Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “SNP analysis”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 415 records · Page 23Linked to original sources
PubMed2004

Human UGT1A6 pharmacogenetics: identification of a novel SNP, characterization of allele frequencies and functional analysis of recombinant allozymes in human liver tissue and in cultured cells.

BACKGROUND: UDP-glucuronosyltransferase (UGT) enzymes catalyze the glucuronidation and typically inactivation of endogenous and exogenous molecules including steroid hormones, bilirubin and many drugs. The UGT1A6 protein is expressed predominantly in liver and metabolizes small phenolic drugs including acetaminophen, salicylates and many beta-blockers. Interindividual variation in the capacity of humans to glucuronidate drugs has been observed. RESULTS: We have identified a novel common single nucleotide polymorphism (SNP) in the human UGT1A6 gene resulting in a Ser7Ala change in encoded amino acid. We have further functionally characterized that polymorphism in the context of two previously reported polymorphisms, Thr181Ala and Arg184Ser. These non-synonymous cSNPs define four common haplotypes. Alleles appear with similar frequencies in Caucasian and African-American populations with distributions adhering to Hardy-Weinberg equilibrium. UGT1A6 genotype, rate of substrate glucuronidation and level of immunoreactive UGT1A6 protein was determined. A 25-fold variation in the rate of substrate glucuronidation and an 85-fold variation in level of immunoreactive protein were measured. Liver tissue samples that were homozygous for UGT1A6*2 exhibited a high rate of glucuronidation relative to tissues with other genotypes. Biochemical kinetic studies of recombinant UGT1A6 expressed in HEK293 cells indicated that the UGT1A6*2 allozyme, expressed homozygously, had almost two-fold greater activity toward p-nitrophenol than UGT1A6*1 and when expressed heterozygously (UGT1A6*1/*2) it was associated with low enzyme activity. CONCLUSIONS: These data suggest that common genetic variation in human UGT1A6 confers functionally significant differences in biochemical phenotype as assessed in human tissue and cultured cells expressing recombinant allozymes. This genetic variation might impact clinical efficacy or toxicity of drugs metabolized by UGT1A6.

Black or African American↗
PubMed2006

Pitfalls of homozygosity mapping: an extended consanguineous Bardet-Biedl syndrome family with two mutant genes (BBS2, BBS10), three mutations, but no triallelism.

The extensive genetic heterogeneity of Bardet-Biedl syndrome (BBS) is documented by the identification, by classical linkage analysis complemented recently by comparative genomic approaches, of nine genes (BBS1-9) that account cumulatively for about 50% of patients. The BBS genes appear implicated in cilia and basal body assembly or function. In order to find new BBS genes, we performed SNP homozygosity mapping analysis in an extended consanguineous family living in a small Lebanese village. This uncovered an unexpectedly complex pattern of mutations, and led us to identify a novel BBS gene (BBS10). In one sibship of the pedigree, a BBS2 homozygous mutation was identified, while in three other sibships, a homozygous missense mutation was identified in a gene encoding a vertebrate-specific chaperonine-like protein (BBS10). The single patient in the last sibship was a compound heterozygote for the above BBS10 mutation and another one in the same gene. Although triallelism (three deleterious alleles in the same patient) has been described in some BBS families, we have to date no evidence that this is the case in the present family. The analysis of this family challenged linkage analysis based on the expectation of a single locus and mutation. The very high informativeness of SNP arrays was instrumental in elucidating this case, which illustrates possible pitfalls of homozygosity mapping in extended families, and that can be explained by the rather high prevalence of heterozygous carriers of BBS mutations (estimated at one in 50 in Europeans).

Adolescent↗
PubMed2006

Impact of the DISC1 Ser704Cys polymorphism on risk for major depression, brain morphology and ERK signaling.

Disrupted-in-schizophrenia 1 (DISC1), identified in a pedigree with a familial psychosis with the chromosome translocation (1:11), is a putative susceptibility gene for psychoses such as schizophrenia and bipolar disorder. Although there are a number of patients with major depressive disorder (MDD) in the family members with the chromosome translocation, the possible association with MDD has not yet been studied. We therefore performed an association study of the DISC1 gene with MDD and schizophrenia. We found that Cys704 allele of the Ser704Cys single-nucleotide polymorphism (SNP) was associated with an increased risk of developing MDD (P=0.005, odds ratio=1.46) and stronger evidence for association in a multi-marker haplotype analysis containing this SNP (P=0.002). We also explored possible impact of Ser704Cys on brain morphology in healthy volunteers using MR imaging. We found a reduction in gray matter volume in cingulate cortex and a decreased fractional anisotropy in prefrontal white matter of individuals carrying the Cys704 allele compared with Ser/Ser704 subjects. In primary neuronal culture, knockdown of endogenous DISC1 protein by small interfering RNA resulted in the suppression of phosphorylation of ERK and Akt, whose signaling pathways are implicated in MDD. When effects of sDISC1 (Ser704) and cDISC1 (Cys704) proteins were examined separately, phosphorylation of ERK was greater in sDISC1 compared with cDISC1. A possible biological mechanism of MDD might be implicated by these convergent data that Cys704 DISC1 is associated with the lower biological activity on ERK signaling, reduced brain gray matter volume and an increased risk for MDD.

Adult↗
PubMed2007

Deletion mapping in Xp21 for patients with complex glycerol kinase deficiency using SNP mapping arrays.

Infantile or complex glycerol kinase deficiency (cGKD) is a contiguous gene deletion syndrome caused by a loss of GK (MIM# 300474), along with its neighboring genes, Duchenne muscular dystrophy (DMD; MIM# 300377) and/or Nuclear Receptor Subfamily 0, Group B, Member 1 (NR0B1; MIM# 300473). Patients with cGKD present with glyceroluria and hyperglycerolemia in association with DMD and/or adrenal hypoplasia congenita (AHC). The purpose of these investigations was to determine whether the Affymetrix GeneChip Mapping Array (SNP chip) could be utilized to detect and map breakpoints in patients with cGKD. Genomic DNAs from several primary lymphoblastoid cell lines from patients with cGKD were analyzed on the Affymetrix platform. The Affymetrix SNP chip is a high-density oligonucleotide array that allows a standardized, parallel interrogation of thousands of SNPs across the entire genome (except for the Y chromosome). Analysis of the array features' hybridization intensities enabled clear delineation of the patient deletions with a high degree of confidence. Many of these patient deletions had been mapped by PCR and their breakpoints confirmed by sequencing. This study demonstrates the utility of the Affymetrix Mapping GeneChips for molecular cytogenetic analysis, beyond the SNP genotyping for which the arrays were initially designed. With one out of 160 live births (approximately 25,000 U.S. neonates annually) reported to have cytogenetic disorders, we envision a significant need for such a standardized platform to carry out rapid, high-throughput, genomic analyses for molecular cytogenetics applications.

Cells, Cultured↗
PubMed2004

Whole genome DNA copy number changes identified by high density oligonucleotide arrays.

Changes in DNA copy number are one of the hallmarks of the genetic instability common to most human cancers. Previous microarray-based methods have been used to identify chromosomal gains and losses; however, they are unable to genotype alleles at the level of single nucleotide polymorphisms (SNPs). Here we describe a novel algorithm that uses a recently developed high-density oligonucleotide array-based SNP genotyping method, whole genome sampling analysis (WGSA), to identify genome-wide chromosomal gains and losses at high resolution. WGSA simultaneously genotypes over 10,000 SNPs by allele-specific hybridisation to perfect match (PM) and mismatch (MM) probes synthesised on a single array. The copy number algorithm jointly uses PM intensity and discrimination ratios between paired PM and MM intensity values to identify and estimate genetic copy number changes. Values from an experimental sample are compared with SNP-specific distributions derived from a reference set containing over 100 normal individuals to gain statistical power. Genomic regions with statistically significant copy number changes can be identified using both single point analysis and contiguous point analysis of SNP intensities. We identified multiple regions of amplification and deletion using a panel of human breast cancer cell lines. We verified these results using an independent method based on quantitative polymerase chain reaction and found that our approach is both sensitive and specific and can tolerate samples which contain a mixture of both tumour and normal DNA. In addition, by using known allele frequencies from the reference set, statistically significant genomic intervals can be identified containing contiguous stretches of homozygous markers, potentially allowing the detection of regions undergoing loss of heterozygosity (LOH) without the need for a matched normal control sample. The coupling of LOH analysis, via SNP genotyping, with copy number estimations using a single array provides additional insight into the structure of genomic alterations. With mean and median inter-SNP euchromatin distances of 244 kilobases (kb) and 119 kb, respectively, this method affords a resolution that is not easily achievable with non-oligonucleotide-based experimental approaches.

Cell Line, Tumor↗
PubMed2005

Refinement of the DFNA41 locus and candidate genes analysis.

We previously mapped the 41rst gene locus (DFNA41) for autosomal dominant hearing loss on chromosome 12q24-qter in a large multi-generational Chinese family. We determined that DFNA41 is located in a 15 cM region, proximal to the marker D12S1609. A maximum two point LOD score of 6.56 at theta = 0.0 was obtained with marker D12S343. In the current study, screening of eight candidate genes within the DFNA41 interval did not reveal the mutation causing deafness in this family. Eight highly informative single nucleotide polymorphisms (SNPs) in the region of D12S343 were selected for linkage and association study. Because the pedigree studied here is a large family with many founders, we applied the transmission/disequilibrium (TDT) test. To account for the dependence of small families and the relatively small sample size, simulations were performed to obtain P-values. For three nearby SNPs spanning a 7 kb interval, we found significant evidence of linkage and association. The highest Z score of linkage and association of 3.6 (P < or = 0.0001) was obtained for SNP rs1566667. Haplotype analysis revealed that affected individuals were heterozygous for one core SNP (rs1027560-rs1027557-rs1566667-rs1463865-rs2078105) CAGTC haplotype, confirming location and autosomal dominant inheritance of the DFNA41 locus. Examination of pairwise LD calculation identified a major haplotype block defined by the four most centromeric SNPs. This study represents a significant refinement of the DFNA41 locus and should facilitate positional cloning of the disease gene.

Centromere↗
PubMed2005

[Retrospective comprehensive assessment of the treatment effect of children with growth hormone deficiency].

The most often cause of hormonal microsomy is a growth hormone deficit on the consequence of hypofuncion of the pituitary anterior lobe (SNP). The aim of the study was a retrospective analysis of children with SNP treated with a synthetic growth hormone (rhGH). Analyzed was the growth velocity in dependence of the dose and developmental period of the patients. Additional analyzed was the influence of the relative body mass (BMI) index and the degree of growth hormone deficit on the result of the therapy with the recombined growth hormone. Analyzed was also the maturity of the bone age during the therapy with growth hormone. A statistical analysis was performed of the influence of the particular parameters on the growth velocity of the investigated patients on support on the one - or multifunctional variant analysis MANOVA. Observed was, that the growth velocity was the highest in children treated with the highest dose of growth hormone. A dependence between the degree of growth hormone deficit and the growth velocity during the therapy with growth hormone was not evidenced. Not shown was also difference in the growth velocity in dependence on the body mass index. Bone age after the therapy during the three years do not achieve the calendar age in the investigated children. The comparison of the therapeutic results in children in a different phase of maturity shows that the best growth velocity was achieved in children in whom the therapy was started before the age of six years. Therefore the beginning of the therapy with growth hormone was recommended at the earliest. The performed examination evidenced also, that children treated with present doses of growth hormone do not attain the provided height, therefore necessary is a further optimalisation of the therapy of SNP with higher doses of rhGH.

Adolescent↗
PubMed2004

Sequence variants of the gene encoding chemoattractant receptor expressed on Th2 cells (CRTH2) are associated with asthma and differentially influence mRNA stability.

The gene, CRTH2, encoding a receptor for prostaglandin D(2) (PGD(2)), is located within the peak linkage region for asthma on chromosome (Chr.) 11q reported in African American families. Family-based analysis of asthma and two common SNPs [G1544C and G1651A (rs545659)] in the 3'-untranslated region of CRTH2 showed significant evidence of linkage in the presence of disequilibrium for the 1651G allele (P = 0.003) of SNP rs545659. Haplotype analysis yielded additional evidence of linkage disequilibrium for the 1544G-1651G haplotype (P < 0.001). Population-based case-control analyses were conducted in two independent populations, and demonstrated significant association of the 1544G-1651G haplotype with asthma in an African American population (P = 0.004), and in a population of Chinese children (P < 0.001). Moreover, in the Chinese children the frequency of the 1651G allele in near-fatal asthmatics was significantly higher than mild-to-moderate asthmatics (P = 0.001) and normal controls (P < 0.001). The 1651G allele of SNP re545659 was also associated with a higher degree of bronchial hyperresponsiveness (P < 0.027). Transcriptional pulsing experiments showed that the 1544G-1651G haplotype confers a significantly higher level of reporter mRNA stability, when compared with a non-transmitted haplotype (1544C-1651A), suggesting that the CRTH2 gene on Chr. 11q is a strong candidate gene for asthma.

3' Untranslated Regions↗
PubMed2006

A polymorphism in Toll-interleukin 1 receptor domain containing adaptor protein is associated with susceptibility to meningeal tuberculosis.

BACKGROUND: Although meningitis is the most severe form of infection caused by Mycobacterium tuberculosis, the immunopathogenesis of this disease is poorly understood. We tested the hypothesis that polymorphisms in Toll-interleukin 1 receptor domain containing adaptor protein (TIRAP), an adaptor protein that mediates signals from Toll-like receptors activated by mycobacteria, are associated with susceptibility to tuberculosis (TB). METHODS: We used a case-population study design in Vietnam with cord-blood control samples (n = 392) and case patients (n = 358) who had either pulmonary (n = 183) or meningeal (n = 175) TB. RESULTS: The TIRAP single-nucleotide polymorphism (SNP) C558T was associated with increased susceptibility to TB, with a 558T allele frequency of 0.035 in control samples versus 0.074 in case patients (odds ratio [OR], 2.25; P < .001). Subgroup analysis revealed that SNP 558T was more strongly associated with susceptibility to meningeal TB (OR, 3.02; P < .001) than to pulmonary TB (OR, 1.55; P = .22). In comparison to the 558CC genotype, the 558TT genotype was associated with decreased whole-blood interleukin-6 production, which suggests that TIRAP influences disease susceptibility by modulating the inflammatory response. CONCLUSIONS: These results provide the first evidence of an association of a TIRAP SNP with the risk of any disease and also suggest that the Toll-like receptor pathway influences susceptibility to meningeal and pulmonary TB by different immune mechanisms.

Adult↗
PubMed2005

Linkage disequilibrium analysis identifies an FGFR1 haplotype-tag SNP associated with normal variation in craniofacial shape.

Mutations in FGFR1 and TWIST1 have been reported to affect the timing of calvarial suture fusion resulting in craniosynostosis and facial abnormalities. We screened nonpathologic populations for genetic polymorphisms that may associate with normal craniofacial variation. We identified 17 single-nucleotide polymorphisms (SNPs) in FGFR1, 6 of which were novel (g.8591855G-->A, g.8593685G-->A, g.8602303C-->T, g.8602475A-->G (p.Ile293Val), g.8605849C-->T, g.8607868G-->A). No SNPs were found in TWIST1. FGFR1 SNP haplotypes were reconstructed for Caucasian, Asian, Australian Aboriginal, and African American populations. All populations shared two linkage disequilibrium blocks, with one haplotype-tag SNP (htSNP) tagging each block. The htSNP g.8592931G-->C was found to have a significant negative correlation with the cephalic index for all populations (R = -0.187, p = 0.036), with larger correlations in Asians and females. This finding is a starting point in the identification of a set of SNPs that can be genotyped to determine both normal and disease craniofacial phenotypes.

Black or African American↗
PubMed2004

Functional characterization of the peptide transporter PEPT2 in primary cultures of human upper airway epithelium.

This study characterizes the expression and function of the peptide transporter hPepT2 (SLC15A2) in differentiated primary cultures of human upper airway lung epithelia obtained from six human donors. Genotype analysis of a SNP in exon 15 of hPepT2 genotypes in six donors revealed an expected distribution of the two main variants present at similar frequency (two AA homozygotes, two BB homozygotes, and two AB heterozygotes). Real-time PCR analysis of the hPepT2 mRNA message revealed no significant differences among genotypes. hPEPT2 was expressed on the apical membrane in all donor specimens, demonstrated by cell surface biotinylation and Western analysis (104 kD). We then compared transepithelial transport of the prototypical substrate (3)H-glycylsarcosine in all donor cultures in the absence and presence of known inhibitors of hPEPT2 to ascertain the phenotype of functionally expressed hPepT2 in the upper airway epithelium. An array of inhibitors included dipeptides, beta-lactam antibiotics, bestatin, and ACE inhibitors. hPEPT2 exhibited saturable Michaelis-Menten-type kinetic parameters for GlySar, corroborating previously reported values for K(T) and J(max). Donor-to-donor variation of transport for different substrates did not correlate with hPepT2 haplotypes in this sample cohort. These findings demonstrate functional hPEPT2 transporter expression in primary cultures of human lung epithelial cells. hPEPT2-mediated transport could serve as a strategy for noninvasive systemic delivery of peptides and peptidomimetics drugs.

Alleles↗
PubMed2005

Streamlined analysis of pooled genotype data in SNP-based association studies.

Several groups have developed methods for estimating allele frequencies in DNA pools as a fast and cheap way for detecting allelic association between genetic markers and disease. To obtain accurate estimates of allele frequencies, a correction factor k for the degree to which measurement of allele-specific products is biased is generally applied. Factor k is usually obtained as the ratio of the two allele-specific signals in samples from heterozygous individuals, a step that can significantly impair throughput and increase cost. We have systematically investigated the properties of k through the use of empirical and simulated data. We show that for the dye terminator primer extension genotyping method we have applied, the correction factor k is substantially influenced by the dye terminators incorporated, but also by the terminal 3' base of the extension primer. We also show that the variation in k is large enough to result in unacceptable error rates if association studies are conducted without regard to k. We show that the impact of ignoring k can be neutralized by applying a correction factor k(max) that can be easily derived, but this at the potential cost of an increase in type I error. Finally, based upon observed distributions for k we derive a method allowing the estimation of the probability pooled data reflects significant differences in the allele frequencies between the subjects comprising the pools. By controlling the error rates in the absence of knowledge of the appropriate SNP-specific correction factors, each approach enhances the performance of DNA pooling, while considerably streamlining the method by reducing time and cost.

Alleles↗
PubMed2001

Assessment and management of single nucleotide polymorphism genotype errors in genetic association analysis.

Single nucleotide polymorphisms (SNP) may be used in case-control designs to test for association between a marker (the SNP) and a disease. However, such designs usually assume that the genotype data are reported without error. We propose a method, the reduced penetrance model method (RPM) that allows for errors in a case-control design, as compared to the full penetrance model method (FPM), that assumes data are errorless. Pearson's chi 2 applied to a 2 x 2 contingency table is the test statistic considered. Additionally, we provide a likelihood method to estimate error rates using SNP genotype data in CEPH pedigrees. We test our method (RPM) against the standard method (FPM) using simulated data. All SNP loci are assumed to have two alleles, coded 1 and 2. We consider three pairs of error rates, two different sample sizes, and two sets of allele frequencies for the SNP locus. SNP genotype data in two populations are simulated under a null hypothesis (allele frequencies equal in both populations) and under an alternative hypothesis (allele frequencies differ between two populations). The total number of simulations is 24; 12 simulations under the null hypothesis, and 12 simulations under the alternative. The significance level threshold is 5%. For the null case, 9/12 (75%) of the simulations show no increase in type I error under RPM, while 3/12 (25%) show a slight increase (rejecting the null for at most 7% of the replicates). There is no increase in the type I error rate for FPM method, which can also be shown analytically. For the alternative case (power), there is a consistent increase in power for the RPM method as compared to FPM method, and average increase of 0.02 for the simulations considered. When sample sizes are large there is virtually no difference in power between RPM and FPM methods. Also, the RPM method provides consistently more accurate allele frequency estimates for the various populations. Our likelihood method to estimate error rates with CEPH pedigrees provides good estimates on average. The largest difference between a true error rate and our average estimated error rate is 0.006. However, there is a fair amount of variability in the estimates, suggesting the need for multiple experiments or larger numbers of CEPH pedigrees. Researchers may use the methods presented in this paper to (1) estimate error rates for their automated genotyping process, and (2) allow for such errors in association analyses, thereby increasing power to detect differences between allele frequencies in case and control populations when errors are present.

Alleles↗
PubMed2004

Bioinformatics tools for single nucleotide polymorphism discovery and analysis.

Single nucleotide polymorphisms (SNPs) are a valuable resource for investigating the genetic basis of disease. These variants can serve as markers for fine-scale genetic mapping experiments and genome-wide association studies. Certain of these nucleotide polymorphisms may predispose individuals to illnesses such as diabetes, hypertension, or cancer, or affect disease progression. Bioinformatics techniques can play an important role in SNP discovery and analysis. We use computational methods to identify SNPs and to predict whether they are likely to be neutral or deleterious. We also use informatics to annotate genes that contain SNPs. To make this information available to the research community, we provide a variety of Internet-accessible tools for data access and display. These tools allow researchers to retrieve data about SNPs based on gene of interest, genetic or physical map location, or expression pattern.

Chromosome Mapping↗
PubMed2003

Single-nucleotide polymorphisms in soybean.

Single-nucleotide polymorphisms (SNPs) provide an abundant source of DNA polymorphisms in a number of eukaryotic species. Information on the frequency, nature, and distribution of SNPs in plant genomes is limited. Thus, our objectives were (1) to determine SNP frequency in coding and noncoding soybean (Glycine max L. Merr.) DNA sequence amplified from genomic DNA using PCR primers designed to complete genes, cDNAs, and random genomic sequence; (2) to characterize haplotype variation in these sequences; and (3) to provide initial estimates of linkage disequilibrium (LD) in soybean. Approximately 28.7 kbp of coding sequence, 37.9 kbp of noncoding perigenic DNA, and 9.7 kbp of random noncoding genomic DNA were sequenced in each of 25 diverse soybean genotypes. Over the >76 kbp, mean nucleotide diversity expressed as Watterson's theta was 0.00097. Nucleotide diversity was 0.00053 and 0.00111 in coding and in noncoding perigenic DNA, respectively, lower than estimates in the autogamous model species Arabidopsis thaliana. Haplotype analysis of SNP-containing fragments revealed a deficiency of haplotypes vs. the number that would be anticipated at linkage equilibrium. In 49 fragments with three or more SNPs, five haplotypes were present in one fragment while four or less were present in the remaining 48, thereby supporting the suggestion of relatively limited genetic variation in cultivated soybean. Squared allele-frequency correlations (r(2)) among haplotypes at 54 loci with two or more SNPs indicated low genome-wide LD. The low level of LD and the limited haplotype diversity suggested that the genome of any given soybean accession is a mosaic of three or four haplotypes. To facilitate SNP discovery and the development of a transcript map, subsets of four to six diverse genotypes, whose sequence analysis would permit the discovery of at least 75% of all SNPs present in the 25 genotypes as well as 90% of the common (frequency >0.10) SNPs, were identified.

DNA Primers↗
PubMed2001

Information technology tools for efficient SNP studies.

We are currently facing a new era of studies involving single nucleotide polymorphisms (SNPs). This increased attention is stimulated by interest in individual differences in disease susceptibility as well as individual responses to drug treatment and the falling cost of genotyping. This review is a guide to the numerous public data repositories and Information Technology (IT) tools that may aid planning, preparation, running and analysis of studies involving SNPs. I will also highlight areas where researchers will have to resort to home-made IT solutions. Unfortunately, both information and IT tools are scattered throughout the internet and a lack of data exchange conventions can hamper the efficient use of these existing resources. This can lead to situations where the planning, preparation and analysis of a SNP study can actually cost more than the actual genotyping. We propose that only a customizable backbone IT infrastructure for SNP studies can help reduce costs associated with SNP data handling and tool launching.

Genetic Diseases, Inborn↗
PubMed2006

FCRL3 promoter 169 CC homozygosity is associated with susceptibility to rheumatoid arthritis in Dutch Caucasians.

BACKGROUND: Human leucocyte antigen is the only genetic risk factor for rheumatoid arthritis (RA) that has been consistently observed in different populations. A number of other genes such as PTPN22 and PADI4 showed population-specific association with RA susceptibility. Recently, Fc receptor-like 3 (FCRL3) gene was found to be associated with RA susceptibility in Japanese, but with conflicting results in other populations. OBJECTIVE: To investigate the association of FCRL3 polymorphism with RA susceptibility and severity in Dutch Caucasian patients with RA, as well as to perform a meta-analysis to reveal the contribution of this gene to RA susceptibility. METHODS: A total of 931 Dutch RA cases and 570 unrelated Dutch controls were genotyped for four FCRL3 single-nucleotide polymorphisms (SNPs). Genotyping was performed using the MassArray matrix-assisted laser desorption ionisation-time-of-flight mass spectrometry. Association of the FCRL3 SNPs with susceptibility to RA was examined by single-marker, carrier and haplotype analysis. RESULTS: Carrier analysis of the SNP (rs7528684) revealed the association of CC genotype with a higher risk of developing RA as compared with TT and TC carriers (p = 0.039 and OR = 1.31). There was no significant difference in the genotype and allele frequencies of all investigated SNPs between cases and controls. Meta-analysis of all studies comparing 9467 individuals showed that the OR for the CC genotype to develop RA was 1.2 and the p value <0.001. CONCLUSION: A promoter polymorphism of FCRL3 (rs7528684) is associated with an increased risk of developing RA in Dutch Caucasians, suggesting that this association is relevant for RA in both Japanese and Caucasian populations.

Adult↗