in the last few years a number of candidate genes have been reported as harbouring risk 
 alleles for oa . these candidates have been chosen principally on the basis that the proteins 
 that they code for are regulators of joint formation and of joint maintenance . table 1 lists examples of some of the genes studied . 
 what has become apparent from these reports is that oa risk alleles often show ethnic 
 stratification , with association in asians or in europeans but not typically in both . this 
 can be attributed to differences between ethnic groups in ( 1 ) the frequencies of the risk 
 alleles , ( 2 ) the genetic background on which the risk alleles are operating and ( 3 ) 
 nongenetic ( environmental ) factors that modulate the impact of the risk alleles . it is also 
 apparent that the oa associations are often to a particular joint rather than to several 
 different joints . in the eight examples listed in table 
 1 , five associations are to either the hip or to the knee whereas only three are to 
 both joints this is an important observation as it suggests that there is only a limited 
 sharing of the effects of particular oa risk alleles between skeletal sites . from a genetics 
 perspective , oa is not therefore a systemic disease of the whole skeleton but is instead a 
 more site - specific disease . table 1.examples of genes reported as associated with osteoarthritis ( oa ) through candidate 
 gene studiesgenechromosomeassociated polymorphismproteinprotein functionjointethnic grouprefs 
 gdf5 
 20q11.22rs143383growth differentiation factor 5regulator of cell growth and differentiationknee and hipasians and europeans79 
 smad3 
 15q22.33rs12901499mothers against decapentaplegic homologue 3signal transducer and transcriptional modulatorknee and hipeuropeans noasian reports yet 
 10 

 aspn 
 9q22.31triplet repeat of the codon for aspartic acidasporincartilage extracellular protein , member of the small 
 leucine - rich proteoglycan familykneeasiansnot europeans 
 11 

 edg2/lpar1 
 9q31.3rs10980705lysophosphatidic acid receptor 1lysophosphatidic acid receptorkneeasiansnot europeans12,13 
 calm1 
 14q24-q31rs12885713calmodulinsubunit of phosphorylase kinasehipasiansnot europeans14,15 
 dio2 
 14q31.1rs225014 and rs12885300type ii iodothyronine deiodinasecatalyses the activation of thyroid hormonehipeuropeans and asians 
 16 

 dio3 
 14q32.31rs945006type iii iodothyronine deiodinasecatalyses the inactivation of thyroid hormoneknee and hipeuropeansno asian reports yet 
 17 

 srebf2 
 22q13.2rs2228314sterol regulatory element - binding protein 2transcription factor controlling cholesterol 
 homeostasiskneeeuropeansno asian reports yet 
 18 
  examples of genes reported as associated with osteoarthritis ( oa ) through candidate 
 gene studies of the genes listed in table 1 
 gdf5 and smad3 deserve further comment . gdf5 is the most compelling candidate association signal so far reported 
 for oa , with the rs143383 single nucleotide polymorphism ( snp ) showing association in both 
 europeans and asians and at a significance level of 
 p  <  5.0    10 , a threshold that is commonly applied to 
 assess the veracity of genome - wide association signals ( refs 7 , 8 , 9 ) . the gene codes for a growth factor that is part of the transforming 
 growth factor - beta ( tgf- ) superfamily and the associated polymorphism , snp rs143383 , have 
 also been reported to be associated with a variety of other musculoskeletal phenotypes 
 ( reviewed in ref . polymorphism in this gene 
 appears therefore to have a broad impact on skeletal health . smad3 
 codes for an intracellular signal transducer that also operates in the tgf- pathway and 
 since the association of rs12901499 to oa has so far been reported in only one publication 
 ( ref . 10 ) , further studies are needed to support 
 the role of this snp in oa susceptibility . nevertheless , it is intriguing that rare and 
 penetrant haploinsufficient mutations within smad3 give rise to the 
 aneurysms - oa syndrome , characterised by early - onset oa and aortic lesions ( ref . it therefore appears that snps such as rs12901499 , 
 which like most common polymorphisms are expected to have relatively moderate effects on 
 gene function , and rare but highly detrimental mutations are acting on 
 smad3 to give rise to the same broad oa phenotype . however , this is so far the only clear 
 example of this phenomenon in oa . since individuals with the smad3 
 haploinsufficient mutations have aortic abnormalities there is the possibility that carriers 
 of the oa risk allele of rs12901499 may be at increased risk of vascular deformities . candidate gene studies have the advantage of targeting the known , combined with the 
 attraction that the investigating team has only to genotype a relatively small number of 
 polymorphisms to cover the gene of interest . these studies , however , have the clear 
 disadvantage that what is known is rarely comprehensive and that novel signals will not 
 therefore be uncovered . the genome - wide association scan ( gwas ) circumvents these 
 deficiencies and , when performed on large cohorts and with replication , has the power to 
 overcome the issue of multiple testing . in oa there have so far been three reports of gwas 
 studies combining the key requirements of extensive coverage , large cohorts and replication 
 in additional cohorts ( table 2 ) . table 2.genome-wide association scans performed utilising high genome coverage and large 
 cohortsstudyethnicity of discovery cohort and 
 cohort sizeethnicity of replication cohort and 
 overall cohort size for discovery and replication combinedoutcomerefsrotterdameuropean  netherlands1341 cases and 3496 
 controlseuropean and north american of european 
 descent14 938 cases and 39 000 controlsone signal , at chromosome 7q22 
 21 
 tokyoasian  japanese899 cases and 3396 controlsasian and european1879 cases and 3396 controlsone signal , at the hla locus 
 22 
 arcogeneuropean  uk3177 cases and 4894 controlseuropean and north american of european 
 descent13 768 cases and 53 286 controlsthree signals 
 23 
 european  uk7410 cases and 11 009 controlseuropean14 883 cases and 53 947 controlseight signals 
 24 
  genome - wide association scans performed utilising high genome coverage and large 
 cohorts the rotterdam study reported a single association signal for knee oa with a 
 p - value of 8    10 to a region of chromosome 7q22 encompassing 
 six known protein - coding genes ( ref . 21 , table 3 ) , none of which had previously been implicated 
 in oa . a subsequent analysis with additional cohorts marginally increased the significance 
 of the association ( ref . the tokyo study 
 reported an association signal to two snps located within a 340 kb region of the hla locus 
 on chromosome 6p , with p - values < 7    10 ( ref . initially , a gwas was performed on 3177 cases and three 
 association signals were reported , but none surpassed the genome - wide significance threshold 
 of p    5.0    10 ( ref . the signals were to mical3 in knee and/or hip oa with a 
 p - value of 2.3    10 , to c6orf130 in knee oa 
 with a p - value of 2.7    10 and to col11a1 in 
 hip oa with a p - value of 1.2    10 . the number of cases 
 genotyped was then increased to 7410 and the gwas was re - run . this enhanced power identified 
 eight novel signals , five of which were genome - wide significant ( ref . five of the 
 arcogen signals encompass two or more protein - coding genes with the remaining three signals 
 containing single genes . several of the genes are plausible functional candidates , including 
 runx2 , which codes for a transcription factor active in joint tissues , 
 and chst11 , which codes for an enzyme that sulfates cartilage proteoglycan . however , the majority of the genes have not previously been suggested to have a role in oa 
 meaning that the arcogen study has provided very novel insights into oa aetiology . body mass 
 index ( bmi ) is a known risk factor for oa but only one of the arcogen signals , to 
 fto , was attenuated after bmi adjustment ; polymorphism in 
 fto is one of the strongest associations so far reported for bmi and 
 obesity risk . table 3.the signals from the rotterdam genome - wide association scan ( gwas ) and from the full 
 arcogen gwasstudysnpchromosomep - valuestratumgeneprotein namesummary of protein functionrotterdamrs38151487q228.0    10knee 
 prkar2b 
 protein kinase - camp - dependent - regulatory - type ii-regulator of camp signalling 
 hpb1 
 hmg - box transcription factor 1transcription factor 
 cog5 
 component of oligomeric golgi complex 5golgi morphology and function 
 gpr22 
 g protein - coupled receptor 22receptor and membrane protein 
 dus4l 
 dihydrouridine synthase 4-likeunknown 
 bcap29 
 b - cell receptor - associated protein 29unknownarcogenrs69763p21.17.24    10tjr 
 stab1 
 stabilin-1transmembrane receptor 
 nt5dc2 
 5-nucleotidase domain - containing protein 2unknown 
 pbrm1 
 polybromo-1chromatin remodeling and transcriptional 
 activation 
 gnl3 
 guanine nucleotide - binding protein - like 3nuclear protein important for stem cell 
 proliferation 
 glt8d1 
 glycosyltransferase 8 domain - containing protein 1glycosyltransferase 
 spcs1 
 signal peptidase complex subunit 1unknown 
 nek4 
 serine / threonine - protein kinase nek4kinase 
 itih1 
 inter - alpha - trypsin inhibitor heavy chain h1serine protease inhibitor  plasma 
 itih3 
 inter - alpha - trypsin inhibitor heavy chain h3serine protease inhibitor  plasma 
 itih4 
 inter - alpha - trypsin inhibitor heavy chain h4serine protease inhibitor plasma 
 mustn1 
 musculoskeletal embryonic nuclear protein 1nuclear protein  expressed during skeletogenesis 
 tmem110 
 transmembrane protein 110unknownarcogenrs121070363q286.71    10tkr - f 
 tp63 
 tumor protein 63transcription factorarcogenrs109481726p21.17.92    10male 
 supt3h 
 transcription initiation protein spt3 homologueunknown 
 runx2 
 runt - related transcription factor 2transcription factorarcogenrs93505916q13-q14.12.42    10hip 
 col12a1 
 collagen -1(xii ) chainfacit collagen , interacts with type i collagen 
 cox7a2 
 cytochrome c oxidase subunit 7a2 , mitochondrialone of the polypeptides of cytochrome c oxidase 
 tmem30a 
 cell cycle control protein 50atransmembrane protein , transporter 
 filip1 
 filamin - a - interacting protein 1interacts with filamin filamins bind to actin 
 senp6 
 sentrin - specific protease 6ubiquitin - like molecule ligated to target 
 proteins 
 myo6 
 myosin - viintracellular vesicle and organelle transport 
 impg1 
 interphotoreceptor matrix proteoglycan 1chondroitin sulfate proteoglycan expressed in the 
 retinaarcogenrs48367329q33.16.11    10thr - f 
 pappa 
 pappalysin-1secreted metalloproteinase 
 astn2 
 astrotactin-2neural migration 
 trim32 
 e3 ubiquitin - protein ligase trim32protein ubiquitination in innate immunityarcogenrs1049236712p11.221.48    10hip 
 klhdc5 
 kelch domain - containing protein 5protein ubiquitination 
 pthlh 
 parathyroid hormone - related proteinhormonearcogenrs83548712q23.31.64    10thr 
 chst11 
 carbohydrate sulfotransferase 11chondroitin sulfationarcogenrs804476916q12.26.85    10female 
 fto 
 -ketoglutarate - dependent dioxygenase ftounknowntjr , total joint replacement ; tkr - f , total knee replacement in females ; thr - f , 
 total hip replacement in females ; thr , total hip replacement . the signals from the rotterdam genome - wide association scan ( gwas ) and from the full 
 arcogen gwas tjr , total joint replacement ; tkr - f , total knee replacement in females ; thr - f , 
 total hip replacement in females ; thr , total hip replacement . one key observation from the arcogen study was that stratification by sex , by joint and by 
 the oa ascertainment criteria used was critical in the discovery of the association signals . regarding sex , the chromosome 6p21.1 signal was only relevant to male disease whereas the 
 3q28 , 9q33.1 and 16q12.2 signals were only relevant to female disease . regarding joint , the 
 3q28 signal was only relevant to knee oa whereas the 6q13-q14.1 , 9q33.1 , 12p11.22 and 
 12q23.3 signals were only relevant to hip oa . regarding ascertainment criteria , all the 
 arcogen cases had radiographic evidence of oa but in over 80% of the cases the disease was 
 so severe that the individuals had also undergone hip or knee joint replacement surgery . a 
 focus on these more severe cases aided the identification of several of the signals . the minor allele frequencies ( mafs ) of the snps that marked the arcogen association signals 
 were quite common , all > 10% . an analysis of the initial arcogen gwas for less common 
 alleles identified another association , with snp rs11842874 ( ref . this snp has a maf of 7% and resides within an intron of 
 mcf2l , which codes for the protein guanine nucleotide exchange factor 
 dbs . the association surpasses the genome - wide significance threshold , with a 
 p - value of 2.1    10 . the large arcogen dataset has so far been used in two related studies , the first 
 investigating an association between dna variants of the mitochondrial genome and oa and the 
 second investigating an overlap between alleles for height , bmi and oa . for many years 
 dysfunction of mitochondria has been implicated in oa aetiology and there is some evidence 
 that polymorphism of mitochondrial dna may mediate this , although the genetic studies so far 
 performed have been on relatively small cohorts ( reviewed in ref . the array used by arcogen provided robust genotype data for 48 
 common mitochondrial variants , which provided good coverage of the mitochondrial genome . however , no association with oa was observed in the comparison of 7393 arcogen cases and 
 5122 controls ( ref . it appears unlikely 
 therefore , that common mitochondrial dna variants are major contributors to oa 
 susceptibility , at least not in the north european population that is represented by the 
 arcogen study . it has been postulated that there may be overlap between the development of 
 oa and natural variation in skeletogenesis , based on the assumption that efficient 
 developmental patterning of the skeleton is essential for creation and maintenance of 
 healthy joints . the discovery that gdf5 snp rs143383 is one of the many 
 polymorphisms associated with natural variation in height ( ref . furthermore , the subsequent 
 discovery that due to its correlation with height , the oa - associated t - allele of this snp is 
 subjected to positive selection implies that oa genetic aetiology may partly be hitchhiking 
 onto the evolution events of skeletogenesis ( ref . however , although there was some initial suggestion from the arcogen study of 
 an excess overlap of association signals between oa and height and between oa and bmi , only 
 the bmi signal at fto replicated ( ref . this suggests that , apart from a few clear examples , there is not yet any 
 compelling evidence of a major correlation between the alleles for height and oa or between 
 the alleles for bmi and oa . having identified compelling genetic signals , the next step is the functional analyses of 
 these to assess how the associated alleles modulate gene or protein function . in this 
 regard , studies on oa - associated snp rs143383 act as an exemplar . rs143383 is a c to t transition located within the 5 untranslated region ( 5utr ) of 
 gdf5 , which codes for the extracellular signalling molecule growth 
 differentiation factor 5 . in the paper that first reported the association between rs143383 
 and oa , the investigators demonstrated that the oa - risk t - allele of the snp - mediated reduced 
 mrna expression relative to the c - allele in an in vitro luciferase assay conducted in a 
 chondrocyte cell line ; chondrocytes are the only cell type present in cartilage ( ref . this experiment therefore highlighted rs143383 as 
 the actual functional snp responsible for the association signal . gdf5 protein is an 
 anabolic extracellular signalling molecule required for joint formation and maintenance and 
 this functional study implied that oa susceptibility at rs143383 acts by reducing the levels 
 of gdf5 protein . soon after this in vitro study , it was demonstrated that the t - allele 
 correlated with reduced expression of gdf5 in cartilage ( ref . this result was obtained by an analysis of the 
 expression of the gene using rna directly extracted from the cartilage of oa patients , who 
 had undergone elective joint replacement surgery . the patients studied were heterozygous for 
 rs143383 , allowing a direct comparison of the expression of the t - allele versus the 
 c - allele . the allelic expression imbalance ( aei ) between the c- and t - alleles of rs143383 
 also occurs in other joint tissues ( ref . a second gdf5 5utr 
 snp , rs143384 , was discovered that modulates the effect that rs143383 has on gene 
 expression . this result revealed that the activity of an oa susceptibility allele could be 
 context - specific . a search of the gdf5 3utr then identified rs56366915 as 
 a snp that also causes aei , but independently of rs143383 ( ref . 34 ) . the subsequent use of electrophoretic mobility shift assays 
 ( emsas ) , emsa - supershifts , chromatin immunoprecipitation ( chip ) and rna knockdown identified 
 the trans - acting factors sp1 , sp3 , p15 and deaf-1 as binding differentially to the t- and 
 c - alleles of rs143383 and mediating the aei ( ref . 35 ) . a summary of these functional studies is listed in table 4 . table 4.functional studies performed on gdf5 snp rs143383functional studyoutcomerefsluciferase assay in chondrocytic cell line hcs-2/8t - allele shows reduced expression relative to the 
 c - allele 
 32 
 gdf5 allelic expression analysis 
 ( aei ) on cartilage rna from oa patientst - allele shows reduced expression relative to the 
 c - allele 
 33 
 gdf5 aei on rna extracted from other 
 joint tissuest - allele shows reduced expression relative to the 
 c - allele 
 34 
 investigation of additional gdf5 
 5utr snpsrs143383s effect on gene expression is modulated by 
 rs143384 
 34 
 investigation of gdf5 3utr snpsrs56366915 independently influences gene expression 
 34 
 emsa , chip and rna knockdown in liposarcoma cell line 
 sw872sp1 , sp3 , p15 and deaf-1 bind differentially to the 
 rs143383 alleles 
 35 
 cpg dna methylation analysisdemethylation exacerbates the aei mediated by rs143383 
 40 
  functional studies performed on gdf5 snp rs143383 rs143383 , rs143384 and rs56366915 are common snps . a sequence analysis of 
 gdf5 in a cohort of 992 oa cases and 944 controls did not detect any 
 additional common variants , implying that there are no other gdf5 
 polymorphisms that can , at the population level , influence oa susceptibility ( ref . this sequence analysis did however detect six 
 unique variants , one of which is located in the promoter of gdf5 . a 
 subsequent functional study demonstrated that this promoter variant is a binding site for 
 the trans - acting factor yy1 and that the unique a - allele of the variant can neutralise the 
 reduced expression that is mediated by the oa - associated t - allele of rs143383 ( ref . this result again demonstrates that the activity 
 of a susceptibility allele is context - specific whereas yy1 , such as sp1 , sp3 , p15 and 
 deaf-1 , is a trans - acting factor that can modulate gdf5 expression and 
 which could therefore be exploited to potentially alleviate the oa risk coded for by this 
 gene . in their c - allele forms such sites are potentially 
 amenable to epigenetic regulation by dna methylation . since epigenetic mechanisms are known 
 to play a role in chondrogenesis and oa pathogenesis ( refs 38 , 39 ) it was hypothesised that rs143383 
 and rs143384 may be targets for epigenetic control and that was indeed shown to be the case 
 ( ref . methylation of the gdf5 
 5utr was demonstrated to occur in cell lines and in joint tissues , with demethylation 
 leading to increased gdf5 expression . in a cell line heterozygous for 
 rs143383 , this demethylation was found to exacerbate the aei mediated by rs143383 . this 
 result clearly demonstrated that the genetic effect that rs143383 has on 
 gdf5 expression is modifiable by nongenetic factors . there are as yet no animal models directly targeting the gdf5 snps 
 discussed above . however , the brachypodism mouse has offered an opportunity to assess what 
 effect a reduction in gdf5 has on joint physiology . the brachypodism mutation is a frame 
 shift of gdf5 that causes a premature termination codon , resulting in a 
 null allele . homozygotes display a number of musculoskeletal defects whereas heterozygotes 
 show no such developmental abnormalities but are at risk of developing an oa phenotype when 
 challenged ( ref . 41 ) . by being subjected to a 
 reduction rather than a total loss of gdf5 the brachypodism heterozygote 
 mimics the effect of rs143383 in human oa and emphasises the need to maintain appropriate 
 levels of gdf5 to ensure healthy joint function . there have been published reports on the functional analysis of other oa loci , with 
 particularly insightful data generated recently for the 7q22 signal from the rotterdam study 
 and for dio2 . as mentioned earlier , the rotterdam study reported an association signal to a region of 
 chromosome 7q22 encompassing six known protein - coding genes ( table 3 ) . the expression of these genes was assessed using cells 
 extracted and cultured from the joint tissues of oa patients . the results revealed that all 
 the genes showed a near universal expression pattern , apart from gpr22 
 ( refs 21 , 25 ) . a subsequent study that examined the expression of the genes using rna directly 
 extracted from patient joint tissues discovered that genotype at the 7q22 association signal 
 correlated with expression of hbp1 in cartilage ( ref . it would appear likely therefore that part , or all , of the 7q22 
 association signal is accounted for by a regulatory polymorphism that modulates 
 hbp1 expression . dio2 codes for iodothyronine - deiodinase enzyme type 2 ( d2 ) , a 
 selenoprotein that converts intracellular inactive thyroid hormone to its active form . a 
 common dio2 haplotype composed of the c - allele of snp rs225014 and the 
 c - allele of snp rs12885300 is associated with oa in europeans and asians ( ref . an analysis of dio2 expression revealed that the gene was subject to aei 
 with the c - allele of rs225014 correlating with increased expression in cartilage ( ref . furthermore , immunohistochemistry revealed an 
 increased amount of d2 positive cells in oa versus healthy cartilage . these results suggest 
 that modulating the level of active thyroid hormone in joint tissues , via the increased 
 expression of dio2 and the subsequent availability of d2 , is a contributing 
 factor in oa aetiology . methylation analysis of cpg sites within and close to 
 dio2 in both oa diseased cartilage and intact cartilage have revealed that , 
 as for gdf5 , the gene is also subjected to epigenetic regulation related to 
 disease status ( ref . gdf5 , hbp1 and dio2 are all examples of 
 where the oa risk allele mediates its effect by altering gene expression . as more 
 susceptibility loci are identified for common human diseases it is becoming apparent that 
 the majority of associated alleles contribute to disease risk by influencing gene 
 expression , typically by modulating rates of transcription or of transcript stability ( ref . 
 45 ) . oa genetic susceptibility is following this 
 trend and as such the initial functional test on all new oa signals should be an assessment 
 of the effect that the risk allele has on gene expression . one of the early translational aims of the genetic investigation of common complex diseases 
 was that it would offer a predictive capacity to clinicians in their attempts to identify 
 individuals at risk of disease initiation and progression . however , it has become apparent 
 that the vast majority of disease risk alleles contribute individually only very modestly to 
 heritability and as such there is limited current scope for their use as predictive tools 
 ( ref . 46 ) . clearly , this scenario is likely to 
 change as more risk alleles are identified ( see below ) but for the vast majority of diseases 
 this is realistically a medium term goal at best . alternatively , by identifying the 
 principal pathways that are the recipients of genetic susceptibility then there is scope for 
 exploiting these insights for new treatment development . as yet the number of oa risk loci 
 is quite small but it does appear from the list of genes in tables 1 and 3 that 
 regulation of cell differentiation could be one of the key pathways for future 
 exploitation . one of the clear messages to have emerged from the gwass performed on common diseases is 
 that the case - control sample sizes used have to be large in order to detect what are small 
 individual contributions from the risk alleles . of the three gwass listed in table 2 only arcogen had adequate sample size if additional novel oa signals are to be 
 discovered , it is critical that genotyping at the genome - wide level continues on all 
 available samples and with the concurrent use of meta - analyses . the number of oa cases will 
 also need to be expanded to provide the power to account for susceptibility differences 
 between ethnic groups , between the two sexes and between different joints ; without case 
 sample sizes in the tens of thousands the vast majority of oa susceptibility alleles will go 
 undetected . it has also become evident that rare variants can also contribute to common 
 disease risk ( refs 47 , 48 ) and that these are often not captured by the current gwas arrays . 
 as such imputation , re - sequencing and exome and whole - genome analyses ( ref . 49 ) are likely to have a role in the discovery of rare 
 risk alleles for oa . oa genetic studies have quite sensibly focused on clinical forms of the disease but it is 
 becoming apparent that breakthroughs can also be achieved by studying alternative but 
 related phenotypes and a very clear example of this has recently been published . the 
 rotterdam group who discovered the 7q22 locus subsequently examined joint - space width ( jsw ) 
 at the hip in their population cohorts ( ref . a 
 gwas was performed and an association was detected with snp rs12982744 , with a 
 p - value of 1.1    10 . the g - allele of the snp was associated 
 with an increase in jsw and a secondary analysis revealed that this allele also correlated 
 with a reduced risk of hip oa . the p - value for the oa association was more 
 modest than that for jsw , at 1.0    10 , but the principle was clearly 
 established that the use of a proxy phenotype can further our understanding of oa . as the name implies , this 
 enzyme is a histone methyltransferase that methylates lysine-79 of histone h3 . using the 
 mouse atdc5 chondrogenesis model and micromass cultures the investigators demonstrated that 
 knockdown of dot1l leads to reduced proteoglycan and collagen content and 
 that this may be mediated by modulation of the wnt signalling pathway . pain is a symptom of clinical oa and has been considered a logical therapeutic target for 
 oa treatment . however , the current clinical trial data on the use of targeted pain biologics 
 have revealed that adverse events can outweigh any benefits of managing oa pain ( ref . nevertheless , there have been several reports 
 testing for genetic association between known pain loci and oa pain , including to the genes 
 p2rx7 , pace4 and trpv1 ( refs 52 , 53 , 54 ) . in comparison with the oa gwas studies discussed 
 above , the significant p - values obtained were relatively modest . despite 
 this , these studies do support a more comprehensive and powered analysis of the genetics of 
 oa pain . gene expression microarray analyses provide an opportunity to assess which particular 
 pathways are implicated in disease initiation and progression , or in the establishment of a 
 particular cell type . as such they have enhanced our understanding of oa pathogenesis and 
 table 5 provides details of six such recent 
 studies including a summary of their key findings ( refs 55 , 56 , 57 , 58 , 59 , 60 ) . one clear conclusion is that 
 gene expression varies qualitatively and quantitatively between cartilage collected from 
 different skeletal sites , such as the knees and the hips ( refs 57 , 58 ) . this is reminiscent 
 of the genetic discovery discussed earlier of oa risk alleles rarely being systemic in their 
 effects and often showing joint - specific effects . the microarrays have also highlighted 
 genes that show significant up- or down - regulation in oa and several of the genes from 
 within the arcogen signals are among these , including col12a1 , 
 myo6 , chst11 and pappa . in the future , 
 rna sequencing ( rnaseq ) will supersede microarrays , as it offers a number of advantages 
 including the ability to discover novel transcripts and alternative splice forms ( refs 61 , 62 ) . a 
 natural progression from gene expression is proteomic analysis but this is only now 
 receiving the detailed and comprehensive attention that it deserves . investigators have , for 
 example , characterised the protein profiles in the joint tissues and fluids of oa patients 
 and then compared these with the profiles from healthy groups and from patients with a 
 different joint disease , such as rheumatoid arthritis ( refs 63 , 64 ) . the aim has been to enlighten our understanding of the pathophysiology of the 
 disease and to assist in the identity of biomarkers that may be used to assess disease 
 status and disease progression ( ref . it is 
 clear from these studies that there are significant differences between the oa and the 
 non - oa proteome profiles and that some of the protein differences are detectable in 
 accessible fluids such as urine , which makes their use in future clinical trials of oa 
 therapeutics a realistic possibility . table 5.recent global gene - expression microarray studies relevant to human osteoarthritis 
 ( oa)joint or cell typekey findingsrefsknee cartilagediseased and nondiseased knee cartilage from the same 
 donors demonstrates significant differences in the expression of a range of 
 genes , including wisp1 and igfbp3.whether this 
 reflects a causal role in oa or is instead a consequence of the disease was not 
 determined 
 55 
 trabecular bone from the iliac crestthe gene profile of iliac crest from oa patients is 
 significantly different from the gene profile of iliac crest from younger non - oa 
 patients and from older non - oa patients , particularly for genes coding for 
 proteins regulating bone , implying a systemic bone phenotype related to oa 
 56 
 knee cartilagethe gene profile of knee cartilage from patients with 
 knee oa is significantly different from that of knee cartilage from patients 
 without knee oa . genes that showed differential expression included those coding 
 for proteins involved in bone formation , in the synthesis of collagens , 
 cytokines and growth factors 
 57 
 hip cartilagethe gene profile of hip cartilage from patients with 
 hip oa is significantly different to that of hip cartilage from patients without 
 hip oa . gene expression in oa hip cartilage demonstrates a number of pathway 
 overlaps with that of oa knee cartilage but also a striking number of 
 differences , implying major aetiological variability between oa at the two sites 
 58 
 cultured fibroblasts from knee synovial tissuecompared with fibroblasts from the synovia of healthy 
 knees , gene expression in oa fibroblasts clustered tightly and has an expression 
 profile significantly distinct from healthy and from rheumatoid arthritis 
 fibroblasts 
 59 
 cartilage and growth platea comparison of gene expression between the 
 growth - plate and articular cartilage of healthy adolescent donors identified the 
 wnt pathway and several downstream target genes as brakes on chondrocyte 
 hypertrophy , which is a known key step in oa progression 
 60 
  recent global gene - expression microarray studies relevant to human osteoarthritis 
 ( oa ) as noted earlier , epigenetics contributes to oa pathogenesis as a regulator of gene 
 expression irrespective of genotype and as a modulator of genetic risk ( refs 38 , 39 , 40 ) . much more work , however , needs to be performed 
 before we get even a vague understanding of the actual impact of epigenetics on the disease . careful decisions will have to be made between which tissues to analyse and although 
 cartilage is an obvious priority tissue , it is clear that all joint tissues have to be 
 considered . the developmental time points studied will also be critical since epigenetic 
 events are likely to be temporally regulated . the type of epigenetic mark is also an issue , 
 with dna cpg methylation and micrornas amenable to relatively high - throughput analyses 
 whereas histone modifications currently are not . ultimately the goal of all such genetic , transcriptomic and epigenetic datasets will be 
 their integration to identify the regulatory pathways and networks that are definitive of 
 and causal to the disease ( ref . at that point 
 we may be in a position to use our genetic insights for informed development of new 
 biological treatments for oa .
recent genome - wide association scans ( gwass ) along with several adequately powered 
 candidate gene studies have yielded a number of risk alleles for osteoarthritis ( oa ) . 
 this 
 number is now sufficiently large to allow conclusions to be drawn regarding the nature of 
 genetic susceptibility , including the fact that the risk alleles have variable effects 
 depending on sex , ethnicity and on the skeletal site of the disease . 
 several of the 
 alleles that have emerged from the gwass are within or close to highly plausible candidate 
 genes , including runx2 and chst11 . 
 however , the majority 
 of risk alleles do not map to genes previously reported to play a role in musculoskeletal 
 biology , indicating that the gwas datasets are telling us something new about the oa 
 disease process . 
 functional studies have so far revealed that effects on gene expression 
 are likely to be one of the main mechanisms through which oa susceptibility is acting . 
 epigenetic mechanisms such as dna methylation also influence oa risk , and integration of 
 genetic , transcriptomic and epigenetic data will allow us to use the genetic discoveries 
 for informed development of new oa biological treatments .