Objectives. To characterize a large extended family with early-onset OA of the knee and investigate its associations with the COL2A1 gene. Methods. Phenotype assessments were conducted in a ...six-generation family to identify individuals affected with OA. Short tandem repeat polymorphic (STRP) markers and DNA sequencing were performed to investigate the involvement of the COL2A1 gene in this family. Results. The kindred affected with OA showed autosomal dominant inheritance. The mean age of onset was 37.3 ± 19.2, 29.8 ± 13.7 and 12.0 ± 7.2 years for generations IV, V and VI, respectively, and 25 ± 16.1 years for males and 34.3 ± 15.5 years for females. The height of the affected males was shorter than the unaffected males (155.9 ± 11.4 vs 164.5 ± 16.0 cm, P = 0.010). Arm span in the affected males was also significantly shorter than the unaffected males (158.4 ± 12.5 vs 165.3 ± 16.7 cm, P = 0.027). However, both height and arm span were not reduced in the affected female OA patients. STRP markers surrounding COL2A1 locus did not show linkage of the COL2A1 locus with the OA. Sequencing of COL2A1 gene revealed three single nucleotide polymorphisms but no mutation was found in the affected patients. Conclusions. The COL2A1 was not a susceptibility gene responsible for the OA phenotype in a large extended kindred with familial early-onset OA. The availability of DNA samples will allow genome-wide linkage study to identify the susceptibility locus.
•We have developed a nanoprobe-based colorimetric method for single-nucleotide polymorphism (SNP) genotyping.•The only equipment involved in the assay is a standard thermal cycler, allowing for easy ...deployment and cost-effective genetic testing.•The method is successfully used to gauge three SNPs that are associated with warfarin sensitivity.•The warfarin sensitivity assay kit has been validated with 249 human genomic DNA samples in four independent institutes.
Plasmonic nanoprobes functionalized with morpholino oligos have been developed for genotyping of single-nucleotide polymorphisms (SNPs) based on colorimetric signals that could be easily visualized. The assay was conducted with a standard thermal cycler that would be available in any molecular diagnostic laboratory, facilitating assay deployment and allowing for cost-effective genetic testing with rapid turnaround time. Specifically, a warfarin sensitivity testing kit gauging three SNPs has been created and validated with 249 human genomic DNA samples in four independent institutes, demonstrating the robustness of our new platform.
This study aimed to determine clinical utility of genotype-guided dosing for warfarin in Han-Chinese.
A total of 320 patients were randomly assigned International Warfarin Pharmacogenetic Consortium ...algorithm, Taiwan algorithm and optimal clinical care arms. The primary outcome of the study was the percentage of time in the therapeutic range during the first 90 days of treatment.
The percentage of time in the therapeutic range of the clinical care group in the first 2 weeks was significantly higher than the algorithm groups. This difference was no longer observed after 4 weeks. No difference in excessive anticoagulation (international normalized ratio ≥4.0) and adverse events was observed.
Genotype-guided dosing did not provide significant benefit. Loading dose with frequent international normalized ratio monitoring could provide sufficient control of anticoagulation.
Back pain is a common and debilitating disorder with largely unknown underlying biology. Here we report a genome-wide association study of back pain using diagnoses assigned in clinical practice; ...dorsalgia (119,100 cases, 909,847 controls) and intervertebral disc disorder (IDD) (58,854 cases, 922,958 controls). We identify 41 variants at 33 loci. The most significant association (OR
= 0.92, P = 1.6 × 10
; OR
= 0.92, P = 7.2 × 10
) is with a 3'UTR variant (rs1871452-T) in CHST3, encoding a sulfotransferase enzyme expressed in intervertebral discs. The largest effects on IDD are conferred by rare (MAF = 0.07 - 0.32%) loss-of-function (LoF) variants in SLC13A1, encoding a sodium-sulfate co-transporter (LoF burden OR = 1.44, P = 3.1 × 10
); variants that also associate with reduced serum sulfate. Genes implicated by this study are involved in cartilage and bone biology, as well as neurological and inflammatory processes.
Sulfonylureas, the first available drugs for the management of type 2 diabetes, remain widely prescribed today. However, there exists significant variability in glycemic response to treatment. We ...aimed to establish heritability of sulfonylurea response and identify genetic variants and interacting treatments associated with HbA
reduction.
As an initiative of the Metformin Genetics Plus Consortium (MetGen Plus) and the DIabetes REsearCh on patient straTification (DIRECT) consortium, 5,485 White Europeans with type 2 diabetes treated with sulfonylureas were recruited from six referral centers in Europe and North America. We first estimated heritability using the generalized restricted maximum likelihood approach and then undertook genome-wide association studies of glycemic response to sulfonylureas measured as HbA
reduction after 12 months of therapy followed by meta-analysis. These results were supported by acute glipizide challenge in humans who were naïve to type 2 diabetes medications,
expression quantitative trait loci (eQTL), and functional validation in cellular models. Finally, we examined for possible drug-drug-gene interactions.
After establishing that sulfonylurea response is heritable (mean ± SEM 37 ± 11%), we identified two independent loci near the
and
genes associated with HbA
reduction at a genome-wide scale (
< 5 × 10
). The C allele at rs1234032, near
, was associated with 0.14% (1.5 mmol/mol),
= 2.39 × 10
), lower reduction in HbA
. Similarly, the C allele was associated with higher glucose trough levels (β = 1.61,
= 0.005) in healthy volunteers in the SUGAR-MGH given glipizide (
= 857). In 3,029 human whole blood samples, the C allele is a
eQTL for increased expression of
(β = 0.21,
= 2.04 × 10
). The C allele of rs10770791, in an intronic region of
, was associated with 0.11% (1.2 mmol/mol) greater reduction in HbA
(
= 4.80 × 10
). In 1,183 human liver samples, the C allele at rs10770791 is a
eQTL for reduced
expression (
= 1.61 × 10
), which, together with functional studies in cells expressing
, supports a key role for hepatic
(encoding OATP1B1) in regulation of sulfonylurea transport. Further, a significant interaction between statin use and SLCO1B1 genotype was observed (
= 0.001). In statin nonusers, C allele homozygotes at rs10770791 had a large absolute reduction in HbA
(0.48 ± 0.12% 5.2 ± 1.26 mmol/mol), equivalent to that associated with initiation of a dipeptidyl peptidase 4 inhibitor.
We have identified clinically important genetic effects at genome-wide levels of significance, and important drug-drug-gene interactions, which include commonly prescribed statins. With increasing availability of genetic data embedded in clinical records these findings will be important in prescribing glucose-lowering drugs.
The aim of this study was to evaluate, for the first time, the differences in gene expression profiles of normal and osteoarthritic (OA) subchondral bone in human subjects.
Following histological ...assessment of the integrity of overlying cartilage and the severity of bone abnormality by micro-computed tomography, we isolated total RNA from regions of interest from human OA (n = 20) and non-OA (n = 5) knee lateral tibial (LT) and medial tibial (MT) plateaus. A whole-genome profiling study was performed on an Agilent microarray platform and analyzed using Agilent GeneSpring GX11.5. Confirmatory quantitative reverse-transcription polymerase chain reaction (qRT-PCR) analysis was performed on samples from 9 OA individuals to confirm differential expression of 85 genes identified by microarray. Ingenuity Pathway Analysis (IPA) was used to investigate canonical pathways and immunohistochemical staining was performed to validate protein expression levels in samples.
A total of 972 differentially expressed genes were identified (fold change ≥ ± 2, P ≤0.05) between LT (minimal degeneration) and MT (significant degeneration) regions from OA samples; these data implicated 279 canonical pathways in IPA. The qRT-PCR data strongly confirmed the accuracy of microarray results (R2 = 0.58, P <0.0001). Novel pathways were identified in this study including Periostin (POSTN) and Leptin (LEP), which are implicated in bone remodeling by osteoblasts.
To the best of our knowledge, this study represents the most comprehensive direct assessment to date of gene expression profiling in OA subchondral bone. This study provides insights that could contribute to the development of new biomarkers and therapeutic strategies for OA.
Uterine fibroids (UF) are common pelvic tumors in women, heritable, and genome-wide association studies (GWAS) have identified ~ 30 loci associated with increased risk in UF. Using summary statistics ...from a previously published UF GWAS performed in a non-Hispanic European Ancestry (NHW) female subset from the Electronic Medical Records and Genomics (eMERGE) Network, we constructed a polygenic risk score (PRS) for UF. UF-PRS was developed using PRSice and optimized in the separate clinical population of BioVU. PRS was validated using parallel methods of 10-fold cross-validation logistic regression and phenome-wide association study (PheWAS) in a seperate subset of eMERGE NHW females (validation set), excluding samples used in GWAS. PRSice determined
p
t
< 0.001 and after linkage disequilibrium pruning (
r
2
< 0.2), 4458 variants were in the PRS which was significant (pseudo-
R
2
= 0.0018,
p
= 0.041). 10-fold cross-validation logistic regression modeling of validation set revealed the model had an area under the curve (AUC) value of 0.60 (95% confidence interval CI 0.58–0.62) when plotted in a receiver operator curve (ROC). PheWAS identified six phecodes associated with the PRS with the most significant phenotypes being 218 ‘benign neoplasm of uterus’ and 218.1 ‘uterine leiomyoma’ (
p
= 1.94 × 10
–23
, OR 1.31 95% CI 1.26–1.37 and
p
= 3.50 × 10
–23
, OR 1.32 95% CI 1.26–1.37). We have developed and validated the first PRS for UF. We find our PRS has predictive ability for UF and captures genetic architecture of increased risk for UF that can be used in further studies.
The P2Y12 receptor inhibitor clopidogrel is widely used in patients with acute coronary syndrome, percutaneous coronary intervention, or ischemic stroke. Platelet inhibition by clopidogrel shows wide ...interpatient variability, and high on-treatment platelet reactivity is a risk factor for atherothrombotic events, particularly in high-risk populations. CYP2C19 polymorphism plays an important role in this variability, but heritability estimates suggest that additional genetic variants remain unidentified. The aim of the International Clopidogrel Pharmacogenomics Consortium (ICPC) is to identify genetic determinants of clopidogrel pharmacodynamics and clinical response.
Based on the data published on www.clinicaltrials.gov, clopidogrel intervention studies containing genetic and platelet function data were identified for participation. Lead investigators were invited to share DNA samples, platelet function test results, patient characteristics, and cardiovascular outcomes to perform candidate gene and genome-wide studies.
In total, 17 study sites from 13 countries participate in the ICPC, contributing individual patient data from 8,829 patients. Available adenosine diphosphate–stimulated platelet function tests included vasodilator-stimulated phosphoprotein assay, light transmittance aggregometry, and the VerifyNow P2Y12 assay. A proof-of-principle analysis based on genotype data provided by each group showed a strong and consistent association between CYP2C19*2 and platelet reactivity (P value=5.1 × 10−40).
The ICPC aims to identify new loci influencing clopidogrel efficacy by using state-of-the-art genetic approaches in a large cohort of clopidogrel-treated patients to better understand the genetic basis of on-treatment response variability.
The cytochrome P450 (CYP)4F2 gene is known to influence mean coumarin dose. The aim of the present study was to undertake a meta‐analysis at the individual patients level to capture the possible ...effect of ethnicity, gene—gene interaction, or other drugs on the association and to verify if inclusion of CYP4F2*3 variant into dosing algorithms improves the prediction of mean coumarin dose. We asked the authors of our previous meta‐analysis (30 articles) and of 38 new articles retrieved by a systematic review to send us individual patients’ data. The final collection consists of 15,754 patients split into a derivation and validation cohort. The CYP4F2*3 polymorphism was consistently associated with an increase in mean coumarin dose (+9% (95% confidence interval (CI) 7–10%), with a higher effect in women, in patients taking acenocoumarol, and in white patients. The inclusion of the CYP4F2*3 in dosing algorithms slightly improved the prediction of stable coumarin dose. New pharmacogenetic equations potentially useful for clinical practice were derived.
Summary Objective To evaluate the interaction of articular cartilage (AC) and subchondral bone (SB) through analysis of osteoarthritis (OA)-related genes of site-matched tissue. Design We developed a ...novel method for isolating site-matched overlying AC and underlying SB from three and four regions of interest respectively from the human knee tibial plateau ( n = 50). For each site, the severity of cartilage changes of OA were assessed histologically, and the severity of bone abnormalities were assessed by microcomputed tomography. An RNA isolation procedure was optimized that yielded high quality RNA from site-matched AC and SB tibial regions. Quantitative polymerase chain reaction (Q-PCR) analysis was performed to evaluate gene expression of 61 OA-associated genes for correlation with cartilage integrity and bone structure parameters. Results A total of 27 (44%) genes were coordinately up- or down-regulated in both tissues. The expression levels of 19 genes were statistically significantly correlated with the severity of AC degeneration and changes of SB structure; these included: ADAMTS1 , ASPN , BMP6 , BMPER , CCL2 , CCL8 , COL5A1 , COL6A3 , COL7A1 , COL16A1 , FRZB , GDF10 , MMP3 , OGN , OMD , POSTN , PTGES , TNFSF11 and WNT1. Conclusions These results provide a strategy for identifying targets whose modification may have the potential to ameliorate pathological alterations and progression of disease in both AC and SB simultaneously. In addition, this is the first study, to our knowledge, to overcome the major difficulties related to isolation of high quality RNA from site-matched joint tissues. We expect this method to facilitate advances in our understanding of the coordinated molecular responses of the whole joint organ.
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