Association between a variation in LRCH1 and knee osteoarthritis: A genome‐wide single‐nucleotide polymorphism association study using DNA pooling

Abstract

Objective. To perform a large-scale association analysis of single-nucleotide polymorphisms (SNPs) in patients with radiographically defined osteoarthritis (OA) of the knee.Methods. We examined >25,000 SNPs located within ϳ14,000 genes for associations with radiographically defined knee OA, using polymerase chain reaction and MassExtend amplification techniques. Allele frequencies were estimated initially in DNA pools from 335 female patients with knee OA and 335 asymptomatic and radiographically negative female control subjects. All were of northern European ancestry. Significant allele frequency differences were validated by genotyping of individual DNA samples. Confirmed significant findings were verified in 2 additional case-control samples from the UK (443 cases and 303 controls) and Newfoundland (346 cases and 264 controls). Chondrosarcoma cell lines were used to test for potential differences in gene expression.Results. The marker most strongly associated with the risk of knee OA was rs912428, a C/T polymorphism in intron 1 of LRCH1, a gene on chromosome 13q14 that encodes a novel protein of as-yet-unknown function. The frequency of the T allele compared with controls was consistently increased by 40% across all 3 case-control groups. Additional subanalyses in casecontrol samples with hip OA and hand OA suggested similar trends, but did not reach statistical significance. Association fine-mapping using 10 additional SNPs in LRCH1 confirmed intron 1 as the region of highest association but failed to reveal variations with significance stronger than the marker SNP, as did the haplotype analysis. LRCH1 was not up-regulated or overexpressed in chondrosarcoma cell lines exposed to inflammatory stimuli, suggesting a possible structural role.Conclusion. A genetic variant in LRCH1 was consistently associated with knee OA in 3 samples from 2 populations. Our results also suggest that the same association with OA may exist at other sites. Additional genetic and experimental work is needed to elucidate the precise mechanism by which the LRCH1 gene influences OA risk.Osteoarthritis (OA) is a degenerative joint disease that primarily affects the knees, hips, hands, and spine (1). The biology and epidemiology of OA seem to differ between sites, with a different balance of risk factors and age at onset for different sites. For genetic purposes, site-specific classification is likely to be important, with differential linkage and association results for the hip and the spine (2).

Lack of association of single nucleotide polymorphism in LRCH1 with knee osteoarthritis susceptibility

“…Sample size was not the explanation for the discrepancy, either. The sample size of the Chinese population was comparable with previous studies (Spector et al 2006), and that of Japanese population was much larger. Therefore, our results were much more powerful to detect an effect on OA susceptibility of the SNP.…”

“…Significant differences in distribution of genotype and allele frequencies were detected between Han Chinese and UK Caucasians (both P \ 0.000001) (Snelling et al 2007). As in the European populations previously reported (Spector et al 2006;Snelling et al 2007), the most common genotype was CC in both patients and controls. The genotype frequency of CC in Han Chinese was similar to that in Japanese and much higher than that in European Caucasians.…”

“…By scanning more than 25,000 single nucleotide polymorphisms (SNPs), Spector et al (2006) detected a sound association with knee OA and a C/T transition SNP (rs912428) located in intron 1 of the LRCH1 gene that encodes a novel protein of as-yet-unknown function. Combined with UK and Newfoundland OA cases, they show a positive association of the T allele of the SNP was a risk factor for knee OA in both genders after stratification.…”

“…To integrate the previous contradicting studies (Spector et al 2006;Snelling et al 2007) and evaluate the global significance of the association, we performed a meta-analysis for all the association studies. We did not detect association between LRCH1 and knee OA.…”

When is a replication not a replication? Or how to spot a good genetic association study

“…This point takes on even more importance when designing a replication study around genome-wide association studies, such as one by our group (10), in which 25,000 "random" SNPs were tested in a DNA pooling analysis. After an initial replication, the association of the gene LRCH1 with knee OA was replicated in 2 separate populations.…”