 19. The method according to claim 18, wherein the salivary short-chain fatty acids (SCFAs), selected from: butyric acid, lactic acid and 2-hydroxybutyric acid show near-linear penetrance of 5-year caries progression in persons assigned to a GS subtype.

[0234] 20. A method for assessing the susceptibility of a person for the development of dental caries, the method comprising:

[0235] a) providing a biological sample obtained from the person;

[0236] b) extracting from the sample information on CNV1 and CNV2 copy number variation patterns of DMBT1 and on allelic phenotypes of acid PRPs and optionally genotypes corresponding to the allelic acid PRPs;

[0237] c) assigning the allelic phenotype is selected from any one of the following PRP groups: P4a: heterozygous at PRH1 (Db-PIF) combined with homozygous at PRH2 (PRP1-PRP1) [Db, PIF, PRP1, PRP1]; P7: heterozygous at PRH1 (Db-Pa) combined with heterozygous at PRH2 (PRP1-PRP2) [Db-Pa-PRP1-PRP2]; P8: heterozygous atPRHl (Db-PIF) combined with heterozygous atPRH2 (PRP-l-PRP-2) [Db-PIF-PRP1-PRP2]; P6: heterozygous atPRHl (Pa, PIF) combined with heterozygous at PRH2 (PRP1, PRP2) [Pa, PIF, PRP1, PRP2]; Pl: homozygous at PRH1 (PIF, PIF) combined with homozygous at PRH2 (PRP1-PRP1) [PIF,PIF, PRP1, PRP1]; P4b: homozygous at PRH1 (Db, Db) combined with homozygous at PRH2 (PRP1-PRP1) [Db, Db, PRP1, PRP1]; P5: homozygous atPRHl (PIF, PIF) combined with heterozygous at PRH2 (PRP1, PRP2) [PIF, PIF, PRP1, PRP2]; P10: homozygous at PRH1 (Pa, Pa) combined with homozygous at PRH2 (PRP2-PRP2) [Pa, Pa, PRP2-PRP2]; wherein groups P4a, P8 and P7 are attributed to immunodeficiency and high incidence of dental caries; groups P5 and P6 are attributed to low to moderate incidence of dental caries; and groups P1, P4b, P1, P10 attributed to lifestyle and low incidence of dental caries. d) assigning the CNV1 and CNV2 deletion patterns to one of the following CNV groups: CNV group 1: CNV1 = 0 and CNV2 < 4; CNV group 2: CNV1 = 1 and CNV2 < 4; CNV group 3: CNV1 = 1 and CNV2 > 4; CNV group 4: CNV1 = 2 and CNV2 < 4; CNV group 5: CNV1 = 2 and CNV2 > 4; where

[0238] group 1 and 5 are attributed (assigned to) a low incidence / susceptibility of dental caries, group 2 is attributed (assigned to) a moderate incidence of dental caries, group 3 and 4 are attributed (assigned to) a high incidence of dental caries;

[0239] e) stratifying at least a PRP group with the CNV groups thereby obtaining CNV stratified PRP groups;

[0240] d) assigning the person to the CNV stratified PRP group selected from any one of:

[0241] i) genetically susceptible (GS) caries subtypes:

[0242] GS1: P4a and CNV groups 2 and 3; GS2: P7 and CNV groups 2 and 4; and GS3: P8 and CNV groups 2, 3 and 4; genetically resistant (GR) caries subtypes: GR1: P4a and CNV groups 4 and 5; GR2: P7 and CNV groups 3 and 5; GR3: P8 and CNV group 5; GR-P4b: P4b combined with CNV groups 1-5; GR-P1: P1 combined with CNV groups 1-5; GR-P5: P5 combined with CNV groups 1-5; GR-P6: P6 combined with CNV groups 1-5; and GR-P10: P10 combined with CNV groups 1-5.

[0243] 21. The method according to claim 20, wherein CNV stratified PRP groups GS1, GS2, GS3 show linear penetrance as to salivary biomarkers.

[0244] 22. The method according to claim 21, wherein salivary biomarkers are selected from any one of: ratio PRP3 / 1, DMBT1 amount, short chain fatty acids, and plaque mass.

[0245] 23. The method according to any one of the preceding claims, wherein the biological sample is selected from any one of: tissue and tissue fluids such as blood, saliva, faces, skin, and any tissue with human cells with a nucleus.24. The method according to any one of the preceding claims, wherein the extraction of information related to DMBT1 (CNV1 and CNV2) is selected from Paralogue Ratio Test (PRT), next generation sequencing (NGS), PCR such as Digital Droplet PCR (ddPCR), Array Comparative Genomic Hybridization (aCGH), Multiplex Ligation-dependent Probe Amplification (MLPA), and SNP genotyping arrays.; and for allelic phenotype of PRPs is selected from Native alkaline polyacrylamide gel electrophoresis (PAGE), High-Performance Liquid Chromatography (HPLC), Mass Spectrometry (MS) - proteomics, Immunoassay — Western blot / ELISA, TaqMan SNP genotyping, Illumina SNP array.

[0246] 25. A method for assessing the susceptibility of a person for the development of dental caries, having established the following stratifications on the genetic level and the phenotype level:

[0247] i) Stratification at the genetic level based on copy number variation pattern at CNV1 and CNV2 of the DMBT1 gene, wherein said copy number variation pattern is characterized by a diploid copy number at CNV1 and a diploid copy number at CNV2 assigned to one of the following CNV groups:

[0248] • CNV group 1: CNV1 = 0 and CNV2 < 4

[0249] • CNV group 2: CNV1 = 1 and CNV2 < 4

[0250] • CNV group 3: CNV1 = 1 and CNV2 > 4

[0251] • CNV group 4: CNV1 > 2 and CNV2 < 4

[0252] • CNV group 5: CNV1 > 2 and CNV2 > 4

[0253] wherein group 1 and 5 are indicative of low incidence of dental caries; group 2 is indicative of moderate incidence of dental caries; and group 3 and 4 are indicative to high incidence of dental caries;

[0254] ii) Stratification at the phenotype level based on an allelic phenotype of acidic proline-rich proteins (PRPs) encoded by PRH1 and PRH2, selected from any one of the following PRP groups:

[0255] • P4a: Db heterozygous at PRH1 (Db-PIF) combined with PRP1 homozygous at PRH2 (PRP 1 -PRP 1) [Db, PIF, PRP1, PRP1];

[0256] • P7: Db heterozygous at PRH1 (Db-Pa) combined with PRP1 / PRP2 heterozygous atPRH2 (PRP1-PRP2) [Db-Pa-PRP1-PRP2];

[0257] • P8: Db heterozygous at PRH1 (Db-PIF) combined with PRP1 / PRP2 heterozygous atPRH2 (PRP-l-PRP-2) [Db-PIF-PRP1-PRP2];• P4b: homozygous at PRH1 (Db, Db) combined with homozygous at PRH2 (PRP1-PRP1) [Db, Db, PRP1, PRP1];

[0258] • P1: homozygous at PRH1 (PIF, PIF) combined with homozygous at PRH2 (PRP1-PRP1) [PIF, PIF, PRP1, PRP1];

[0259] • P5: homozygous at PRH1 (PIF, PIF) combined with heterozygous at PRH2 (PRP1, PRP2) [PIF, PIF, PRP1, PRP2];

[0260] • P6: heterozygous at PRH1 (Pa, PIF) combined with heterozygous at PRH2 (PRP1, PRP2) [Pa, PIF, PRP1, PRP2];

[0261] • P10: homozygous at PRH1 (Pa, Pa) combined with homozygous at PRH2 (PRP2-PRP2) [Pa, Pa, PRP2-PRP2];

[0262] iii) Combining the stratification based on at CNV1 and CNV2 of the DMBT1 gene and the phenotype level based on an allelic phenotype of acidic proline-rich proteins (PRPs) encoded by PRH1 and PRH2, thereby forming the following genetically susceptible dental caries groups:

[0263] • GS1: P4a combined with CNV group 2 or CNV group 3;

[0264] • GS2: P7 combined with CNV group 2 or CNV group 4;

[0265] • GS3: P8 combined with CNV groups 2, 3 or 4;

[0266] • GR1: P4a combined with CNV groups 4 and 5;

[0267] • GR2: P7 combined with CNV groups 3 and 5;

[0268] • GR3: P8 combined with CNV group 5;

[0269] • GR-P4b: P4b combined with CNV groups 1 to 5;

[0270] • GR-P1: Pl combined with CNV groups 1 to 5;

[0271] • GR-P5: P5 combined with CNV groups 1 to 5;

[0272] • GR-P6: P6 combined with CNV groups 1 to 5;

[0273] • GR-P10: PIO combined with CNV groups 1 to 5;

[0274] the method comprising;

[0275] a) providing a biological sample obtained from the person;

[0276] b) extracting from the sample of said person information on CNV1 and CNV2 copy number variation patterns of DMBT1 and on allelic phenotypes of acid PRPs and optionally genotypes corresponding to the allelic acid PRPs; andc) assigning the person to one group selected from GS1, GS2, GS3, GR1, GR2, GR3,, GR-P4b, GR-P1, GR-P5, GR-P6, GR-P10.

[0277] 26. The method for assessing the susceptibility of a person for the development of dental caries, wherein the stratification at the phenotype level based on an allelic phenotype of acidic proline-rich proteins (PRPs) encoded by PRH1 and PRH2 is selected from any one of the following PRP groups:

[0278] • P4a: Db heterozygous at PRH1 (Db-PIF) combined with PRP1 homozygous at PRH2 (PRP 1 -PRP 1) [Db, PIF, PRP1, PRP1];

[0279] • P7: Db heterozygous at PRH1 (Db-Pa) combined with PRP1 / PRP2 heterozygous atPRH2 (PRP1-PRP2) [Db-Pa-PRP1-PRP2];

[0280] • P8: Db heterozygous at PRH1 (Db-PIF) combined with PRP1 / PRP2 heterozygous atPRH2 (PRP-l-PRP-2) [Db-PIF-PRP1-PRP2]; and

[0281] combining the stratification based on at CNV1 and CNV2 of the DMBT1 gene and the phenotype level based on an allelic phenotype of acidic proline-rich proteins (PRPs) encoded by PRH1 and PRH2, thereby forming the following genetically susceptible dental caries groups:

[0282] • GS1: P4a combined with CNV group 2 or CNV group 3;

[0283] • GS2: P7 combined with CNV group 2 or CNV group 4;

[0284] • GS3: P8 combined with CNV groups 2, 3 or 4; and

[0285] assigning the person to one group selected from GS1, GS2, GS3.

[0286] 27. An analytical kit for determining the predisposition of a person developing dental caries, comprising: means for extracting fingerprint information defined by any one of claims 1 to 8 and attributing the person to any one of the groups defined in any one of claims 1 to 8.

[0287] 28. The analytical kit according to claim 27, therein the means for genetic fingerprints are selected from Paralogue Ratio Test (PRT), generation sequencing (NGS), PCR such as Digital Droplet PCR (ddPCR), Array Comparative Genomic Hybridization (aCGH), Multiplex Ligation-dependent Probe Amplification (MLPA), SNP genotyping arrays, means for phenotype fingerprints are selected from Native alkaline polyacrylamide gel electrophoresis (PAGE), High-Performance Liquid Chromatography (HPLC), Mass Spectrometry (MS) -proteomics, Immunoassay - Western blot / ELISA, TaqMan SNP genotyping, Illumina SNP array; and means for protein concentration are selected from Slot-blot immunoassay, ELISA, and Proximity Extension Assay (PEA, Olink).CONTENT OF TABLES

[0288] Table 1. Caries progression in DM TL PRH L PRH2 genetically susceptible (GS) and genetically resistant (GR) phenotypes.

[0289] Table 2. Summery of genetically (GS) and genetically resistant (GR) caries types. Table 3. Stratification of CNV groups2'5against PRH1, PRH2 phenotypes.

[0290] Table 4. Proportion (%) of GS1-3 across caries progression severity levels.

[0291] Table 5. Association of SCFAs on 5-year caries increment in GS and GR caries. Table 6. GS and GR caries prediction models.

[0292] Table 7. VIP values from PLS models against 5-year caries progression.

[0293] Table 8. Quantitative number of DNA or protein repeats do not correlate with caries progression in GS and GR caries types.

[0294] Table 9. DMBT1 isoforms related to caries progression GS and GR groups.Table 1. Caries progression in DMBT1, PRH1, PRH2 genetically susceptible (GS) and genetically resistant (GR) phenotypes

[0295] Genetic characteristics3Caries scoresb

[0296] PRH1, PRH2 DMBT1 DeFS-12y DeFS-17y ADeFS-5y eno Designation Type PRH1 PRH2 CNV. „.., n % Mean ± SD p n Mean ± SD p Mean ± SD p type •1. Influential

[0297] S'1’1- CNV site

[0298] GS GS1-3 46 10 3 -4 ± 3 -5 0 127 40 ll -9 ± 8-9 <0 001 8-2 ± 7-8 <0 001 GR non-GSl-3 405 90 2-5 ± 2-6 Ref. 349 6-3 ± 7-2 Ref. 3 -8 ± 5-7 Ref. GS-P4a P4a-CNV1’5P4a Db-PIF PRP1-PRP1 1-5 84 19 3 -2 ± 3 -3 0-030 71 8- l ± 8-3 0-031 4-7 ± 6-6 0-292 GS1 P4a-CNV2-3P4a Db-PIF PRP1-PRP1 2, 3 1 27 6 3 -7 ± 4- l 0- 110 22 12-2 ± 10-5 0-001 8-3 ± 8-6 0-001 GR1 P4a-CNV4-5P4a Db-PIF PRP1-PRP1 4, 5 - 57 13 3 -0 ± 2-8 0-073 49 6-2 ± 6-4 0-449 3 -2 ± 4-9 0-518 GS-P7 P7-CNV1’5P7 Db-Pa PRP1-PRP2 1-5 33 7 2-6 ± 2-8 0-661 28 7-9 ± 6-7 0-037 4-8 ± 4-5 0-038 GS2 P7-CNV2-4P7 Db-Pa PRP1-PRP2 2, 4 2 13 3 2-7 ± 2-0 0-298 12 9-9 ± 5-7 0-002 6-7 ± 5-0 0-008 GR2 P7-CNV3-5P7 Db-Pa PRP1-PRP2 3, 5 - 19 4 2-0 ± 2-6 0-532 15 4-5 ± 3.7 0-883 2-6 ± 1.9 0-802 GS-P8 P8-CNV1’5P8 Db-PIF PRP1-PRP2 1-5 11 2 2-7 ± 3 -5 0-957 11 9- 1 ± 8-7 0- 102 6-4 ± 8-5 0- 131 GS3 P7-CNV2-4P8 Db-PIF PRP1-PRP2 2, 3, 4 1, 2 6 1 3 -8 ± 4-2 0-388 6 13 -8 ± 9- 1 0-004 10-3 ± 10-0 0-005 GR3 P7-CNV5P8 Db-PIF PRP1-PRP2 5 - 5 1 1-4 ± 2.2 0-385 5 3-4 ± 3 -5 0-503 1 -7 ± 1 -8 0-446

[0299] PTF- GR-P1 Pl-CNV1’5Pl PRP1-PRP1 1-5 - 143 32 2-2 ± 2-3 Ref. 118 5-7 ± 6-5 Ref. 3 -6 ± 5 1 Ref.

[0300] PIF

[0301] aPRHl, PRH2 alleles; diploid DMBT1 copy number of SRCR-SID repeats at CNV1, CNV2 (range 7-14) influential on 5-year caries progression:

[0302] low numbers (1, <4) marks influential deletions; - marks that CNV at the site are non-influential.

[0303] bCaries DeFS scores at 12 and 17 years of age and ADeFS-5y incremental increase over 5 years.Table 2. Summary of genetically susceptible (GS) and genetically resistant (GR) caries types

[0304] Caries subtypes3

[0305] Variables'3Susceptible types Resistant types GS1 GS2 GS3 GR-P1 Prevalence, n(%) 27 (6) 13 (3) 6 (1) 143 (32) Caries DeFS score High High High Low Baseline DeFSc3-7 2-3 3-8 2-2 5-yearADeFSd8-3 6-7 10-3 3-6 R2, Q2(PLS)e0-84, 0-25 0-53, -0 1 0-98, 0-76 0-36, 0 006 Dependence onf

[0306] Salivary proteins

[0307] PRP3 / 1Ccleavage ratio -0-692 (0-013) -0-821 (0-023) NA -0-58 (0-670) DMBT1 (cone.) 0-510 (0-090) -0-679 (0 094) NA 0 050 (0-711) Salivary SCFAs

[0308] Butyrate n.i. -0-797 (0-002) n.i. n.i. Lactate 0-374 (0.087) -0-741 (0-006) -0-943 (0-005) n.i. 2-Hydroxybutyrate -0-428 (0-047) -0-559 (0-059) -0-886 (0-019) n.i. Inflammatory markers

[0309] SIRT2 -0-72 (<0-001) n.i. n.i. n.i. GDNF n.i. -0-88 (0-004) n.i. n.i. SCF -0-55 (0-012) n.i. 0-83 (0-042) n.i. Biofilm, lifestyle

[0310] Plaque (PLI) amount® 0-466 (0-033) 0-374 (0-287) 0-257 (0-623) 0-196 (0-038) Toothbrushing frequency® -0-557 (0-007) -0-028 (0-931) -0-926 (0-008)11-0-165 (0-075)aGS and GRcaries types based on DMBT1, PRH1, PRH2 variation.

[0311] bn.i. = non-influential on caries. NA = not analyzed.

[0312] cCaries DeFS (Decayed, enamel included, Filled Surfaces) score at 12 years old.

[0313] d5-year prospective caries sADeFS-5y increment from 12 to 17 years old.

[0314] ePartial least squares (PLS) regression of biomarker blocks against caries ADeFS-5y progression;

[0315] blocks = salivary protein, SCFA, Inflammatory, biofilm and lifestyle biomarkers.

[0316] R2= explained variance, Q2= predictive accuracy.

[0317] fSpearman’s rank correlation against 5-year caries ADeFS-5y progression,

[0318] r (p): r = correlation coefficient, p = significance level.

[0319] 8PLI= Plaque load index = percentage of tooth surfaces with visible plaque at 17 years old.

[0320] Toothbrushing frequency was coded as: l=irregular; 2=once per day; 3=twice per day; 4=more than twice per day.

[0321] 11Significant for DeFS at 17 years old (p < 005), but borderline significance for ADeFS-5y.Table 3. Stratification of the predominant DMBT1 copy number variation (CNV) deletion groups 2-5 against PRH1, PRH2 caries phenotypes to generate the GS1-3 caries types in 452 adolescents

[0322] Genetic characteristics Caries measures’11Genetic DMBT1ADeFS-12y DeFS-17 ADeFS-5y group PRHI-PRH2' Grp CNV1 CNV2 n Mean± SD p n Mean± SD p Mean± SD p Total 1 0 < 4 9 1-6 + 1-9 0-268 8 4-414 0 0-599 2-913-1 0-861

[0323] 2 1 < 4 44 2-5 ± 2-4 0-942 39 7-7 ± 8-4 0-344 5-3 + 8 3 0-298 3 1 > 4 64 2-8 ± 3-5 0-762 57 8-9 + 10-7 0 084 6-118-6 0 008 4 >2 < 4 108 2-6 ± 2-5 0-905 92 7-116-6 0 083 4-4 ± 4-7 0 013

[0324]

[0325] 5 >2 > 4 224 2-6 ± 2-7 Ref. 192 6-116-7 Ref. 3-5 ± 5-2 Ref. GS-P4a Db-PIF-PRPl-PRPl 84 3-2 ± 3-3 0-030 71 8-118-3 0 031 4-7 + 6 6 0-292

[0326] 1 0 < 4 2 2-5 + 2- 1 0-676 2 6 018-5 0-835 3-917 0 0-972 2 1 < 4 10 2-3 + 1-8 0-280 8 10-4 ± 12-8 0-797 8-7 + 13-2 0-395 3 1 > 4 17 4-5 + 4 8 0-839 14 13-2 + 9-3 0 010 8-015 0 0 002 4 >2 < 4 15 1-5 + 1-7 0-015 13 3-812 0 0-310 2-2 + 1-8 0-766 5 >2 > 4 40 3-613 0 Ref. 34 7-117-3 Ref. 3-5 ± 5-6 Ref. GS1 2+3 27 3-7 + 4- 1 0-718 22 12-2 + 10-5 0 008 8-3 + 8 6 0 002 GR1 4+5 55 3-012-8 Ref. 47 6-2 ± 6-4 Ref. 3-2 ± 4-8 Ref. GS-P7 Db-Pa-PRP1-PRP2 33 2-5 ± 2-8 0-663 28 7-9 ± 6-7 0 038 4-8 ± 4-5 0 038

[0327] 1 0 < 4 2 0-010 0 0- 157 1 3 0 - 3-8

[0328] 2 1 < 4 4 3-5 + 1 0 0- 160 4 9-8 + 2 9 0 035 5-9 + 2 8 0 078 3 1 > 4 3 3-014-4 0-897 3 4-714 0 1 000 1-6 + 0-8 0-533 4 >2 < 4 9 2-3 ± 2-3 0-674 8 10-8 + 6-7 0 046 7-5 + 6 2 0 126 5 >2 > 4 14 2-112-4 Ref. 11 4-614-0 Ref. 2-812-1 Ref. GS2 2+4 13 2-7 + 2 0 0-348 12 10-4 + 5-6 0 010 7 0 + 5-2 0 022 GR2 3+5 17 2-2 ± 2-7 Ref. 14 4-6 ± 3-8 Ref. 2-5 ± 1-9 Ref. GS-P8 Db-PIF-PRP1-PRP2 11 2-7 ± 3-5 0-957 11 9 118-7 0 103 6-4 + 8 5 0 131

[0329] 1 0 < 4 0 - - 0 - 2 1 < 4 3 7-013-6 0-067 3 13-3 + 6-7 0 035 7-013-9 0 072 3 1 > 4 2 1 0 + 1-4 1-000 2 17-5 + 16-3 0-324 16-7 + 18-8 0 171 4 >2 < 4 1 0 0 - 1 8-0 - 7-6

[0330] 5 >2 > 4 5 1-4 ± 2-2 Ref. 5 3-4 ± 3-5 Ref. 1-7 ± 1-8 Ref. GS3 2+3+4 6 3-8 + 4 2 0-337 6 13-8 + 9 1 0 022 10-3 + 10 0 0 022 GR3 5 5 1-4 ± 2-2 Ref. 5 3-4 ± 3-5 Ref. 1-7 ± 1-8 Ref. GR-P1 PIF-PIF-PRP1-PRP1 143 2-2 ± 2-3 Ref. 118 5-7 ± 6-5 Ref. 3-615-1 Ref.

[0331] 1 0 < 4 3 1-3 + 2-3 0-467 3 2-7 + 2 5 0-539 1 111-3 0-558 2 1 < 4 12 2-3 + 1-8 0-576 10 8-118-9 0-219 5-5 + 8 2 0-300 3 1 > 4 18 1-912-0 0-793 16 4-7 + 4 3 0-970 3-012-9 0-693 4 >2 < 4 34 2-4 ± 2-6 0-780 26 6 116-3 0-367 3-7 + 4 5 0 195 5 >2 > 4 75 2-2 ± 2-3 Ref. 62 5-7 ± 6-8 Ref. 3-5 ± 5-3 Ref. GR-P6 Pa-PIF-PRP1-PRP2 123 2-5 ± 2-5 0-426 112 6-6 + 7 6 0-289 4 015-6 0-476

[0332] 1 0 < 4 1 4 0 - 1 8 0 - 4-8

[0333] 2 1 < 4 6 1-3 + 1-5 0-475 6 3-5 + 5 2 0 148 2-013-5 0-268 3 1 > 4 16 2-2 ± 3-5 0-464 15 8 1 + 14-6 0-542 6 0 + 11-4 0-858 4 >2 < 4 36 3-3 ± 2-5 0 039 32 8-117-6 0-206 4-5 + 4 9 0-357 5 >2 > 4 63 2-2 ± 2-3 Ref. 58 5-7 ± 4-8 Ref. 3-3 ± 3-5 Ref.aCaries DeFS scores at 12 and 17 years of age, and the incremental increase (ADeFS-5y) over 5 years. DeFS: Decayed, enamel included, Filled Surfaces.

[0334] b2-sided p-value from Mann-Whitney U-test compared to the reference (Ref.).

[0335] cPRH1, PRH2 phenotypes based on alleles at PRH1 (PIF, Db, Pa) and PRH2 (PRP1, PRP2).

[0336] dDMBT1 CNV groups (1-5) based on diploid copy numbers at two sites: CNV1 and 2.Table 4. Proportion (%) of GS1-3 across caries progression severity levels

[0337] Canes progressiona3ADeFocSaaT,otxal G, S1xh-3, GRxhGS Oddsn95_ CIap-va,lued

[0338] (n) (n)D(n)Dproportion1- ratio GSa

[0339] Total6390 40 350 1<}%

[0340] No progression = 0 94 4 90

[0341] Progression > 0 296 36 259 12% 3.13 1.1-9.0 0.035

[0342] Progression Severity1:

[0343] > median: > 3 182 32 149 18% 5.37 2.4-12.0 4.11 x 10'5

[0344] >75 percentile: > 6 91 21 69 23% 4.49 2.3-8.8 1.28 x 10'5

[0345] >90 percentile: > 10 39 11 27 4.52 2.0-10.0 2.88 x 104

[0346] >95 percentile: > 15 20 6 14 4.22 1.5-11.7 0.006

[0347] aThe incremental increase (ADeFS-5y) over 5 years. DeFS: Decayed, enamel included, Filled Surfaces.

[0348] bGS = genetically susceptible, GR= genetically resistant caries phenotypes based on DMBT1, PRH1,

[0349] PRH2 variation.

[0350] ‘ Proportion of GS in the total sample (n = 390) and across caries progression severity levels.

[0351] dRisk of caries progression for GS across severity levels, shown as odds ratios with 95% confidence

[0352] intervals and p-values from binary logistic regression.

[0353] ‘ A total of 390 of the 452 adolescents were examined at both 12 and 17 years of age.

[0354] fCut-off values for different caries progression severity levels were defined using the 50th, 75th, 90th, and

[0355]

[0356] 95th percentiles of caries progression (ADeFS), with values rounded up to whole numbers (0 decimals).

[0357] Table 5. Association of salivary short chain fatty acids on 5-year caries increment in GS and GR caries Short chain fatty Genetic-susceptible typesab_ Genetic-resistant typesab_

[0358] acid6dGS1 GS2 GS3 GR1 GR2 GR3 GR-P1 GR-P6 Acetic.... 0-744 (0002)

[0359] Succnic - - - - -... Propionic.... 0-794 (<0-001)

[0360] Butyric - -0-797 (0-002) - - -... Isobutyric.... 0-827 (<0-001)

[0361] 2-Hydroxybutyric -0-428 (0-047) -0-559 (0-059) -0.886 (0 019) - -... 2-Methylbutyric.... 0-638 (0-014)

[0362] Valeric.... 0-737 (0-003)

[0363] Isovaleric.... 0-702 (0-005)

[0364] Isocapronic.... 0-647 (0-012)

[0365] Lactic -0-374 (0-087) -0-741 (0-006) -0-943 (0 005) - -...aGS = genetically susceptible, GR= genetically resistant caries phenotypes based onDMBTl, PRH1, PRH2 variation.

[0366] bindicates non-influential, p > 0 09

[0367] 6Concentrations of short-chain fatty acids (SCFAs) in whole saliva collected at 12 years of age.

[0368] dThe associations between 5-year caries increment and salivary short-chain fatty acid concentrations (pM / pL), evaluated using Spearman’s rank correlation and reported as correlation coefficients (r) with corresponding p-values, r(p).Table 6. GS and GR risk prediction models of 5-year \DeFS caries progression by blocks

[0369] of salivary biomarkers and clinical symptoms. _

[0370] Prediction models (R2, _ Genetically Susceptible3Genetically Resistant3

[0371] Q2)bcGS1 GS2 GS3 GR-P1

[0372] Total model 0-84 (0-25) 0-532 (-0 10) 0-98 (0-76) 0-36 (0-01)

[0373] Saliva protein 0 09 (-0-1)

[0374] I

[0375]

[0376] nflammatory markers 0-49 (-0-1)

[0377] Biofilm 0-42 (0 08) 0-80 (-0-10) 0-96 (0'37) 0 18 (0 12)

[0378] Lifestyle 0-28 (0 19) 0 004 (-0 10) 0-93 (0-80) 0 09 (0 06)

[0379] Baseline caries 0 14 (0 04) 0 03 (-0 1) 0 08 (-0 1) 0 14 (0 12)

[0380] 3GS = genetically susceptible, GR= genetically resistant caries phenotypes based onDMBTl, PRH1, PRH2 variation.

[0381] bSalivary protein, inflammatory, biofilm, and lifestyle biomarkers; baseline caries lesions and total risk model without

[0382] baseline caries symptoms / lesions.

[0383] - Partial least square (PLS) models; R2= explanatory, Q2predictive values

[0384] Table 7. VIP values from PLS modelling of salivary blocks of biomarkers against 5-year caries progression.

[0385] Genetic groupaBlock Variables GS1 GS2 GS3 GR-P1 Nomenclature PRP3 / 1 ratio L96 1-47 0-6 Ratio of PRP3 / PRP1 amounts in parotid saliva Db ratio 2 -64 0 -48 Ratio of small / large Db amounts in parotid saliva PRPl.amount L42 1 15 2-88 Amount of large PRP1 in parotid saliva PRP3.amount 0-68 0-87 0-88 Amount of small PRP3 in parotid saliva Dbs.amount L21 0 -65 Amount of Dbs (large Db) in parotid saliva Dbf.amount 1 11 0-93 Amount of Dbf (small Db) in parotid saliva PRPtot 0-73 0-91 1-73 Total amount of acidic PRPs in parotid saliva •S DMBT1 amount L52 1-63 0 09 Total amount of DMBT1 in parotid saliva £ DMBTl la 0-76 0-45 L84 0 12 Presence of isoform la (+, -) in parotid saliva DMBT1 lb 0 -73 0 0 0 16 Presence of isoform lb (+, -) in parotid saliva DMBTl II 0-67 0-89 0 0-68 Presence of isoform II (+, -) in parotid saliva DMBTl III 0 17 0-84 0-26 1 15 Presence of isoform III (+, -) in parotid saliva DMBTl Iva 0-35 0 0-7 0-92 Presence of isoform IVa (+, -) in parotid saliva DMBTl Ivb 0-81 0 0-66 0-37 Presence of isoform IVb (+, -) in parotid saliva WS 0-61 0-33 1-25 0-49 Whole saliva secretion rate (mL / min) PS 0-87 0-81 0-28 0 14 Parotid saliva secretion rate (mL / min) 2-Hydroxybutyric acid 0-76 1-42 1 18 1 11 short chain fatty acid in whole saliva 2-Methylbutyric acid 0-32 0-81 1-52 0-34 short chain fatty acid in whole saliva Acetic acid 0 18 0-52 1-77 0-35 short chain fatty acid in whole saliva Butyric acid 0-24 1-58 0-88 0-35 short chain fatty acid in whole saliva Formic acid 0 -84 0 -42 0 -97 0 -39 short chain fatty acid in whole saliva g Isobutyric acid 0 15 1 02 1-61 0-2 short chain fatty acid in whole saliva1 / 3Isocaproic acid 0-42 0-47 1-57 0 11 short chain fatty acid in whole saliva Isovaleric acid 0-26 0-87 1-76 0-44 short chain fatty acid in whole saliva Lactic acid 0-72 1-93 1-32 0-55 short chain fatty acid in whole saliva Propionic acid 0-34 1-35 1-77 0-41 short chain fatty acid in whole saliva

[0386]

[0387] Succinic acid 0-21 0-43 0-23 0-31 short chain fatty acid in whole salivaValeric acid 0-44 0-67 0-99 0 17 short chain faty acid in whole saliva 4E-BP1 2 07 1-39 0-71 0-63 Eukaryotic translation initiation factor 4E-binding protein 1 ADA 1-76 0-77 0-2 1-33 Adenosine Deaminase

[0388] ARTN 0-46 0-9 0-57 1-5 Artemin

[0389] AXIN1 1-59 0-64 0-87 0-99 Axin-1

[0390] Beta-NGF 0-42 0-79 0 18 0-73 Beta-nerve growth factor

[0391] CASP-8 0-49 0-92 1-85 0-69 Caspase-8

[0392] CCL11 1-35 1 06 0-31 0-23 Eotaxin

[0393] CCL19 0-62 1 03 1-58 0-67 C-C motif chemokine 19

[0394] CCL20 0 16 0-99 1-25 0-85 C-C motif chemokine 20

[0395] CCL23 1-4 1-33 1-72 0-74 C-C motif chemokine 23

[0396] CCL25 1-55 0-62 0-38 0-37 C-C motif chemokine 25

[0397] CCL28 0-74 1-22 0-41 0 09 C-C motif chemokine 28

[0398] CCL3 0-7 1 01 1-72 0-89 C-C motif chemokine 3

[0399] CCL4 0-63 1-54 1-48 0 13 C-C motif chemokine 4

[0400] CD244 1 01 0-62 0-38 1 Natural killer cell receptor 2B4

[0401] CD40 0-95 1 01 1-38 1 08 CD40L receptor

[0402] CD5 0-52 1 15 0-92 0-65 T-cell surface glyocprotein

[0403] CD6 1 1 0-65 0-28 1-26 T-cell surface glycoprotein CD6 isoform

[0404] CD8A 1-28 0-47 1-68 0 06 T-cell surface glycoprotein CD8 alpha chain CDCP1 0-36 1 08 0-51 0-31 CUB domain-containing protein 1

[0405] CSF-1 0-63 1-33 1-66 0-49 Macrophage colony -stimulating factor 1

[0406] CST5 0-65 0-99 0-36 0-65 Cystatin D

[0407] CX3CL1 1 17 0-91 0-42 0-67 Fractalkine

[0408] CXCL1 0-3 1-27 1-52 0-44 C-X-C motif chemokine 1

[0409] CXCL10 0-41 0-94 0 07 1 08 C-X-C motif chemokine 10

[0410] CXCL11 0-35 0-89 0-31 1 22 C-X-C motif chemokine 11

[0411] CXCL5 0-7 0-9 1-48 0-55 C-X-C motif chemokine 5

[0412] CXCL6 0-56 1 04 1-81 0-68 C-X-C motif chemokine 6

[0413] CXCL9 0-36 0-53 0-56 0-55 C-X-C motif chemokine 9

[0414] DNER 1 18 1-22 0-4 1 91 Delta and Notch-like epidermal growth factor receptor EN-RAGE 0-5 1 04 1-43 0-73 Protein S100-A12

[0415] FGF-19 1 1-28 1 14 1 02 Fibroblast growth factor 19

[0416] FGF-21 1-67 0-73 0-46 0-29 Fibroblast growth factor 21

[0417]

[0418] FGF-23 0-53 0-96 1-35 0-29 Fibroblast growth factor 23

[0419] FGF-5 1-24 0-44 0-66 0-37 Fibroblast growth factor 5

[0420] Flt3L 2 03 1 15 0 09 0-85 Fms-related tyrosine kinase 3 ligand

[0421] GDNF 1-2 2 04 0-79 0-41 Glial cell line-derived neutrotrophic factor

[0422] HGF 0-68 1-21 0-35 0 08 Hepatocyte growth factor

[0423] IFN-gamma 0-4 1 19 0-26 1-5 Interferon gamma

[0424] IL-1 alpha 0-38 1-43 1 03 0-33 Interleukin- 1 alpha

[0425] IL-10RA 1-44 1-38 1-38 0-75 Interleukin- 10 receptor subunit alpha

[0426] IL-10RB 0-77 1-47 1 51 1-69 Interleukin- 10 receptor subunit beta

[0427] IL-12B 0-92 0-76 1 09 0-68 Interleukin- 12 subunit beta

[0428] IL-15RA 1-34 1 13 0-95 1-41 Interleukin-15 receptor subunit afpha

[0429] IL-17A 0-8 0-96 1 0-75 Interleukin 17A

[0430] IL-17C 1-36 0-42 0-27 0-39 Interleukin 17C

[0431] IL-18R1 1-24 1-47 1-23 1 18 Interleukin-18 receptor 1

[0432] IL-20 1-56 0-28 0-49 1-2 Interleukin-20

[0433] IL-20RA 1 1 0-24 1 0 15 Interleukin-20 receptor subunit alpha

[0434] IL-22 RAI 0-37 1-2 0-62 1-5 Interleukin-22 receptor subunit alpha- 1

[0435] IL-24 0-89 0-85 0-53 0-26 Interleukin-24

[0436] IL-2RB 0-75 1 02 1-39 0-57 Interleukin-2 receptor subunit beta

[0437] IL10 1 11 0-93 0-58 1-76 Interleukin- 10

[0438] IL13 0-91 0-6 0-43 0-84 Interleukin 13

[0439] IL18 1 09 1 12 0-37 0-21 Interleukin 18IL2 1-38 0-57 0-3 0 12 Interieukin-2 IL33 1-51 0-9 0-51 0 15 Interleukin-33 IL4 0-82 1-22 0-85 2-4 Interleukin-4 IL5 0-54 0-93 0-26 1 15 Interleukin-5 IL6 0-48 0-71 1-74 0-87 Interleukin-6 IL7 0-49 1-3 0-37 1-77 Interleukin-7 IL8 0-22 1-28 1-86 0 15 Interleukin-8 LAP TGF -beta- 1 0-63 0-71 0-22 0 13 Latency-associated peptide transforming growth factorb-1 LIF 0-36 1-28 1-35 0-29 Leukemia inhibitory factor LIF-R 0-87 1 02 0-32 1-71 leukemia inhibitory factor receptor MCP-1 0-53 0-68 0-7 1 09 Monocyte chemotactic protein- 1 MCP-2 0-39 1 0 18 0-28 Monocyte chemotactic protein-2 MCP-3 1-74 1 09 0-34 0-75 Monocyte chemotactic protein-3 MCP-4 1-23 0-57 0-74 0-87 Monocyte chemotactic protein-4 MMP-1 0-37 1 0-49 0-52 Matrix metalloproteinase- 1 MMP-10 0-48 1-26 1 11 0-52 Matrix metalloproteinase-10 NRTN 0-86 0-69 0-72 1-75 Neurturin NT-3 1-22 0-4 0-23 0-42 Neutrotrophin-3 OPG 0-35 0 15 0-55 0-61 Osteoprotegerin OSM 0-44 0-27 1-79 0-24 Oncostatin-M PD-L1 0-79 1-78 1 19 0-62 Programmed cell death 1 ligand 1 SCF 1-77 1-53 0-6 0-58 Stem cell factor SIRT2 2 01 1 02 0-41 0-73 SIR2 -like protein SLAMF1 1-53 0-44 0-55 1-32 Signaling lymphocyte activation molecule family 1 ST1A1 0-93 1 06 1-73 0 02 Sulfotransferase 1A1 STAMBP 0-64 1 18 0-36 0-74 STAM-binding protein TGF-alpha 1-85 0-46 0-53 0-61 Transforming growth factor alpha TNF 0-66 0-87 1-44 1-98 tumor necrosis factor TNFB 1 16 1-56 0-35 0-59 tumor necrosis factor-beta TNFRSF9 1-41 0-47 1-64 0-31 tumor necrosis factor receptor superfamily member 9 TNFSF14 0-78 0 18 1-77 0 03 tumor necrosis factor ligand superfamily member 14 TRAIL 0-53 1-59 0 09 0-52 TNF-related apoptosis-induced ligand TRANCE 1-37 1 07 0-86 0-74 TNF-related activation-induced cytokine TSLP 0-83 0-76 0-33 0-59 Thymic stromal lymphopoietin TWEAK 0 17 1 01 0 11 0 07 Tumor necrosis factor (Ligand) superfamily member 12 uPA 0-37 1 01 0-94 0-36 Urokinase-type plasminogen activator VEGFA 0-46 0-93 1-58 1-72 Vascular endothelial growth factor A PI 17 1-36 1-24 0-98 1-47 Plaque load (index) at 17 years old ms 12 0-3 0-58 1-55 1-93 S. mutans counts at 12 years old in whole saliva lbc 12 1 18 0-93 0 09 1 18 Lactobacilli counts at 12 years old in whole saliva strept 12 1 19 0-52 1-44 0-85 Oral streptococci counts at 12 years old in whole saliva a S Percentms l2 0-26 0-6 0-43 1-7 % S. mutans / oral streptococci in whole saliva 2 ms pl 12 0-56 0-45 0-82 2-37 S. mutans counts at 12 years old in plaque streptp! 12 0-96 0-76 0-72 0 02 Oral streptococci counts at 12 years old in plaque Percent ms pl 12 0 -68 0 -66 0 -74 2 -48 % S. mwtonx / oral streptococci in plaque SmIB adh 1 11 1-72 0-55 saliva adhesion of S. mutans strain IB ActinoLY7 adh 1-31 0 -44 3 04 saliva adhesion of Actinomyces strain LY7 i Oh 12 1-62 0 13 1-44 1-77 Oral hygiene, S Drinks 12 0-21 0-26 1-75 0-56 Intake frequency of sweet drinks 3 Sweets_12 0 -49 0 -72 1-8 0 -76 Intake frequency of sweets

[0440]

[0441] aVIP = Variable of Importance in projection in PLS modelling; VIP> 1.0, influential and > 1.5, highly influentialTable 8. The quantitative number of DMBT1 DNA and protein domain repeats do not correlate with caries progression in GS and GR groups

[0442] „ Total SRCR-SIDbDMBT1 isoform size variation^ Cj ClldlC 2610111}TB, m R32p Bm n Rt2p

[0443]

[0444] All -0 174 0 006 0 13 -1 03 0 024 0 006 GS1-3 -0 187 0 002 0-81 0.718 0 009 0-659 GR -0-014 0 0-91 -0-974 0 021 0 013 GS1 -0-457 0-004 0-77 2-37 0 182 0 190 GR1 0 07 0-001 0-79 0-789 0 012 0-478 GS2 0-201 0-007 0-79 -0.316 0 001 0-907 GS3 0-965 0-011 0-84

[0445] GR-P1 0-071 0-002 0-67 -0-728 0 019 0 183aGS = genetically susceptible, GR = genetically resistant caries phenotypes based onDMBTl, PRH1, PRH2 variation.bEffect size (B), explained variance (R2), and significance (p) of SRCR diploid copy number count and isoform size variation as predictors of caries progression (5 -year prospective caries increment from 12 to 17 years). DMBT1CNN sites 1 and 2 were non-significant in relation to caries progression.

[0446]

[0447] ' Isoform sizes ranked as: Ib< Ia< II< III.Table 9. DMBT1 isoforms and caries measures in GS and GR groups, and individuals undergoing orthodontic treatment., Caries measures'*C,1C'CDMBT DeFS-12y DeFS-17y ADeFS-5y isoformdn Mean± SD p n Mean± SD p Mean± SD p Total lb < small 20 2-7 ± 2-3 0-240 16 11-4 ± 14-5 0-014 7-3 ± 11 0 0-009 la small 71 3 0 ± 3-4 0- 132 57 7-2 ± 6- l 0-002 4-2 ± 4-7 0-007 II intermediate 166 2-8 ± 2-7 0-012 143 7-2 ± 7-4 0-015 4-5 ± 5-9 0-022 III large 108 2- l ± 2-3 Ref. 98 5-l ± 5-8 Ref. 2-944-1 Ref. IVa small double 35 2-7 ± 2-9 0-306 29 10-2 ± ll-l 0-036 7-7 ± 10-7 0-020 IVb large double 48 2-4 ± 2-7 0-665 43 6-146-6 0-428 3-5 ± 4-7 0-375 GS1-3 I 16 4-3 ± 4-6 0-608 8 11-9 ± 10-3 1 000 7 048 1 0-840

[0448] II 10 2-2 ± l-7 0-931 2 12 0 ± 7 0 0-509 9 145-6 0-229 III 3 3-0 ± 3-6 Ref. 1 9-3 ± 2-3 Ref. 5-3 ± 3-7 Ref. GR I 75 2-6 ± 2-8 0-210 60 7-3 ± 8-2 0 002 4-4 ± 6-3 0 004

[0449] II 156 2-9 ± 2-7 0-009 134 6-8 ± 7-4 0 021 4-145-8 0 043 III 105 2-0 ± 2-3 Ref. 95 5 045-8 Ref. 2-8 ± 4-l Ref. GR-P1 lb 8 2-6 ± 1-8 0- 104 6 7-3 ± 3-9 0 047 4-143 0 0 079 la 21 l-9 ± 2-7 0-949 15 5-4 ± 2-2 0-029 3-842 1 0-015 II 48 2-8 ± 2-4 0-011 40 6-9 ± 7-9 0 013 4-3 ± 6-2 0 076 III 40 1-6 ± 1-9 Ref. 36 4-0 ± 4-8 Ref. 2-3 ± 3-5 Ref. IVa 10 2-l ± 2-4 0-564 7 8-7 ± ll-l 0- 198 6-5 ± 9-6 0- 139 IVb 16 2-3 ± 2-2 0-293 14 5-146-7 0-683 2-8 ± 4-8 0-824. I 13 4-5 ± 3-8 0-291 13 9-9 ± 7-9 0 015 4-8 ± 5-3 0 007 Orthodontic II 26 2-l ± 2-l 0-632 23 6 145-9 0 188 3-7 ± 4-7 0 025 treatment JJJR 2-7 ± 2-8 Ref. 11 3-9 ± 4-6 Ref. 0-8 ± 2-6 Ref. Dependency I + 53 3-7 ± 3-5 0-272 42 10-4 ± 10-7 0.029 6.2 ± 8.3 0.021 on S.m. II + 80 3-7 ± 2-8 0-070 66 9-7 ± 8-7 0.029 6.2 ± 7.2 0.028 infection6III + 48 2-8 ± 2-5 Ref. 46 6-5 ± 6-6 Ref. 3.5 ± 4.8 Ref.

[0450] I - 38 l-8 ± 2-3 0-474 31 5 142-8 0 009 3-142.2 0-033 II - 86 2-0 ± 2-3 0-098 77 4-9 ± 5-3 0 120 3 0 ± 3.9 0-282 III - 60 1-5 ± 1-9 Ref. 52 4-0 ± 4-7 Ref. 2-3 ± 3.2 Ref.aCaries DeFS scores (mean ± SD) at 12 and 17 years of age, and the incremental increase (ADeFS-5y) over 5 years. DeFS: Decayed, enamel included, Filled Surfaces.b2-sided p-value from Mann- Whitney U-test compared to the reference (Ref.).

[0451] 6GS = genetically susceptible, GR = genetically resistant caries phenotypes based on DMBT1, PRH1, PRH2 variation.dDMBTl size isoforms in individual parotid saliva samples measured using western blot assay.

[0452]

[0453] 6S.mutans infection status (+ / -).References

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Claims

1. CLAIMS1. A genetic origin fingerprint (stratification at the genetic level) for predisposition to dental caries, the fingerprint comprising a copy number variation pattern at CNV1 and CNV2 of the DMBT1 gene, wherein said copy number variation pattern is characterized by a diploid copy number at CNV1 and a diploid copy number at CNV2 assigned to one of the following CNV groups:CNV group 1: CNV1 = 0 and CNV2 < 4CNV group 2: CNV1 = 1 and CNV2 < 4CNV group 3: CNV1 = 1 and CNV2 > 4CNV group 4: CNV1>2 and CNV2 < 4CNV group 5: CNV1>2 and CNV2 > 4;wherein group 1 and 5 are indicative of low incidence of dental caries;group 2 is indicative of moderate incidence of dental caries; andgroup 3 and 4 are indicative to high incidence of dental caries.

2. A phenotype origin fingerprint for predisposition to dental caries, the phenotype fingerprint being an allelic phenotype of acidic proline-rich proteins (PRPs) encoded by PRH1 and PRH2, wherein said allelic phenotype is selected from any one of the following PRP groups: P4a: heterozygous at PRH1 (Db-PIF) combined with PRP1 homozygous at PRH2 (PRP1-PRP1) [Db, PIF, PRP1, PRP1];P7: heterozygous at PRH1 (Db-Pa) combined with heterozygous at PRH2 (PRP1-PRP2) [Db-Pa-PRP1-PRP2];P8: heterozygous at PRH1 (Db-PIF) combined with heterozygous at PRH2 (PRP-l-PRP-2) [Db-PIF-PRP1-PRP2];P6: heterozygous at PRH1 (Pa, PIF) combined with heterozygous at PRH2 (PRP1, PRP2) [Pa, PIF, PRP1, PRP2];Pl: homozygous at PRH1 (PIF, PIF) combined with homozygous at PRH2 (PRP 1 -PRP 1) [PIF, PIF, PRP1, PRP1];P4b: homozygous at PRH1 (Db, Db) combined with homozygous at PRH2 (PRPl-PRPl) [Db, Db, PRP1, PRP1];P5: homozygous at PRH1 (PIF, PIF) combined with heterozygous at PRH2 (PRP1, PRP2) [PIF, PIF, PRP1, PRP2];P10: homozygous at PRH1 (Pa, Pa) combined with homozygous at PRH2 (PRP2-PRP2) [Pa, Pa, PRP2-PRP2];wherein groups P4a, P8 and P7 are attributed to immunodeficiency and high incidence of dental caries; groups P5 and P6 are attributed to low to moderate incidence of dental caries; and groups P1, P4b, P1, P10 attributed to lifestyle and low incidence of dental caries.

3. The phenotype origin fingerprint according to claim 2, wherein the allelic phenotype is selected from any one of the following PRP groups:P4a: heterozygous at PRH1 (Db-PIF) combined with homozygous at PRH2 (PRP1-PRP1) [Db, PIF, PRP1, PRP1];P7: heterozygous at PRH1 (Db-Pa) combined with heterozygous at PRH2 (PRP1-PRP2) [Db-Pa-PRP1-PRP2];P8: heterozygous at PRH1 (Db-PIF) combined with heterozygous at PRH2 (PRP-l-PRP-2) [Db-PIF-PRP1-PRP2];P6: heterozygous at PRH1 (Pa, PIF) combined with heterozygous at PRH2 (PRP1, PRP2) [Pa, PIF, PRP1, PRP2];Pl: homozygous at PRH1 (PIF, PIF) combined with homozygous at PRH2 (PRP 1 -PRP 1) [PIF, PIF, PRP1, PRP1];wherein groups P4a, P8 and P7 are attributed to immunodeficiency and high incidence of dental caries; group P6 is attributed to low to moderate incidence of dental caries; and group Pl attributed to lifestyle and low incidence of dental caries.

4. A phenotype origin fingerprint according to claim 2, wherein the allelic phenotype of acidic proline-rich proteins (PRPs) encoded by PRH1 and PRH2, wherein said allelic phenotype is selected from any one of the following PRP groups:P4a: heterozygous at PRH1 (Db-PIF) combined with homozygous at PRH2 (PRP1-PRP1) [Db, PIF, PRP1, PRP1];P7: heterozygous at PRH1 (Db-Pa) combined with heterozygous at PRH2 (PRP1-PRP2) [Db-Pa-PRP1-PRP2];P8: heterozygous at PRH1 (Db-PIF) combined with heterozygous at PRH2 (PRP-l-PRP-2) [Db-PIF-PRP1-PRP2];wherein groups P4a, P8 and P7 are attributed to immunodeficiency and preferably high incidence of dental caries that is independent of Streptococcus mutans infection status.

5. A fingerprint from genetic and phenotype origin according to claim 1, and 2 for predisposition to dental caries, the fingerprint comprising the following CNV stratified RPR groups, CNV-PRP groups:CNV-PRP group 1: [P4a-CNV group 2],CNV-PRP group 2: [P4a-CNV group 3],CNV-PRP group 3: [P4a-CNV group 2-CNV group 3],CNV-PRP group 4: [P4a-CNV group 4-CNV group 5],CNV-PRP group 5: [P7-CNV group 2],CNV-PRP group 6: [P7-CNV group 4],CNV-PRP group 7: [P7-CNV group 2-CNV group 4],CNV-PRP group 8: [P7-CNV group 3-CNV group 5],CNV-PRP group 9: [P8-CNV group 2],CNV-PRP group 10: [P8-CNV group 3],CNV-PRP group 11: [P8-CNV group 4],CNV-PRP group 12: [P8-CNV group 2-CNV group- 3 - CNV group 4],CNV-PRP group 13: [P8-CNV group 5],CNV-PRP group 14: [P4b- CNV groups 1-5],CNV-PRP group 15: [Pl - CNV groups 1-5],CNV-PRP group 16: [P5- CNV groups 1-5],CNV-PRP group 17: [P6- CNV groups 1-5],CNV-PRP group 18: [PIO- CNV groups 1-5],6. A fingerprint from genetic and phenotype origin according to claim 1, and 4 for predisposition to dental caries, the fingerprint comprising the following CNV stratified RPR groups, CNV-PRP groups:CNV-PRP group 1: [P4a-CNV group 2],CNV-PRP group 2: [P4a-CNV group 3],CNV-PRP group 3: [P4a-CNV group 2-CNV group 3],CNV-PRP group 4: [P4a-CNV group 4-CNV group 5],CNV-PRP group 5: [P7-CNV group 2],CNV-PRP group 6: [P7-CNV group 4],CNV-PRP group 7: [P7-CNV group 2-CNV group 4],CNV-PRP group 8: [P7-CNV group 3-CNV group 5],CNV-PRP group 9: [P8-CNV group 2],CNV-PRP group 10: [P8-CNV group 3],CNV-PRP group 11: [P8-CNV group 4],CNV-PRP group 12: [P8-CNV group 2-CNV group- 3 - CNV group 4],CNV-PRP group 13: [P8-CNV group 5],7. A fingerprint from genetic and phenotype origin for predisposition to dental caries, by the provision of the following two groups / entities: a genetically susceptible dental caries (GS) group and a genetically resistant dental caries (GR) group, the genetic fingerprint comprising:(i) a copy number variation pattern at CNV1 and CNV2 of the DMBT1 gene assigned to a CNV group as defined in claim 1; and(ii) an allelic phenotype of acid PRPs encoded by PRH1 and PRH2 assigned to a PRP group as defined in any one of claim 2 to 4;wherein the fingerprint is a GS fingerprint when the combination of CNV group and PRP group is any one of GS or GR groups:GS1: P4a combined with CNV group 2 or CNV group 3;GS2: P7 combined with CNV group 2 or CNV group 4;GS3: P8 combined with CNV groups 2, 3 and 4;and wherein the genetic fingerprint is a GR fingerprint when the combination is:GR1: P4a combined with CNV group 4 or CNV group 5;GR2: P7 combined with CNV group 3 or CNV group 5;GR3: P8 combined with CNV group 5;GR-P4b: P4b combined with CNV groups 1-5;GR-P1: P1 combined with CNV groups 1-5;GR-P5: P5 combined with CNV groups 1-5;GR-P6: P6 combined with CNV groups 1-5; andGR-P10: P10 combined with CNV groups 1-5.

8. A fingerprint as defined by any one of claims 1 to 7 showing penetrance such as linear penetrance, as to biomarkers such as proteins, salivary short-chain fatty acids (SCFAs), inflammatory biomarkers in parotid saliva, and biofilm.

9. A method for assessing the susceptibility (predisposition) of a person for the development of dental caries, the method comprising:a) providing a biological sample obtained from the person;b) from the biological sample extracting one or more fingerprints as defined by any one of claims 1 to 7; andc) attributing the person to any one of the CNV groups; PRP groups, CNV-PRP group and GS, GR groups.

10. A method for assessing the susceptibility (predisposition) of a person for the development of dental caries, the method comprising:a) providing a biological sample obtained from the person;b) from the biological sample extracting the genetic origin fingerprint of claim 1; and c) attributing the person to one of the CNV groups.

11. A method for assessing the susceptibility (predisposition) of a person for the development of dental caries, the method comprising:a) providing a biological sample obtained from the person;b) from the biological sample extracting the phenotype origin fingerprint of any one of claims 2 to 4; andc) attributing the person to one of the PRP groups.

12. A method for assessing the susceptibility (predisposition) of a person for the development of dental caries, the method comprising:a) providing a biological sample obtained from the person;b) from the biological sample extracting the fingerprint from genetic and phenotype origin of claim 5 or 6; andc) attributing the person to one of the CNV-PRP groups; or GS or GR groups.

13. The method according to claim 10, further comprising from the sample extracting information on allelic phenotypes of acid PRPs; stratifying the PRP group by the CNV groups; and assigning the person to a CNV stratified PRP group.

14. The method according to claim 10, wherein the PRP groups are one or more of the following: P4a (Db, PIF, PRP-1, PRP-1), P6 (Pa, PIF, PRP-1I, PRP-2), Pl (PIF, PIF, PRP-1, PRP-1), P8 (Db-PIF -PRP-1 -PRP-2), and P7 (Db-Pa-PRP-1 -PRP-2), wherein groups P4a, P8 and P7 are attributed to immunodeficiency and high incidence of dental caries; group P6 is attributed to low to moderate incidence of dental caries; and group Pl attributed to lifestyle and low incidence of dental caries.

15. The method according to claim 13 or 14, further comprising assigning the person to a genetically susceptible (GS) caries subtype based on the stratification of PRH1, PRH2 allelic phenotype (PRP groups) with DMBT1 CNV group(s) and, thereby providing the GS subtypes:GS1: P4a and CNV groups 2 and 3;GS2: P7 and CNV groups 2 and 4; andGS3: P8 and CNV groups 2, 3 and 4.

16. The method according to claim 15, further comprising assigning the person to a genetically resistant (GR) caries subtype based on the stratification of PRH1, PRH2 allelic phenotype (PRP groups) with DMBT1 CNV group(s) and, thereby providing the GR subtypes:GR1: P4a and CNV groups 4 and 5;GR2: P7 and CNV groups 3 and 5;GR3: P8 and CNV group 5;GR-P4b: P4b combined with CNV groups 1-5;GR-P1: P1 combined with CNV groups 1-5;GR-P5: P5 combined with CNV groups 1-5;GR-P6: P6 combined with CNV groups 1-5; andGR-P10: P10 combined with CNV groups 1-5.

17. The method according to claim 15 or 16, further from a saliva sample obtained from the person extracting information selected from the group of salivary proteins such as amount of DMBT1 and ratio of small / large acidic PRPs, salivary short-chain fatty acids (SCFAs), inflammatory markers and microbiota and lifestyle biomarkers, preferably from the salivary proteins as the amount of DMBT1 and ratio of small / large acidic PRPs.

18. The method according to any one of claims 15 to 17, wherein further from a saliva sample obtained from the person extracting information selected from salivary short-chain fatty acids (SCFAs), preferably from butyric acid, lactic acid and 2-hydroxybutyric acid.

19. The method according to claim 18, wherein the salivary short-chain fatty acids (SCFAs), selected from: butyric acid, lactic acid and 2-hydroxybutyric acid show near-linear penetrance of 5-year caries progression in persons assigned to a GS subtype.

20. A method for assessing the susceptibility of a person for the development of dental caries, having established the following stratifications on the genetic level and the phenotype level:i) Stratification at the genetic level based on copy number variation pattern at CNV1 and CNV2 of the DMBT1 gene, wherein said copy number variation pattern is characterized by a diploid copy number at CNV1 and a diploid copy number at CNV2 assigned to one of the following CNV groups:• CNV group 1: CNV1 = 0 and CNV2 < 4• CNV group 2: CNV1 = 1 and CNV2 < 4• CNV group 3: CNV1 = 1 and CNV2 > 4• CNV group 4: CNV1 > 2 and CNV2 < 4• CNV group 5: CNV1 > 2 and CNV2 > 4wherein group 1 and 5 are indicative of low incidence of dental caries; group 2 is indicative of moderate incidence of dental caries; and group 3 and 4 are indicative to high incidence of dental caries;ii) Stratification at the phenotype level based on an allelic phenotype of acidic proline-rich proteins (PRPs) encoded by PRH1 and PRH2, selected from any one of the following PRP groups:• P4a: Db heterozygous at PRH1 (Db-PIF) combined with PRP1 homozygous at PRH2 (PRP1-PRP1) [Db, PIF, PRP1, PRP1];• P7: Db heterozygous at PRH1 (Db-Pa) combined with PRP1 / PRP2 heterozygous atPRH2 (PRP1-PRP2) [Db-Pa-PRP1-PRP2];• P8: Db heterozygous at PRH1 (Db-PIF) combined with PRP1 / PRP2 heterozygous atPRH2 (PRP-l-PRP-2) [Db-PIF-PRP1-PRP2];• P4b: homozygous at PRH1 (Db, Db) combined with homozygous at PRH2 (PRP1-PRP1) [Db, Db, PRP1, PRP1];• Pl: homozygous at PRH1 (PIF, PIF) combined with homozygous at PRH2 (PRP1-PRP1) [PIF, PIF, PRP 1, PRP 1];• P5: homozygous at PRH1 (PIF, PIF) combined with heterozygous at PRH2 (PRP1, PRP2) [PIF, PIF, PRP1, PRP2];• P6: heterozygous at PRH1 (Pa, PIF) combined with heterozygous at PRH2 (PRP1, PRP2) [Pa, PIF, PRP1, PRP2];• P10: homozygous at PRH1 (Pa, Pa) combined with homozygous at PRH2 (PRP2-PRP2) [Pa, Pa, PRP2-PRP2];iii) Combining the stratification based on at CNV1 and CNV2 of the DMBT1 gene and the phenotype level based on an allelic phenotype of acidic proline-rich proteins (PRPs) encoded by PRH1 and PRH2, thereby forming the following genetically susceptible dental caries groups:• GS1: P4a combined with CNV group 2 or CNV group 3;• GS2: P7 combined with CNV group 2 or CNV group 4;• GS3: P8 combined with CNV groups 2, 3 or 4;• GR1: P4a combined with CNV groups 4 and 5;• GR2: P7 combined with CNV groups 3 and 5;• GR3: P8 combined with CNV group 5;• GR-P4b: P4b combined with CNV groups 1 to 5;• GR-P1: Pl combined with CNV groups 1 to 5;• GR-P5: P5 combined with CNV groups 1 to 5;• GR-P6: P6 combined with CNV groups 1 to 5;• GR-P10: PIO combined with CNV groups 1 to 5;the method comprising;a) providing a biological sample obtained from the person;b) extracting from the sample of said person information on CNV1 and CNV2 copy number variation patterns of DMBT1 and on allelic phenotypes of acid PRPs and optionally genotypes corresponding to the allelic acid PRPs; andc) assigning the person to one group selected from GS1, GS2, GS3, GR1, GR2, GR3, GR-P4b, GR-P1, GR-P5, GR-P6, GR-P10.

21. The method according to claim 20 for assessing the susceptibility of a person for the development of dental caries, wherein the stratification at the phenotype level based on an allelic phenotype of acidic proline-rich proteins (PRPs) encoded by PRH1 and PRH2 is selected from any one of the following PRP groups:• P4a: Db heterozygous at PRH1 (Db-PIF) combined with PRP1 homozygous at PRH2 (PRP1-PRP1) [Db, PIF, PRP1, PRP1];• P7: Db heterozygous at PRH1 (Db-Pa) combined with PRP1 / PRP2 heterozygous atPRH2 (PRP1-PRP2) [Db-Pa-PRP1-PRP2];• P8: Db heterozygous at PRH1 (Db-PIF) combined with PRP1 / PRP2 heterozygous atPRH2 (PRP-l-PRP-2) [Db-PIF-PRP1-PRP2]; andcombining the stratification based on at CNV1 and CNV2 of the DMBT1 gene and the phenotype level based on an allelic phenotype of acidic proline-rich proteins (PRPs) encodedby PRH1 and PRH2, thereby forming the following genetically susceptible dental caries groups:• GS1: P4a combined with CNV group 2 or CNV group 3;• GS2: P7 combined with CNV group 2 or CNV group 4;• GS3: P8 combined with CNV groups 2, 3 or 4; andassigning the person to one group selected from GS1, GS2, GS3.

22. The method according to claim 20 or 21, wherein CNV stratified PRP groups GS1, GS2, GS3 show linear penetrance as to salivary biomarkers.

23. The method according to claim 22, wherein salivary biomarkers are selected from any one of: ratio PRP3 / 1, DMBT1 amount, short chain fatty acids, and plaque mass.

24. The method according to any one of the preceding claims, wherein the biological sample is selected from any one of: saliva, parotid saliva, whole saliva, buccal scraping or swab, blood, serum, plasma, urine, faeces, cerebrospinal fluid, tissue biopsy, and any other tissue or fluid containing nucleated human cells.

25. The fingerprint of any one of claims 1 to 8, and the method according to any one of claims 20 to 24, wherein the extraction of information related to DMBT1 (CNV1 and CNV2) is selected from Paralogue Ratio Test (PRT), next generation sequencing (NGS), PCR such as Digital Droplet PCR (ddPCR), Array Comparative Genomic Hybridization (aCGH), Multiplex Ligation-dependent Probe Amplification (MLPA), and SNP genotyping arrays.; and for allelic phenotype of PRPs is selected from Native alkaline polyacrylamide gel electrophoresis (PAGE), High-Performance Liquid Chromatography (HPLC), Mass Spectrometry (MS) -proteomics, Immunoassay — Western blot / ELISA, TaqMan SNP genotyping, Illumina SNP array.

26. An analytical kit for determining the predisposition of a person developing dental caries, comprising: means for extracting fingerprint information defined by any one of claims 1 to 8 and attributing the person to any one of the groups defined in any one of claims 1 to 8.

27. The analytical kit according to claim 26, therein the means for genetic fingerprints are selected from Paralogue Ratio Test (PRT), generation sequencing (NGS), PCTR such asDigital Droplet PCT (ddPCR), Array Comparative Genomic Hybridization (aCGH), Multiplex Ligation-dependent Probe Amplification (MLPA), SNP genotyping arrays, means for phenotype fingerprints are selected from Native alkaline polyacrylamide gel electrophoresis (PAGE), High-Performance Liquid Chromatography (HPLC), Mass Spectrometry (MS) -proteomics, Immunoassay - Western blot / ELISA, TaqMan SNP genotyping, Illumina SNP array; and means for protein concentration are selected from Slot-blot immunoassay, ELISA, and Proximity Extension Assay (PEA, Olink).

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