Genome-wide linkage analysis of quantitative biomarker traits of osteoarthritis in a large, multigenerational extended family

Abstract

Objective

The genetic contributions to the multifactorial disorder osteoarthritis (OA) have been increasingly recognized. The goal of the current study was to use OA-related biomarkers of severity and disease burden as quantitative traits to identify genetic susceptibility loci for OA.

Methods

In a large multigenerational extended family (n = 350), we measured 5 OA-related biomarkers: hyaluronan (HA), cartilage oligomeric matrix protein (COMP), N-propeptide of type IIA collagen (PIIANP), C-propeptide of type II procollagen (CPII), and type II collagen neoepitope (C2C). Single-nucleotide polymorphism markers (n = 6,090) covering the whole genome were genotyped using the Illumina HumanLinkage-12 BeadChip. Variance components analysis, as implemented in the Sequential Oligogenic Linkage Analysis Routines, was used to estimate heritabilities of the quantitative traits and to calculate 2-point and multipoint logarithm of odds (LOD) scores using a polygenic model.

Results

After adjusting for age and sex, we found that 4 of the 5 biomarkers exhibited significant heritability (PIIANP 0.57, HA 0.49, COMP 0.43, C2C 0.30; P ≤ 0.01 for all). Fourteen of the 19 loci that had multipoint LOD scores of >1.5 were near to or overlapped with previously reported OA susceptibility loci. Four of these loci were identified by more than 1 biomarker. The maximum multipoint LOD scores for the heritable quantitative biomarker traits were 4.3 for PIIANP (chromosome 8p23.2), 3.2 for COMP (chromosome 8q11.1), 2.0 for HA (chromosome 6q16.3), and 2.0 for C2C (chromosome 5q31.2).

Conclusion

Herein, we report the first evidence of genetic susceptibility loci identified by OA-related biomarkers in an extended family. Our results demonstrate that serum concentrations of PIIANP, HA, COMP, and C2C have substantial heritable components, and using these biomarkers, several genetic loci potentially contributing to the genetic diversity of OA were identified.

Osteoarthritis (OA) is the most common joint disorder worldwide and the most common cause of disability in Western countries, with significant socioeconomic consequences (1). Although many studies have shown that OA has a strong genetic component (2–4), with an estimated heritability ranging from 39% to 74% based on the pattern of joint involvement (5), the genetic and phenotypic heterogeneity of OA presents challenges in the ongoing attempt to identify the genetic contributions to this complex disease (6). Over the last decade, the whole-genome linkage scan approach has led to the mapping of a number of susceptibility loci for OA. These findings were all based on phenotyping using radiography, clinical examination, or clinical history (total joint replacement) (7–15). However, the hallmark of OA is cartilage loss; reflected on radiographs as the joint space width, it is a fairly late stage manifestation of disease with poor sensitivity for detecting OA initiation (16).

An alternative approach, the use of intermediate biomarker traits, has been used successfully in genetic analyses of other diseases (anti–cyclic citrullinated peptide in a study of rheumatoid arthritis [17] and YKL-40 in a study of asthma [18]), but never in OA. Use of existing OA-related biomarkers has the potential to detect disease earlier than is possible using radiography (19), and to reflect not only OA severity but also the total-body burden of disease (20). Moreover, OA is clearly not only a cartilage disorder (21, 22) but rather a disease of the whole joint organ consisting of cartilage, bone, synovium, meniscus, and tendon.

We hypothesized that, using biomarkers representing OA endophenotypes, we could replicate known OA susceptibility genes and identify additional OA-related genes and shared genetic determinants through monitoring of the turnover of the whole joint organ, thereby potentially providing data that could augment existing knowledge of OA etiologic pathways and progression. Based on the strength of previous validation evidence (23), in this study, we chose to analyze 5 serum OA-related biomarkers: hyaluronan (HA), cartilage oligomeric matrix protein (COMP), N-propeptide of type IIA collagen (PIIANP), C-propeptide of type II procollagen (CPII), and type II collagen neoepitope (C2C). Each of these markers has data to support its classification (24, 25) in at least 2 categories of the BIPED (Burden of disease, Investigative, Prognostic, Efficacy of intervention, and Diagnostic) (26) biomarker classification system, as follows: for HA, categories B and P; for COMP, categories B, P, and D; for PIIANP, categories B, P, and D; for CPII, categories P, E, and D; and for C2C, categories P, E, and D.

For these analyses, we studied a unique extended family, the CARRIAGE (Carolinas Region Interaction of Aging, Genes and Environment) family. The CARRIAGE family is one of the most extensively pedigreed existing families in the US and comprises 10 generations with 3,327 pedigreed members originating from 1 founder born in the 1700s. The ethnic origin of this family is primarily African American and American Indian. Because of reduced genetic heterogeneity and confounding by population stratification, linkage analysis of this single-founder lineage provides many advantages for mapping complex traits (27). This family was selected for study because of its size and strong genealogical records and not because of the presence of a particular condition or disease, including OA. Nevertheless, as we have previously reported (28), this cohort has exhibited a prevalence of clinical hand OA of 17% and clinical knee OA of 30%, as determined using the criteria of the American College of Rheumatology (29, 30). The prevalence of knee OA is modestly elevated compared with that in a Dutch population, but the prevalence of hand OA is consistent with estimates for individuals of a mean age of 55 years (the mean age of the ascertained CARRIAGE family members) (31). We have also observed an association of hand OA phenotypes in this cohort with serum OA-related biomarkers (32). Herein, we report the first evidence of genetic linkage in OA using these biomarker traits in this large extended family.

PATIENTS AND METHODS

Family cohort.

Pedigree data on the CARRIAGE family were obtained from 3 sources: a book detailing the genealogy of the descendents of the forefather, family history questionnaires distributed by mail and completed during 3 family reunions over 4 years (2002 and 2004–2006), and genealogical data collected by a family member. These data were combined for genetic database and pedigree management using Progeny software (online at www.progenygenetics.com). We were able to successfully document 3,327 family members from 9 generations, with 2,795 family members completely connected to the original founder. This family came to be studied in the context of health fairs conducted at several large family reunions. Detailed ascertainment of 350 family members (mean age 54 years) was accomplished during 3 family reunions, and further details have been previously reported (28, 32). Written informed consent was obtained from each participant, and the study was approved by the Duke Institutional Review Board. All information and work was conducted under a Federal Certificate of Confidentiality to ensure the privacy of each participating member's clinical and genetic data.

Analysis of serum biomarkers related to OA.

Serum was isolated, aliquoted, and stored within 4 hours of collection at −80°C until biomarker analyses were performed. Serum biomarker analyses were repeated as necessary for samples with a >15% coefficient of variation (CV). We measured 5 OA-related serum biomarkers: 2 type II collagen biomarkers (PIIANP, CPII) indicative of collagen synthesis, a type II collagen biomarker (C2C) indicative of collagen degradation, a glycoprotein biomarker (COMP) originating from cartilage, synovium, and tendon, which is associated with spine and knee OA (33) and impacted by synovitis (33, 34), and a high molecular weight polysaccharide (HA), which is an excellent indicator of the total-body burden of OA, particularly osteophyte (20). When serum from a given individual was collected at more than 1 family reunion, the most recent sample was used.

PIIANP, a marker of a fetal form of type II collagen that is recapitulated in OA, was measured by competitive enzyme-linked immunosorbent assay (ELISA; Linco Research, St. Charles, MO). The minimum detection limit is 17.2 ng/ml, and intraassay and interassay CVs were <6.6% and <7.8%, respectively. Competitive ELISAs (Ibex, Montreal, Quebec, Canada) were also used to measure CPII, which is a marker of the adult form of type II collagen synthesis, and C2C. For CPII, the minimum detection limit is estimated to be 35.1 ng/ml, and intraassay and interassay CVs were <3.7% and <9.1%, respectively. For C2C, the minimum detection limit is reported to be 7.3 ng/ml, and intraassay and interassay CVs were <2.4% and <9.5%, respectively. COMP was measured by an in-house sandwich ELISA, as previously described (35, 36), using monoclonal antibodies 17-C10 (epitope in the epidermal growth factor–like domain) and 16F12 (epitope in the NH2-terminal domain) against human COMP (37). The minimum detection limit is 120 ng/ml, and intraassay and interassay CVs were <5.8% and <8.7%, respectively. HA was measured by enzyme-linked binding protein assay (Corgenix, Westminster, CO). The assay uses enzyme-conjugated hyaluronic acid binding protein from bovine cartilage to specifically capture HA from human serum. The minimum detection limit is established at 10 ng/ml, and intraassay and interassay CVs were <4.7% and <7.0%, respectively.

DNA isolation and quality control.

DNA was isolated from buffy coat (derived from 5 ml fresh EDTA blood) (n = 347) or from saliva (4 ml) (n = 3). Saliva samples were obtained by mail when available blood was insufficient for DNA isolation but sufficient for serum biomarker analyses. DNA was extracted from blood and saliva using the Puregene DNA Purification Kit according to the instructions of the manufacturer (Gentra Systems, Minneapolis, MN). DNA concentration was quantified by NanoDrop spectrophotometry (Thermo Scientific, Wilmington, DE). DNA quality was verified on 0.8% agarose gels (0.8 gm SeaKem, 5 μl ethidium bromide in 100 ml 1× Tris–acetate–EDTA buffer) run at 90V for 1 hour using 0.5-μl aliquots of each sample. A Hind III digest of λ DNA (catalog no. N3012S; New England Biolabs, Ipswich, MA) was used as a reference ladder. DNA was scored 0–5, with a score of ≥4 indicating that a single high molecular weight DNA band was clearly visible and a score of <4 indicating that DNA degradation had occurred and the single high molecular band was accompanied by a visible smear of smaller fragments. Samples with a score of ≥4 (n = 349) were used for whole-genome genetic mapping assays.

Whole-genome genotyping.

Whole-genome genotyping by fluorescence-based methods was performed using the Infinium HumanLinkage-12 Genotyping BeadChip (Illumina, San Diego, CA). The BeadChip included 6,090 single-nucleotide polymorphism (SNP) markers with an average spacing of 0.58 cM across the genome. Two blinded samplings of controls from the Centre d'Etude du Polymorphisme Humain were genotyped for each plate as quality controls to ensure accuracy for these assays. The genotype assignments were determined with BeadStudio genotyping module software (Illumina). A total of 6,015 of the 6,090 SNPs (98.8%) met quality control benchmarks for the accuracy of genotype assignments based on the duplicated genotypes and for genotyping efficiency based on proportion of samples with high-quality genotypes. Two blood-derived DNA samples were not included in the analysis because of low call rate (0.961–0.971). There was no difference in the success of genotyping DNA derived from saliva and blood. The 3 saliva-derived DNA samples had high call rates (average call rate 0.998), which did not differ from the call rates of the 345 blood-derived samples (average call rate 0.999). The distance from the telomere was estimated using a map by deCODE Genetics (Reykjavik, Iceland).

Statistical analysis.

Variance components analysis implemented in the Sequential Oligogenic Linkage Analysis Routines (SOLAR; Southwest Foundation for Biomedical Research/National Institutes of Health, San Antonio, TX) (38) was used for linkage analysis. Heritability (H²r) was estimated by fitting a polygenic variance components model as implemented in SOLAR. Both 2-point and multipoint genome-wide linkage scans using 5 OA-related biomarkers as quantitative traits were performed. Linkage between each of the biomarker traits and marker loci was tested by maximum-likelihood methods, as recommended for multigenerational pedigrees, adjusted by age and sex, and according to the concepts of the variance components approach (39).

The variance component method partitions each biomarker trait into unobserved quantitative trait loci (QTL), residual additive genetic components, and residual nongenetic components. The phenotypic variance–covariance matrix consists of parameters of the kinship coefficient and the identity-by-descent (IBD) probability at a given marker locus between each pair of individuals (40). Due to the complexity of the CARRIAGE pedigree, the IBD probabilities were computed using the Markov chain Monte Carlo algorithm as implemented in the Loki linkage analysis package (41). The Loki IBD files were converted into SOLAR format for subsequent linkage analysis of the full pedigree. The whole-genome linkage used IBD values calculated for 6,015 SNP markers. Biomarker data on all family members (including unaffected members) were included in the QTL analysis with the exception of 7 participants; 2 had known rheumatoid arthritis and were excluded to avoid confounding by other forms of arthritis, and 5 were younger than 25 years of age and were excluded to avoid confounding by high cartilage biomarker concentrations due to cartilage growth plate turnover from skeletal immaturity. Concentrations of OA biomarkers were logarithmically transformed to achieve a normal distribution for SOLAR analyses. For those biomarkers with residual kurtosis >1 (CPII, HA), outliers that exceeded 3 standard deviations from the mean were removed. The resulting residual kurtosis for each biomarker was <0.7. Due to low trait standard deviations, the values for CPII, C2C, and COMP were multiplied by a scaling factor (2.6, 3.8, and 2.4, respectively) to increase the standard deviation above 0.5. The polygenic model that the QTL was built upon was adjusted for age and sex. For all biomarkers, linkage was considered significant if the logarithm of odds (LOD) score equaled or exceeded 3.0. LOD scores of ≥1.5, which are suggestive of linkage, are also reported (12).

RESULTS

Heritability of biomarkers.

Ascertainment was available to anyone attending any of the CARRIAGE family reunions, and serum biomarker analysis and genotyping were performed on all individuals for whom we had biologic samples. Therefore, there was no selection for individuals with OA. Heritability estimates, which reflect effect sizes, were adjusted for age and sex for each OA-related biomarker. After removing the outliers, biomarker and genetic marker data were available on 333 family members for COMP, PIIANP, and C2C, 330 family members for CPII, and 327 family members for HA. The highest residual heritability (after adjusting for age and sex) was observed for PIIANP (57%), followed by HA (49%), COMP (43%), and C2C (30%) (P ≤ 0.01 for all); however, CPII was not significantly heritable (3%) (Table 1). The 4 significantly heritable biomarker traits were used subsequently as quantitative traits in genome-wide linkage analyses using 2-point and multipoint models.

Table 1. Heritability of OA-related serum biomarker quantitative traits*

OA endophenotype (no. of samples analyzed)	Concentration, mean ± SD ln ng/ml†	H^2‡	P
* Heritability (H^2) and P values were calculated using Sequential Oligogenic Linkage Analysis Routines. OA = osteoarthritis; COMP = cartilage oligomeric matrix protein; HA = hyaluronan; PIIANP = N-propeptide of type IIA collagen; CPII = C-propeptide of type II procollagen; C2C = type II collagen neoepitope. † Concentrations were reported in ng/ml prior to natural log transformation. ‡ Adjusted for age and sex.
COMP (333)	7.39 ± 0.45	0.43	0.001
HA (327)	3.60 ± 0.86	0.49	0.001
PIIANP (333)	7.17 ± 0.52	0.57	<0.001
CPII (330)	7.06 ± 0.37	0.03	0.4
C2C (333)	5.35 ± 0.27	0.30	0.01

Genome-wide linkage analyses.

Two-point linkage analysis.

A total of 39 markers with LOD scores of >1.5 were identified by 2-point linkage analysis (Table 2). One marker had a LOD score of >3. The maximum LOD score (3.1) was observed at rs2780701 (chromosome 9q22.2) for PIIANP. The next highest LOD score (2.7) was observed at rs1563796 (chromosome 4q13.1) for PIIANP. For COMP and HA, the maximum LOD scores were 2.23 at rs221924 (chromosome 14q24.2) and 1.79 at rs1020782 (chromosome 1q25.3), respectively. No LOD scores of >1.5 were observed for C2C.

Table 2. SNPs showing evidence for linkage in the CARRIAGE family*

OA endophenotype, chromosome, location	Genetic marker	Peak LOD	Previously reported OA candidate genes near these regions†
* Linkage was defined as a logarithm of odds (LOD) score of ≥1.5, by 2-point linkage analysis. Significant linkage was defined as an LOD score of ≥3. SNPs = single-nucleotide polymorphisms; CARRIAGE = Carolinas Region Interaction of Aging, Genes and Environment (see Table 1 for other definitions). † Previously reported OA candidate genes are <10 cM from the SNP (50–53).
PIIANP
1,133.27 cM	rs1246194	1.79	COL11A1
2,167.91 cM	rs964176	1.58	TNFAIP6, FAP
4
34.5 cM	rs1325107	1.73	SOD3
53.76 cM	rs10023150	1.71	SOD3
76.25 cM	rs1563796	2.65	IGFBP7, ADAMTS3
7
98.06 cM	rs473880	1.56	CD36
179.01 cM	rs6953751	1.88	–
8
1.69 cM	rs763869	1.70	–
2.4 cM	rs4242539	1.66	–
7.79 cM	rs3849827	1.82	–
9
88.03 cM	rs729958	2.52	CTSL, ASPN, OGN
94.51 cM	rs2780701	3.09	CTSL, ASPN, OGN
95.55 cM	rs1316268	1.72	CTSL, ASPN, OGN
100.39 cM	rs6478437	1.67	CTSL, ASPN, OGN
127.84 cM	rs1013324	1.70	EDG2
128.7 cM	rs4679	1.93	–
128.74 cM	rs1571586	2.23	–
136.55 cM	rs913275	1.86	–
138.31 cM	rs1220789	1.65	–
154.29 cM	rs2989726	1.86	–
14, 52.37 cM	rs1950209	1.55	ESR2
15, 132.59 cM	rs2949	1.78	AGC1
16
38.48 cM	rs1389504	1.58	IL4R
41.19 cM	rs724307	1.62	IL4R
57.05 cM	rs1843609	1.75	IL4R
57.1 cM	rs11647994	1.59	IL4R
57.85 cM	rs17734120	1.63	–
17
10.04 cM	rs149245	1.76	–
15.04 cM	rs7221818	1.76	–
33.94 cM	rs2240519	1.56	–
COMP
14, 69.55 cM	rs221924	2.23	ESR2, DIO2
16, 14.53 cM	rs1035564	1.56	–
18, 40.13 cM	rs1893495	2.22	–
HA
1, 181.52 cM	rs1020782	1.79	PTGS2, PLA2G4A
6
64.36 cM	rs722269	1.76	IL17A, IL17F, COL11A2, HLA
101.6 cM	rs1133503	1.63	–
146.82 cM	rs583341	1.54	ESR1
8, 132.31 cM	rs7814955	1.61	TNFRSF11B
19, 63.42 cM	rs4805201	1.56	TGFB1

Multipoint linkage analysis.

Results of multipoint analysis of the genome-wide linkage scan are plotted separately for the 4 highly heritable OA-related biomarkers (Figure 1). A total of 23 loci (from 19 separate nonoverlapping regions) with LOD scores of >1.5 were identified (Table 3). Two significant linkage peaks (LOD score of >3) were observed for chromosome 8, with PIIANP and COMP as quantitative traits (Figure 2A). The highest LOD score (4.33) was observed for PIIANP, yielding linkage to chromosome 8p23.2 (near marker rs3849827). The next highest LOD score (3.18) was observed for COMP, yielding linkage to chromosome 8q11.1 (near marker rs7826304). Another high LOD score (2.5) was observed for COMP, yielding linkage to chromosome 8q24.2 at 149 cM (near marker rs2282).

Figure 1. Quantitative trait loci mapping in 22 chromosomes of the 4 highly heritable osteoarthritis-related biomarkers. A, N-propeptide of type IIA collagen (PIIANP). B, Cartilage oligomeric matrix protein (COMP). C, Hyaluronan (HA). D, Type II collagen neoepitope (C2C). Multipoint logarithm of odds (LOD) scores are shown. LOD scores of ≥3.0 represent significant linkage, while scores of ≥1.5 are suggestive of linkage. Panels were generated using Haploview software.

Table 3. Regions of linkage to quantitative traits in the CARRIAGE family and previously reported OA associations that overlap these regions*

OA endophenotype, chromosome	Multipoint LOD	Location of peak LOD score, cM	1-LOD interval, cM	Overlapping biomarkers	Previously reported OA candidate genes in these regions (cM from peak)†	Previously reported OA linkages overlapping these regions
						OA phenotype	Peak LOD	Distance, cM	Population	Ref.
* Linkage was defined as a logarithm of odds (LOD) score of ≥1.5, by multipoint linkage analysis. Significant linkage was defined as an LOD score of ≥3. CARRIAGE = Carolinas Region Interaction of Aging, Genes and Environment; JSN = joint space narrowing; JSN-sum = sum of JSN scores; U-DIP joint = unaffected distal interphalangeal joint; U-JSN = unaffected JSN; OST = osteophyte; K/L scale sum = sum of Kellgren/Lawrence scale scores; U-OST = unaffected OST (see Table 1 for other definitions). † All candidate genes are <10 cM from the border of the 1-LOD drop support interval, with 2 exceptions. The KL locus is ∼31.4 cM from the HA chromosome 13 peak and the 1-LOD interval is 5–11 cM, but this candidate gene has been retained in the list because it is <10 cM from the 1-LOD drop interval for the C2C chromosome 13 peak (41–51 cM). The HLADRB4 locus is 7.8 cM from the PIIANP chromosome 6 peak, but the candidate gene has been retained in the list because it is <10 cM from the HA chromosome 6 peak.
PIIANP
6	2.25	50	47–52	HA	HFE (0.1), HLADRB4 (13.8), TNF (1.3), COL11A2 (2.4)	Female hip	4.8	53–56	UK	42, 50
7	1.97	98	96–102	–	CD36 (5.4)	–	–	–	–	–
8	4.33	8	5–15	–	–	Hand JSN	1.57	8.3–21.3	UK	13
9	1.85	98	72–108	–	CTSL (9.9), ASPN (2.1), OGN (2.2), LPAR1 (17)	Hand JSN-sum	2.3	76	US	11, 50, 53
13	2.35	50	45–57	C2C	LRCH1 (0.3)	–	–	–	–	–
15	1.63	9	0–14	COMP	–	–	–	–	–	–
COMP
3	1.61	179	173–183	–	–	–	–	–	–	–
5	1.55	127	121–129	–	–	–	–	–	–	–
8	3.18	62	60–70	–	–	Hand U-DIP joint	2.56	41.5–79.4	UK	13
8	2.50	149	145–155	–	WISP1 (4.1)	–	–	–	–	45
14	1.64	40	29–52	–	–	Hand U-DIP joint	1.44	40.5–47.5	UK	13
14	2.57	66	59–82	HA	ESR2 (2.2), DIO2 (14.7), FLRT2 (17.7), GPX2 (1.7), CALM1 (26.5)	Hand U-JSN	2.64	48–57	UK	13, 51, 54
15	1.60	6	2–20	PIIANP	–	–	–	–	–	–
16	1.51	50	45–68	–	IL4R (3.5)	Early-onset hip	2.6	28–47	Iceland	55
						Female hip	1.7	46	UK	14
						Hand U-JSN	2.64	48.5–57.8	UK	13
18	1.82	39	36–49	–	–	–	–	–	–	–
18	1.81	72	65–91	–	–	Hand osteophyte	1.34	71–85	UK	13
						Knee OA	2.41	60.1–86.1	US/UK	56
C2C
5	1.98	139	133–144	–	SLC26A2 (14.8)	–	–	–	–	57
13	1.51	45	41–51	PIIANP	LRCHI (5.3), KL (13.6)	Hand OST	1.28	17.2–25.1	UK	13
						Hand K/L scale sum	1.6	36	US	11
21	1.52	15	6–22	–	–	–	–	–	–	–
HA
6	1.69	44	38–48	PIIANP	HLADRB4 (7.8), HFE (5.9), COL11A2 (8.4), TNXB (7.6)	Female hip	4.8	53–56	UK	42
6	1.96	104	100–108	–	COL10A1 (14.2)	Hand U-OST	1.11	82.6–109.9	The Netherlands	10
13	1.83	7	5–11	–	KL (24.4)	–	–	–	–	–
14	1.57	63	60–67	COMP	ESR2 (0.8), GPX2 (1.2)	Hand U-JSN	2.64	48–57	UK	13

Figure 2. Potential osteoarthritis (OA) candidate genes on chromosomes 8 (A), 6 (B), and 14 (C). Gene names shown in boldface over the peaks represent potential novel candidate genes associated with biomarkers of OA in the current study that, according to the literature, have potential biologic relevance for OA. Genes not shown in boldface represent candidate genes linked to OA in previous studies. # indicates that the genes are <10 cM from the border of the 1-LOD drop support interval. See Figure 1 for other definitions.

Chromosome 6 was notable for overlapping regions of linkage (LOD scores of 1.69–2.25) in the interval 38–52 cM, observed for PIIANP and HA (Figure 2B). This region corresponds to linkage reported in a female UK cohort with hip OA (42). Chromosome 14 was notable for overlapping regions of linkage (LOD scores of 1.57–2.57) in the interval 59–82 cM, observed for COMP and HA (Figure 2C). This region corresponds to linkage reported in a UK cohort with hand OA (13). Overall, PIIANP yielded 3 overlapping regions with HA, C2C, and COMP on chromosomes 6, 13, and 15, respectively. For HA and C2C, the highest LOD scores were observed for additional regions on chromosomes 6q16.3 (LOD score of 1.96, observed for HA) and 5q31.2 (LOD score of 1.98, observed for C2C). In addition to identifying previously reported OA candidate genes within or near our linkage peaks on chromosomes 6, 8, and 14, we also list potential candidates based on their biologic relevance (Figures 2A–C).

DISCUSSION

The current study represents the first linkage study to identify genetic loci associated with OA using biologic markers. In 5 previous genome-wide linkage studies, OA phenotypes were uniformly defined using radiographic evidence, physical examination, or joint replacement, which detect late stages of OA (7–13). There have been few studies investigating the heritability of OA biomarkers. In previous studies of twins and sibling pairs, the heritability of COMP and PIIANP was significant (40–70% and 62%, respectively) (43, 44). To our knowledge, the heritability of serum HA, C2C, and CPII has not been assessed previously. The genetic components in the earlier studies were consistent with our findings, despite differences in the race of study subjects and in study design (43, 44). The genetic influence on OA-related biomarker levels may operate through allelic variation or factors regulating expression of the gene encoding the biomarker protein or through effects on biologic pathways influencing cartilage metabolism and degradation (43). The latter appears most likely, given that the significant linkage regions did not contain the genes encoding the biomarker used for the linkage.

The validity of our overall strategy was borne out by our replication of several previously reported genetic associations with OA identified by other means of phenotyping (Table 3). Overall, we identified 14 regions of linkage to OA-related quantitative traits that overlap or are near (within 10 cM) regions reported in the current literature to have a genetic association with OA. By 2-point linkage, the maximum LOD score (3.1), observed for PIIANP, is within 2 Mb of the asporin gene (ASPN) and within 3 Mb of the cathepsin L gene (CTSL) and the osteoglycin gene (OGN). The next highest LOD score (2.7), also observed for PIIANP, is close to the insulin-like growth factor binding protein 7 (IGFBP7) and ADAMTS3 genes. The maximum LOD scores observed for COMP (2.23) and HA (1.79) are close to the type II deiodinase iodothyronine gene (DIO2) (<10 Mb away) and the prostaglandin-endoperoxide synthase 2 gene (PTGS2) (<5 Mb away), respectively.

In addition, this study provides evidence of 2 novel OA loci on chromosome 8, based on PIIANP and COMP quantitative traits (PIIANP on chromosome 8p23.2 and COMP on chromosome 8q11.1). Suggestive linkage (LOD scores of 1.57 and 2.56) overlapping 2 of these regions has been reported previously by Greig et al based on hand radiographic phenotypes (13), but candidate genes have yet to be identified for these regions. The COMP linkage to chromosome 8q24.2 at 149 cM overlaps a region of linkage previously reported in the Wnt-1–induced secreted protein 1 (WISP1) based on a spinal OA radiographic phenotype in postmenopausal Japanese women (45). The signals observed for the top genomic loci by multipoint analysis (the PIIANP chromosome 8p23.2 QTL, the COMP chromosome 8q11.1 QTL, and the HA chromosome 6q16.3 QTL) were also observed in the 2-point analysis.

Several of the OA-associated loci identified in this study were detected by more than 1 biomarker trait. This supports our hypothesis that a panel of biomarkers could identify shared genetic determinants. Loci identified by more than 1 OA-related biomarker may be of particular interest in future studies since these loci are less likely to represent false-positives and are more likely to represent genes regulating the whole joint organ. We are aware that linkage disequilibrium (LD) can inflate multipoint LOD scores. However, the genotyping platform used was optimized for minimal LD. Inflation of LOD scores due to LD occurs only when there are missing parental genotypes (46). In our study, given the multigenerational nature of the family pedigree, a large number of parental genotypes were included (22 children had both parents genotyped, 73 children had 1 parent genotyped). Using our own study data (examining LD between available married-in unrelated individuals), there was no significant LD (defined as r² > 0.4) between SNPs in the top QTL. Taken together, these data suggest the LD between markers will have minimum impact on the LOD scores reported here.

Of note, we did not observe significant or suggestive linkage peaks covering several genes with known OA association, including frizzled-related protein β (FRZB), growth differentiation factor 5 (GDF5), and von Willebrand factor A domains (DVWA); this may be due to the lack of SNP markers covering these genes in the Infinium HumanLinkage-12 Genotyping BeadChip (Illumina). All 3 of these proteins are related to skeletal morphogenesis and bone morphogenetic cell signaling (15, 47, 48). Our biomarker panel did not include a primary bone marker and so may have failed to account for the metabolic pathways impacted by these genes. These seminal studies (15, 47, 48) were performed using Caucasian or Asian populations, while our study was performed using individuals of mixed African American and American Indian heritage; thus, ethnic variation in genetic etiologies of OA may in part account for the failure to detect these loci in our cohort. Statistical power may also be an issue, as these 3 studies included between 1,696 and 4,361 individuals. Finally, our study was conducted in 1 large extended family, and it would not be reasonable to expect that every possible genetic etiology of OA would be reflected in this 1 family.

A strength of this study is that it is based on data from a large extended family with a pedigree spanning 300 years and 10 generations from a single founder. Statistical power can be increased by the use of biomarkers as quantitative traits (49). Increased statistical power may also come from minimizing genetic variability by studying a cohort originating from a single founder. This family was not ascertained based on having a large number of OA cases and, therefore, was also not ascertained to determine the presence of OA biomarkers, providing an opportunity to perform an unbiased linkage analysis of the biomarker levels. Thus, the strengths of this study stem from the detailed biomarker analysis in a very large family, randomly selected with respect to OA cases. A limitation of the study, however, was the inability to perform radiographic phenotyping due to the health fair setting in which individuals were ascertained. Nevertheless, our study of biomarker traits led to replication of several loci reported in previous OA genetic studies that used radiographic phenotyping. Also, we have previously shown that several of the OA biomarkers used herein were associated with clinical OA phenotypes in this large multigenerational family (32). In addition, all the biologic markers (PIIANP, COMP, C2C, HA, and CPII) have been associated with OA in other studies (26).

In summary, we report the first evidence for OA linkage obtained using quantitative biomarker traits in a large extended family. We not only replicated several loci reported in previous OA genetic studies, but also identified 2 significant novel loci on chromosome 8. Several of the loci were identified by more than 1 OA-related biomarker. Further study of the candidate genes at these loci may provide new insight into the mechanisms of joint metabolism and OA initiation and progression.

AUTHOR CONTRIBUTIONS

All authors were involved in drafting the article or revising it critically for important intellectual content, and all authors approved the final version to be published. Dr. V. Kraus had full access to all of the data in the study and takes responsibility for the integrity of the data and the accuracy of the data analysis.

Study conception and design. Chen, V. Kraus, Stabler, Hauser, Gregory, W. Kraus, Shah.

Acquisition of data. Chen, V. Kraus, Johnson, Stabler, Gregory, W. Kraus, Shah.

Analysis and interpretation of data. Chen, V. Kraus, Li, Nelson, Haynes, Johnson, Hauser, Gregory, W. Kraus, Shah.

Acknowledgements

We would like to thank the CARRIAGE family members for their participation in this study, Dr. Vladimir Vilim for the kind gift of the 16F12/17-C10 anti-COMP monoclonal antibodies, Norine Hall and Milton Campbell for helping to organize the collection of samples from CARRIAGE family members, and everyone who made the family reunions possible.