Tag Single Nucleotide Polymorphisms Research Articles

Genome‐Wide Association Study of Yield and Component Traits in Pacific Northwest Winter Wheat

Grain yield and agronomic traits, key breeding goals for most crops, are under complex genetic control and subject to environmental interactions. Plant breeders require that the genetic architecture of agronomic traits be identified in locally relevant germplasm. Our goal was to conduct a genome‐wide association study to identify quantitative trait loci for eight agronomic traits in a diversity panel containing 402 Pacific Northwest winter wheat (Triticum aestivum L.) lines. Phenotypic evaluations of yield, yield components, phenology, and plant height were conducted under drought, rainfed, and irrigated conditions in 2012, 2013, and 2014. Linkage disequilibrium analysis, using 6492 single nucleotide polymorphism (SNP) markers from the 9K SNP array, determined that 70% of markers were in significant LD with other markers and formed 539 LD blocks with an average distance of 3.5 cM. Population structure analysis was conducted using 719 SNP tags that represent marker distribution. Three genetic subgroups were identified in the population, explaining 3 to 38% of the total phenotypic variation. A mixed linear model with 3653 SNP markers of known genetic position, the first two membership coefficients (Q = 2) of population structure and a compressed kinship (Kc = 192) was used in the association analysis. In this study, a total of 94 marker‐trait associations that were significant (false discovery rate < 0.05) were identified. Multiple trait associations for yield and component traits were identified on chromosomes 2B, 4B, 5A, 5B, 6A, and 7B. These findings highlight the possibility of using historical recombination in northern latitude winter wheat to identify genomic regions associated with desired agronomic traits.

Screening the full leucocyte receptor complex genomic region revealed associations with pemphigus that might be explained by gene regulation

Pemphigus foliaceus (PF) is a blistering autoimmune skin disease rare in most of the world but endemic in certain regions of Brazil. PF is characterized by the detachment of epidermal cells and the presence of autoantibodies against desmoglein 1. In previous studies, we have shown that genetic polymorphisms and variable expression levels of certain leucocyte receptor complex (LRC) genes were associated with PF. However, the role of the LRC on PF susceptibility remained to be investigated. Here, we analysed 527 tag single nucleotide polymorphisms (SNPs) distributed within the 1·5 Mb LRC. After quality control, a total of 176 SNPs were analysed in 229 patients with PF and 194 controls. Three SNPs were associated with differential susceptibility to PF. The intergenic variant rs465169 [odds ratio (OR) = 1·50; P = 0·004] is located in a region that might regulate several immune-related genes, including VSTM1, LILRB1/2, LAIR1/2, LILRA3/4 and LENG8. The rs35336528 (OR = 3·44; P = 0·009) and rs1865097 (OR = 0·57; P = 0·005) SNPs in LENG8 and FCAR genes, respectively, were also associated with PF. Moreover, we found four haplotypes with SNPs within the KIR3DL2/3, LAIR2 and LILRB1 genes associated with PF (P < 0·05), which corroborate previously reported associations. Thus, our results confirm the importance of the LRC for differential susceptibility to PF and reveal new markers that might influence expression levels of several LRC genes, as well as candidates for further functional studies.

Association study between inwardly rectifying potassium channels 2.1 and 4.1 and autism spectrum disorders

Autism spectrum disorders (ASD) are a group of neurodevelopmental disorders involving structural and functional impairment of the brain. Inwardly rectifying potassium (Kir) channels may contribute to the etiology of ASD by altering brain function. This study investigated the associations between genetic variants of KCNJ2 and KCNJ10 genes (encoding Kir2.1 and Kir4.1, respectively) and ASD risk in patients, and Kir channel expression in ASD model rats. This case-control study involved a cohort of 269 Chinese children with ASD and 243 unrelated healthy controls. Twelve tag single nucleotide polymorphisms (SNPs) from the KCNJ2 and KCNJ10 genes were genotyped by Sequenom Mass Array, while a valproic acid (VPA)-induced rat model of ASD was used to evaluate Kir channel expression in the hippocampus. Among the 12 examined SNPs, only KCNJ10 rs1186689 was significantly associated with disease susceptibility; the variant T allele conferred a lower risk of developing ASD [odds ratio (OR) = 0.61, 95% confidence interval (CI) = 0.47–0.80, p false discovery rate (FDR) = 0.012, and OR = 0.63, 95% CI = 0.48–0.84, pFDR = 0.014 at the allelic and genotypic levels, respectively]. Additionally, hippocampal Kir2.1 and Kir4.1 levels were decreased in VPA as compared to control rats. These results demonstrated that KCNJ10 (rs1186689) polymorphisms was correlated with ASD susceptibility in Chinese Han children, and the abnormal expression of Kir2.1 and Kir4.1 in ASD model rats suggested a mechanism by which Kir channels may play a role in ASD.

Voltage-gated calcium channel activity and complex related genes and schizophrenia: A systematic investigation based on Han Chinese population

Schizophrenia (SCZ) is a devastating mental disorder affecting approximately 1% of the worldwide population. Early studies have indicated that genetics plays an important role in the onset and development of SCZ. Accumulating evidence supports that SCZ is linked to abnormalities of synapse transmission and synaptic plasticity. Voltage-gated calcium channel (VGCC) subunits are critical for mediating intracellular Ca2 + influx and therefore are responsible for changing neuronal excitability and synaptic plasticity. To systematically investigate the role of calcium signaling genes in SCZ susceptibility, we conducted a case-control study that included 2518 SCZ patients and 7521 healthy controls with Chinese Han ancestry. Thirty-seven VGCC genes, including 363 tag single nucleotide polymorphisms (SNPs), were examined. Our study replicated the following previously identified susceptible loci: CACNA1C, CACNB2, OPRM1, GRM7 and PDE4B. In addition, several novel loci including CACNA2D1, PDE4D, NALCN, and CACNA2D3 were also identified to be associated with SCZ in our Han Chinese sample. Combined with GTEx eQTL data, we have shown that CASQ2, ITGAV, and TMC2 can be also added into the prioritization list of SCZ susceptible genes. Two-way interaction analyses identified widespread gene-by-gene interactions among VGCC activity and complex-related genes for the susceptibility of SCZ. Further sequencing based studies are still needed to unravel potential contributions of schizophrenia risk from rare or low frequency variants of these candidate genes.

A15972 The characteristic of adrenoceptor related gene polymorphism of hypertension in northwest region Han people of China

Objectives: The aim of this study is to investigate the the characteristic of adrenoceptor related gene polymorphism of hypertension in northwest region Han people of China. Methods: Genetic analysis of the Arg347Cys polymorphism was conducted by polymerase chain reaction/restriction fragment length polymorphism. We have compared cardiovascular risk variables and genotypes using ANOVA, and Chi-square test for univariate comparisons and logistic regression for multivariate comparisons. A case-control study comprising 576 hypertension cases and 576 controls from the general population of Gansu province in China was used to evaluate the association of 13 adrenoceptor tagging single nucleotide polymorphism (tagSNPs) in northwest region Han people of China. Genetic analysis of the adrenoceptor related gene polymorphism was conducted by polymerase chain reaction/restriction fragment length polymorphism Results: Three SNPs were significantly associated with systolic blood pressure (SBP), including rs17327624 (p = 6.167 × 10–4, beta = 5.650), rs3789243 (p = 4.331 × 10–3, beta = 2.800), and rs4148734 (p = 3.514 × 10–3, beta = 3.692). Rs17327624 (p = 2.818 × 10–4, beta = 2.753) and rs3789243 (p = 6.345 × 10–3, beta = 1.497) were significantly associated with diastolic blood pressure (DBP) and rs17327624 was significantly associated with hypertension (p = 1.746 × 10–4, OR = 1.605). These three SNPs (rs17327624, rs3789243 and rs4148734) were also associated with hypertension in female subjects but no significant signal was detected in males. Conclusion: Our results suggest that ABCB1 polymorphisms may contribute to the blood pressure variation in northwest region Han people of China and the effect may be specific in females.

Evaluation of Common Variants in Matrix Metalloproteinase-9 Gene with Lumbar Disc Herniation in Han Chinese Population.

Lumbar disc herniation (LDH) is a common and frequent orthopedic disease with strong genetic determinants. The disruption of the intervertebral disc extracellular matrix has been found to play a key role in the development of LDH, suggesting that abnormal matrix metalloproteinases (MMPs) may promote the degradation of the disc matrix. MMP-9, an important member of the MMP family, is a good candidate for the LDH susceptibility gene. The present study aimed to investigate the association of common variants in the MMP-9 gene with the risk, severity, and clinical characteristic variables of LDH. Fourteen tag single nucleotide polymorphisms (SNPs) entirely covering the region of the MMP-9 gene were analyzed in a sample of 845 patients and 1751 healthy controls. The SNP rs17576 was found to be significantly associated with susceptibility to LDH (OR = 0.77, p = 0.0002), which was also confirmed by haplotype-based analyses (rs79845319-rs17576-rs45437897, global p < 0.001). Our results indicated that the A allele of rs17576 reduced the risk of LDH by ∼23% on average. Furthermore, the G allele of rs17576 was found to correlate with more severe grades of disc degeneration. Our results provide additional evidence supporting an important role of the MMP-9 gene in the pathogenesis of LDH.

A Pilot Study Investigating the Influence of Glucagon-Like Peptide-1 Receptor Single Nucleotide Polymorphisms on Gastric Emptying Rate in Caucasian Men.

Gastric emptying rate in humans is subject to large individual variability, but previous research on the influence of genetics is scarce. Variation in the glucagon-like peptide-1 receptor (GLP1R) gene is a plausible candidate gene to partially explain the high variance. This study aimed to investigate the influence of genetic variation in the GLP1R gene on gastric emptying rate of a glucose solution in humans. Forty eight healthy Caucasian males took part in this investigation. Gastric emptying rate of a 6% glucose solution was assessed using the 13C breath test method and a venous blood sample was obtained from each participant. Participants were genotyped for 27 Tag single nucleotide polymorphisms (SNPs) in the GLP1R locus using Sequenom MassARRAY iPLEX GOLD analysis and MALDI-TOF mass spectrometry. The time at which maximal emptying rate occurred (Tlag) was faster in participants with the CC genotype than in TT and TC genotypes for SNP rs742764: [median (quartiles) CC, 35 (30–36) min vs. TT, 43 (39–46) min, and TC, 41 (39–45) min; P < 0.01]. Tlag was also slower in participants with the AA genotype compared to the TT and TA genotypes for SNP rs2254336: [AA, 43 (39–49) min vs. TT, 36 (34–41) min, and TA, 39 (35–42) min; P < 0.05]. Analysis by phenotype also showed differences in half-emptying time (T12) and Tlag for SNPs rs9283907, rs2268657, and rs2254336. Several neighboring Tag SNPs within the GLP1R gene were found to be associated with gastric emptying rate, and should be further investigated.

FKBP1A rs6041749 polymorphism is associated with allograft function in renal transplant patients.

To investigate the potential impact of single-nucleotide polymorphisms (SNPs) in the FK506-binding protein (FKBP)-calcineurin (CaN)-nuclear factor of activated T cells (NFAT) signaling pathway on the efficacy and safety of tacrolimus (TAC) in Chinese renal transplant patients. Seventy-seven tag SNPs were detected in 146 patients who were on TAC-based maintenance immunosuppression and who followed up for at least 2years. The relationships of these polymorphisms with clinical outcomes such as acute rejection, acute nephrotoxicity, pneumonia, and estimated glomerular filtration rate (eGFR) were explored. For the FKBP1A rs6041749 polymorphism, which has a significant association with renal function over time, a preliminary functional analysis was performed using a dual-luciferase reporter gene system. The patients with FKBP1A rs6041749 TT genotype had a more stable eGFR level than CC and CT carriers (P = 2.08 × 10-8) during the 2years following transplantation. Dual-luciferase reporter assay results showed that the rs6041749 C variant could enhance the relative luciferase activity compared with the T variant, which indicated that the rs6041749 C allele may increase the FKBP1A gene transcription. In addition, we did not find any association between these genetic variants and the risk of acute rejection, acute nephrotoxicity, and pneumonia in renal transplant patients receiving TAC-based immunosuppression. FKBP1A rs6041749 C allele carriers are at higher risk for eGFR deterioration. The variant might serve as a biomarker to predict allograft function in renal transplant patients.

Ethanol (EtOH)-Related Behaviors in α-Synuclein Mutant Mice and Association of SNCA SNPs with Anxiety in EtOH-Dependent Patients.

Data have shown a role of α-synuclein in anxiety and also in addiction, particularly in alcohol use disorders (AUD). Since the comorbidity between AUD and anxiety is very high and because anxiety is an important factor in ethanol (EtOH) relapse, the aim of the present study was to investigate the role of α-synuclein in moderating EtOH intake, the anxiolytic effects of EtOH, and EtOH withdrawal-induced anxiety and convulsions in mice. The study aimed to determine whether SNCA variants moderated anxiety in EtOH-dependent patients. We analyzed the moderator effect of 3 SNCA Tag-single nucleotide polymorphisms (Tag-SNPs) rs356200, rs356219, and rs2119787 on the anxiety symptoms in 128 EtOH-dependent patients. We used the C57BL/6JOlaHsd Snca mutant mice to assess EtOH intake; sensitivity to the anxiolytic effects of EtOH in a test battery comprising the open field, the light-dark box, and the elevated plus maze; and both anxiety and convulsions induced by EtOH withdrawal. Our results demonstrated a reduction in both EtOH intake and preference and also a lack of sensitivity to the anxiolytic effects of EtOH in α-synuclein mutant mice. Results on anxiety-like behavior were mixed, but mutant mice displayed increased anxiety when exposed to a low anxiogenic environment. Mutant mice also displayed an increase in handling-induced convulsion scores during withdrawal after EtOH inhalation, but did not differ in terms of EtOH withdrawal-induced anxiety. In humans, we found a significant association of the rs356219 SNP with a high level of anxiety (Beck Anxiety Inventory score >15) and the rs356200 SNP with a positive familial history of AUD. Our translational study highlights a significant role of α-synuclein in components of AUD.

FADS1-FADS2 and ELOVL2 gene polymorphisms in susceptibility to autism spectrum disorders in Chinese children

BackgroudAutism spectrum disorders (ASD) are a complex group of neurodevelopmental disorders with a genetic basis. The role of long-chain polyunsaturated fatty acids (LC-PUFAs) and the occurrence of autism has been the focus of many recent studies. The present study investigates whether genetic variants of the fatty acid desaturase (FADS) 1/2 and elongation of very long-chain fatty acids protein (ELOVL) 2 genes, which are involved in LC-PUFA metabolism, are associated with ASD risk.MethodsA cohort of 243 ASD patients and 243 unrelated healthy controls were enrolled in this case control study. Sixteen tag single nucleotide polymorphisms from the FADS1–2 and ELOVL2 genes were genotyped using the Sequenom Mass Array.ResultsThere were significant differences in allelic distribution of FADS2 rs526126 (OR = 0.55, 95% CI = 0.42–0.72, pFDR < 0.05) between autistic children and controls. FADS2 rs526126 and ELOVL2 rs10498676 were associated with decreased ASD risk in recessive model (OR = 0.07, 95% CI = 0.02–0.22, pFDR < 0.01; OR = 0.56, 95% CI = 0.35–0.89, pFDR = 0.042), while ELOVL2 rs17606561, rs3756963, and rs9468304 were associated with increased ASD risk in overdominant model (OR = 1.63, 95% CI = 1.12–2.36, pFDR = 0.036; OR = 1.64, 95% CI = 1.14–2.37, pFDR = 0.039; OR = 1.75, 95% CI = 1.22–2.50, pFDR = 0.017). The A/A genotype of rs10498676 was correlated with a decline in the Autism Diagnostic Interview-Revised communication (verbal and nonverbal) domain.ConclusionsThese findings provide evidence of an association between FADS2 and ELOVL2 polymorphisms and ASD susceptibility in Chinese children.

Genetic variants of cGMP-dependent protein kinase genes and salt sensitivity of blood pressure: the GenSalt study.

Genetic mechanisms involved in the susceptibility to salt sensitivity have not been completely clarified. This study aimed to comprehensively examine the association between genetic variants in the cyclic guanosine monophosphate (cGMP)-dependent protein kinase (PKG/PRKG) genes and blood pressure (BP) responses to dietary sodium intervention in a Chinese population. A 7-day low-sodium intervention followed by a 7-day high-sodium intervention was conducted among 1906 Han participants from rural areas of northern China. Nine BP measurements were obtained at baseline and each intervention using a random-zero sphygmomanometer. Linear mixed-effect models were used to assess the additive association of 213 tag single-nucleotide polymorphisms (SNPs) in two PRKG genes (PRKG1 and PRKG2) with salt sensitivity phenotypes. Gene-based analyses were conducted using the truncated product method. The Bonferroni method was used to adjust for multiple testing. Mean systolic BP response to low-sodium intervention significantly decreased with the number of minor T allele of marker rs10997916 in PRKG1 (P = 2.4 × 10-5). Mean systolic BP responses (95% confidence interval) among those with genotypes CC, CT, and TT were -5.6 (-6.0, -5.3), -3.7 (-4.7, -2.8), and -1.3 (-4.6, 2.0) mmHg, respectively, during the low-sodium intervention. Gene-based analyses demonstrated that PRKG1 was significantly associated with systolic BP response to low-sodium intervention (P = 1.2 × 10-3), whereas PRKG2 was nominally significantly associated with diastolic BP responses to high-sodium intervention (P = 2.6 × 10-2). The current study suggested a significant association of genetic variants in the PRKG genes with variation of BP response to dietary sodium intake in Han Chinese population. These novel findings merit further replication in future.

Smoking modifies the effect of two independent SNPs rs5063 and rs198358 of NPPA on central obesity in the Chinese Han population

Obesity is the third most risk factors of death in the middle-income and high-income countries. Whether DNA polymorphisms in CORIN and NPPA genes were associated with obesity, and if these associations could be modified by smoking in the Chinese Han population were unknown, hence a group of 1507 participants were recruited and genotyped for 12 tag single-nucleotide polymorphisms (SNPs) of CORIN and NPPA genes. Regression models were used to test the associations of SNPs with obesity. The potential SNP-smoking interactions were detected in regression models. NPPA SNPs rs5063 and rs198358 were associated with the body mass index (BMI) (P = 0.0053 and 0.0037, respectively). Rs198358 was associated with obesity in both univariate- and multivariable-adjusted analyses (P = 0.0138 and 0.0173, respectively). Rs5063 was associated with central obesity in both univariate- and multivariable-adjusted analyses (P = 0.0454 and 0.0361, respectively). Significant interactions between cigarette smoking and rs5063 and rs198358 were detected (P = 0.0019 and 0.0006, respectively). In subgroup analyses, rs5063 and rs198358 were associated with central obesity in smokers (P = 0.0081 and 0.0037, respectively). The results of our study demonstrated that the effect of NPPA SNPs rs5063 and rs198358 on central obesity might be modified by smoking in the Chinese Han population. Further studies are needed to confirm the associations and elucidate the underlying mechanisms.

Polymorphisms in AURKA and AURKB are associated with the survival of triple-negative breast cancer patients treated with taxane-based adjuvant chemotherapy.

PurposeTriple-negative breast cancer (TNBC) is more than a single disease. Identifying biomarkers to further subdivide TNBC patients with distinct outcome is of great importance. It has been reported that single-nucleotide polymorphisms (SNPs) in Aurora kinase A (AURKA) or Aurora kinase B (AURKB) are associated with the risk and survival of several cancers. But till now, there is no research about these polymorphisms in TNBC patients.Materials and methodsIn this study, we investigated the association between polymorphisms in AURKA or AURKB gene and prognosis of TNBC patients treated with taxane-based adjuvant chemotherapy. A total of 273 TNBC patients were enrolled. Haploview 4.2 software was used to identify Tag SNPs. Genotyping was conducted using the MassARRAY MALDI-TOF system.ResultsWe found that AURKA rs6099128 GG genotype carriers had significantly worse overall survival (OS) than TT+ TG genotype carriers (P = 0.003, HR = 12.499, 95% CI = 2.357–66.298). AURKB rs11651993 TT genotype carriers had better disease-free survival (DFS) than TC + CC genotype carriers (P = 0.018, HR = 1.876, 95% CI = 1.116–3.154). AURKB rs2289590 CC genotype carriers had worse DFS than CA + AA genotype carriers (P = 0.021, HR = 0.536, 95% CI = 0.315–0.912). After subgroup analysis, rs11651993 TC + CC genotype predicted worse DFS in subgroups of age ≤ 50, post-menopausal, grade unknown (UK), tumor size >2 cm, and lymph node negative. Rs2289590 CA + AA genotype could predict favorable DFS in pre-menopausal, grade 3 and lymph node-positive patients.ConclusionWe first demonstrated that polymorphisms in AURKA or AURKB gene might predict the OS or DFS of TNBC patients treated with taxane-based adjuvant chemotherapy.

Association between Vitamin D Deficiency and Single Nucleotide Polymorphisms in the Vitamin D Receptor and GC Genes and Analysis of Their Distribution in Mexican Postmenopausal Women.

Genome-wide association studies in people with European ancestry suggest that polymorphisms in genes involved in vitamin D (VD) metabolism have an effect on serum concentrations of 25-hydroxyvitamin D. However, nothing is known about these polymorphisms in populations with Amerindian ancestry. Our aim was to evaluate the association between genetic variants on the vitamin D receptor (VDR) and the vitamin D binding protein (GC) genes, involved in the VD pathway, and VD deficiency in 689 unrelated Mexican postmenopausal women. We also described the frequencies of these variants in 355 postmenopausal women from different ethnic groups. Based on our preliminary results of 400 unrelated Mexican postmenopausal women, three single nucleotide polymorphisms (SNPs) were selected for genotyping. The SNPs rs4516035 in VDR and rs2282679 in GC were associated with VD deficiency. Additionally, women who carried three risk alleles had a 3.67 times higher risk of suffering VD deficiency, compared to women with no risk alleles (p = 0.002). The rs4516035-C allele frequency in the Amerindian population was enriched in the South East region of Mexico. In contrast, the highest frequency of the rs2298850-C allele, a proxy for the tag SNP rs2282679, was observed in the South region. Our results indicate that genetic variants in VDR and GC genes are associated with VD deficiency in Mexican postmenopausal women. Moreover, an association was observed for the variants rs3794060 and rs4944957 of the DHCR7/NADSYN1 gene with osteopenia/osteoporosis.

Association of genetic variation of the six gene prognostic model for castration-resistant prostate cancer with survival.

We previously identified a blood RNA transcript-based model consisting of six immune or inflammatory response genes (ABL2, SEMA4D, ITGAL, C1QA, TIMP1, and CDKN1A) that was prognostic for survival in cohorts of men with castration-resistant prostate cancer (CRPC). We investigated whether inherited variation in these six genes was associated with overall survival (OS) in men with CRPC. The test cohort comprised 600 patients diagnosed with CRPC between 1996 and 2011 at Dana-Farber Cancer Institute. Genotyping of 66 tagging single nucleotide polymorphisms (SNPs) spanning the six genes was performed on blood derived DNAs. For the top four SNPs (P < 0.05), validation was conducted in an independent cohort of 223 men diagnosed with CRPC between 2000 and 2014. Multivariable Cox regression adjusting for known prognostic factors estimated hazard ratios (HR) and 95% confidence intervals (CI) of the association of genetic variants with OS. Two thirds of patients in both cohorts had metastases at CRPC diagnosis. Median OS from CRPC diagnosis was 3.6 (95%CI 3.3-4.0) years in the test cohort and 4.6 (95%CI 3.8-5.2) years in the validation cohort. Fifty-nine SNPs in Hardy-Weinberg equilibrium were analyzed. The major alleles of rs1318056 and rs1490311 in ABL2, and the minor alleles of rs2073917 and rs3764322 in ITGAL were associated with increased risk of death in the test cohort (adjusted-HRs 1.27-1.39; adjusted-p <0.05; false discovery rate <0.35). In the validation cohort, a similar association with OS was observed for rs1318056 in ABL2 (adjusted-HR 1.44; 95%CI 0.89-2.34) and rs2073917 in ITGAL (adjusted-HR 1.41; 95%CI 0.82-2.42). The associations did not reach statistical significance most likely due to the small sample size of the validation cohort (adjusted-p = 0.142 and 0.209, respectively). Additional eQTL analysis indicated that minor alleles of rs1318056 and rs1490311 in ABL2 are associated with a lower ABL2 expression in blood. These findings corroborate our initial work on the RNA expression of genes involved in immunity and inflammation from blood and clinical outcome and suggest that germline polymorphisms in ABL2 and ITGAL may be associated with the risk of death in men with CRPC. Further studies are needed to validate these findings and to explore their functional mechanisms.

Vitamin D receptor polymorphism rs2228570 is significantly associated with risk of dyslipidemia and serum LDL levels in Chinese Han population

BackgroundThe goal of this study was to determine if vitamin D receptor (VDR) gene polymorphisms underlie susceptibility to dyslipidemia in a Chinese Han population.MethodsThree tag single nucleotide polymorphisms (SNPs) (rs11574129, rs2228570, and rs739837) were genotyped using TaqMan assays to determine VDR SNP associations with dyslipidemia. We genotyped 877 cases of dyslipidemia from a normotensive, non-diabetes mellitus population and 1822 non-dyslipidemia subjects in a stage I study. In a follow-up stage II study, we included a larger sample of 3124 controls and 1679 cases with dyslipidemia. Finally, we explored the potential molecular mechanism for the SNP associations using molecular modeling analysis.ResultsWe found a significant association between SNP rs2228570 and dyslipidemia in the additive (adjusted odds ratio (OR) = 1.255, 95% Confidence Interval (CI) = (1.118–1.409), P < 0.001), dominant (OR = 1.384, 95% CI = 1.384 (1.136–1.6), P = 0.001) and recessive models (OR = 1.356, 95%CI = 1.1–1.671, P = 0.004) in stage I. We further established that the rs2228570 variant was significantly associated with dyslipidemia in the additive (adjusted OR = 1.146, 95% CI = 1.053–1247, P = 0.002), dominant (OR = 1.184, 95%CI =1.018–1.376, P = 0.028) and recessive models (OR = 1.209, 95%CI = 1.064–1.374, P = 0.004) in stage II. The TT genotype was significantly higher (4.93 ± 0.75 mmol/L) compared to the TC (4.67 ± 0.47 mmol/L) or CC (4.66 ± 0.44 mmol/L) genotype (P = 0.01) in cases with elevated low-density lipoprotein cholesterol (LDL-C) levels. In contrast, the cases with the TT genotype had significantly lower serum 25(OH)D levels (18.43 ± 5.04 ng/ mL) compared to the TC (26.24 ± 4.16 ng/mL) and CC (36.76 ± 8.10 ng/ mL) genotypes (P < 0.001). Multivariable linear regression analysis indicated that the rs2228750 genotype significantly correlated with serum low-density lipoprotein-C (LDL-C) levels in cases with dyslipidemia. Using molecular modeling analysis, we further found that the rs2228570 variant changed the structure and the stability of VDR and altered the binding energy of its ligand.ConclusionsThe VDR rs2228570 variant may increase susceptibility to dyslipidemia in the Chinese Han population.

Association study and mutation sequencing of genes on chromosome 15q11-q13 identified GABRG3 as a susceptibility gene for autism in Chinese Han population

Cytogenetic studies suggested that chromosome 15q11-q13 might be a candidate region that increases the risk of autism. Previous association studies in Caucasian populations identified the risk variants of genes in this region. However, the association of these genes with autism in Chinese Han population remains unclear. Herein, 512 autism trios were utilized for a family-based association study of 41 tag single nucleotide polymorphisms (SNPs) in this region to explore the association between protein-coding genes on chromosome 15q11-q13 and autism in Chinese Han population. Furthermore, we sequenced these autism-related genes to detect rare variants in 512 autism trios and 575 healthy controls. Our results showed that the C allele of rs7180500 in GABRG3 was a risk variant for autism (p = 0.00057). The expression quantitative trait loci (eQTL) analysis revealed that the C allele of rs7180500 might be associated with the expression of GABRG3 in the cerebellum (Braineac: p = 0.0048; GTEx: p = 0.0010). Moreover, the sequencing identified two rare variants rs201602655 (p.Val233Met) and rs201427468 (p.Pro365Ser) in GABRG3 and six rare variants in GABRB3 in autistic patients. Among these variants, rs201602655 (p.Val233Met) in GABRG3 were observed in 9 of 512 autistic children and 2 of 575 healthy controls (Pearson χ2-test, χ2 = 5.375, p = 0.020). The functional prediction indicated that rs201602655 (p.Val233Met) might be deleterious. Thus, these findings demonstrated that GABRG3 might contribute to the pathogenesis of autism in Chinese Han population.

Cross-ethnicity tagging SNPs for HLA alleles associated with adverse drug reaction.

Reduction of adverse drug reaction (ADR) incidence through screening of predisposing human leucocyte antigen (HLA) alleles is a promising approach for many widely used drugs. However, application of these associations has been limited by the cost burden of HLA genotyping. Use of single nucleotide polymorphisms (SNPs) that can approximate ('tag') HLA alleles of interest has been proposed as a cost-effective and simple alternative to conventional genotyping. However, most reported SNP tags have not been validated and there is concern regarding clinical utility of this approach due to tagging inconsistency across different populations. We assess the ability of 67 previously reported and 378 novel tagging SNPs, identified here in 5 HLA reference panels, to tag 15 ADR-associated HLA alleles in a panel of 955 ethnically diverse samples. Tags for 8 HLA alleles of interest were identified with 100% sensitivity and >95% specificity. These SNPs may act as a reliable genotyping approach for the routine screening of patients, without the need to account for patient ethnicity.

Smoking is associated with increased disease activity during natalizumab treatment in multiple sclerosis

Background: Smoking has been associated with increased multiple sclerosis (MS) risk, disease worsening, and progression in MS patients. Furthermore, interactions between smoking and human leukocyte antigen (HLA) genes have been shown for MS risk. Recently, we found that smoking was associated with an increased relapse rate in interferon-beta-treated relapsing-remitting multiple sclerosis (RRMS) patients. Objectives: We examined the association between smoking and relapses in natalizumab-treated RRMS patients. Second, we investigated if an interaction between smoking and HLA-DRB1*15:01 or HLA-A*02:01 affected the number of relapses during treatment. Methods: In this observational cohort study, 355 natalizumab-treated RRMS patients were assessed. Prespecified criteria excluded 62 patients. Clinical data from the starting of treatment to the two-year follow-up visit were collected. Smoking status was obtained by a questionnaire survey. TaqMan allelic discrimination was used for genotyping of tag single-nucleotide polymorphisms (SNPs) for HLA-DRB1*15:01 and HLA-A*02:01. Negative binomial regression analysis was used to analyze the association between relapse rate and smoking intensity and HLA. Results: One pack of cigarettes (20 cigarettes) per day during natalizumab treatment increased the relapse rate during treatment with 38% (incidence rate ratio (IRR) = 1.38, 95% confidence interval (CI): 1.08–1.77, p = 0.01). No association or interaction was found between smoking and HLA-DRB1*15:01 or HLA-A*02:01, respectively. Conclusion: Smoking intensity was significantly associated with the number of relapses during natalizumab treatment.

Long-range genomic regulators of THBS1 and LTBP4 modify disease severity in duchenne muscular dystrophy.

Duchenne muscular dystrophy (DMD) is a severe X-linked recessive disease caused by loss-of-function dystrophin (DMD) mutations in boys, who typically suffer loss of ambulation by age 12. Previously, we reported that coding variants in latent transforming growth factor beta (TGFβ)-binding protein 4 (LTBP4) were associated with reduced TGFβ signaling and prolonged ambulation (p = 1.0 × 10-3 ) in DMD patients; this result was subsequently replicated by other groups. In this study, we evaluated whether additional DMD modifier genes are observed using whole-genome association in the original cohort. We performed a genome-wide association study (GWAS) for single-nucleotide polymorphisms (SNPs) influencing loss of ambulation (LOA) in the same cohort of 253 DMD patients used to detect the candidate association with LTBP4 coding variants. Gene expression and chromatin interaction databases were used to fine-map association signals above the threshold for genome-wide significance. Despite the small sample size, two loci associated with prolonged ambulation met genome-wide significance and were tagged by rs2725797 (chr15, p = 6.6 × 10-9 ) and rs710160 (chr19, p = 4.7 × 10-8 ). Gene expression and chromatin interaction data indicated that the latter SNP tags regulatory variants of LTBP4, whereas the former SNP tags regulatory variants of thrombospondin-1 (THBS1): an activator of TGFβ signaling by direct binding to LTBP4 and an inhibitor of proangiogenic nitric oxide signaling. Together with previous evidence implicating LTBP4, the THBS1 modifier locus emphasizes the role that common regulatory variants in gene interaction networks can play in mitigating disease progression in muscular dystrophy. Ann Neurol 2018;84:234-245.