Agena Bioscience Research Articles

Pharmacogenetics of colorectal cancer in a third-level hospital in Valencia

Abstract Objectives Genetic variants with associated pharmacokinetic and pharmacodynamic effects have an impact on the development of adverse drug reactions and survival of patients with colorectal cancer. Methods A selection of genetic variants was performed according to the established chemotherapy and the pharmacogenetic databases. Genotyping was performed using MassArray technology (Agena Bioscience). Variant-toxicity and survival-genotype correlations were assessed using logistic regression (SPSS v.28.0.1.1). Results Genotyping of 25 SNPs was performed in 96 patients. In relation to the DPYD gene, 3.5 % had the rs75017182 mutation; 4.7 % the rs1801158 mutation and 7.1 % the rs1801160 mutation. Genotypic frequencies in the UGT1A1 gene were 39.4 % (*1/*1); 37.9 % (*1/*28); 19.7 % (*28/*28); and 3 % (*1/*36). The genotypes CT of the rs1801160 variant, AT of the rs67376798 variant (DPYD) and *1/*36 (UGT1A1) were associated with low survival (p-value: 0.006, <0.001, and 0.052, respectively). The most frequent adverse reactions were gastrointestinal disorders, followed by neurotoxicity. The CC genotype (rs1801160, DPYD) was associated with a lower risk for developing severe gastrointestinal events, whereas CC (rs1801158, DPYD) was associated with a lower risk of developing severe general hematologic toxicity. Conclusions The population frequencies obtained in our study for rs1801160 and rs75017182 (DPYD); and for *1/*28, *28/*, and *1/*36 (UGT1A1) were inconsistent with the frequencies reported for the Spanish population in the literature. The genotypes CT of rs1801160, AT of rs67376798 (DPYD), and 1/*36 (UGT1A1) were associated with lower survival rates.

Pharmacogenomic Predictors of Antibiotic-Associated Drug-Induced Liver Injury in Critically Ill Children: Observational Study Results

INTRODUCTION. The pathogenesis of antibiotic-associated drug-induced liver injury (DILI) in children has not been fully elucidated to date. Certain genotypes in patients increase the probability of developing DILI. Therefore, the identification of pharmacogenetic markers associated with DILI in children is essential.АIM. This study aimed to identify pharmacogenetic biomarkers of new-onset DILI associated with tigecycline and meropenem in children.MATERIALS AND METHODS. This prospective observational study was conducted in the Morozov Children’s City Clinical Hospital from 1 February 2020 to 1 September 2021. The study analysed the incidence and types of antibiotic-associated adverse drug reactions (ADRs) in 100 critically ill children aged 0 to 17 years (44 boys and 56 girls). Pharmacogenetic testing was performed in children with ADRs (n=30) to identify potential mechanisms involved in the development of their ADRs. The authors isolated and tested DNA from buccal epithelium swabs using the Agena Bioscience iPLEX® PGx Pro-based VeriDose® Core Panel covering 68 single nucleotide polymorphisms (SNPs) or short insertions and deletions (INDELs) and 5 copy number variants (CNVs).RESULTS. The odds of developing DILI associated with meropenem and tigecycline were higher in carriers of the homozygous cytochrome genotype CYP3A5*3/*3 (OR: 12.6; 95% CI: 1.9–79.4, r=6.54, p=0.011) than in patients with the heterozygous genotype CYP3A5*1A/*3. The odds were even higher in patients not carrying the CYP3A5*1A/*3 genotype (OR: 17.14; 95% CI: 1.79–16.3, r=6.24, p=0.013). The detection of the CYP3A5*3/*3 ge­notype had a prognostic accuracy of 76.7%, a sensitivity of 82%, and a specificity of 74% in predicting the risk of DILI associated with meropenem and tigecycline. Moreover, children with DILI carried the heterozygous ge­notype SLCO1B1*1/*5 (rs4149056 polymorphism) more often than children with other adverse reactions ­associated with meropenem and tigecycline (r=9.8, p=0.002).CONCLUSION. The results of this study prove the prognostic significance of the homozygous cytochrome genotype CYP3A*3/*3 as an indicator of a potential risk for developing DILI associated with meropenem and tigecycline in children in critical conditions.The study was registered at ClinicalTrials.gov under No. NCT04141657 on 24 October 2019.

NEW MULTIPLEX SNP GENOTYPING ASSAY TO SIMUTANEOUSLY SCREEN FOR EIGHT VOLTAGE-GATED SODIUM CHANNEL MUTATIONS IN AEDES AEGYPTI

Aedes aegypti has been implicated as the vector responsible for transmission of dengue, chikungunya, and Zika viruses during disease outbreaks in Florida within the past 15 years. Recently, locally acquired dengue cases have increased dramatically, with more than 450 cases documented in Florida since 2019. This mosquito is known to be resistant to pyrethroid-based insecticides in Florida. Resistance of insects to pyrethroids due to knockdown resistance (kdr) is the result of single nucleotide polymorphisms (SNPs) in the voltage-gated sodium channel gene (vgsc). Recently, two novel SNPs, F174I and E478K, and four known SNPs, V410L, S723T, D1763Y, and Q1853R were reported circulating in Floridian Ae. aegypti populations for the first time. The present study provides a more comprehensive estimate of these SNP frequencies through the screening of a larger number of Floridian Ae. aegypti samples using a new custom multiplex SNP assay we developed using the Agena Biosciences iPLEX Assay platform to facilitate the rapid screening of multiple SNPs at an affordable cost. Our assay was successful in screening 162 Ae. aegypti mosquitoes for 8 SNPs from 4 counties in Southern Florida (Broward, Collier, Palm Beach, and Monroe Counties). This new assay can be used for studies examining the association between genetic mutations and pyrethroid-resistant phenotypes in Ae. aegypti populations such as increased time of survival after insecticide exposure.

IL7RA rs10491434 polymorphism is related to spontaneous HIV infection control in naïve HIV-infected patients: A retrospective study.

Interleukin 7 receptor (IL7R) is vital in the adaptive immune response against human immunodeficiency viruses (HIV). We assessed IL7RA polymorphisms (SNPs) in antiretroviral therapy (ART)-naïve HIV patients for their association with spontaneous HIV infection control. We conducted a retrospective cohort study involving 667 ART-naïve patients categorized by HIV progression (ordinal variable): 150 rapid progressors, 334 moderate/typical progressors, 86 long-term nonprogressors elite controllers (LTNPs-EC), and 97 LTNPs-non-EC. We genotyped three IL7RA SNPs using Agena Bioscience's MassARRAY platform. The association between IL7RA SNPs and spontaneous HIV infection control was evaluated using ordinal logistic regression. Individuals carrying the rs10491434 G allele have a higher likelihood of spontaneous HIV infection control (adjusted odds ratio [aOR] = 1.33; p = 0.023). Moreover, the IL7RA GCT haplotype, consisting of three specific SNPs (rs6897932, rs987106, and rs10491434), demonstrated an association with the control of untreated HIV infection (aOR = 1.34; p = 0.050). Remarkably, the rs10491434 SNP and the IL7RA GCT haplotype exhibited similar aOR values, suggesting that rs10491434 may be primarily responsible for the observed effect of the haplotype. IL7RA rs10491434 G allele is associated with a higher likelihood of spontaneous HIV infection control, indicating its significant role in the pathogenesis of HIV, possibly influencing infection course and viral replication control.

WTAP gene variants and susceptibility to ovarian endometriosis in a Chinese population.

Background: Endometriosis is a common chronic gynecologic disorder with a significant negative impact on women's health. Wilms tumor 1-associated protein (WTAP) is a vital component of the RNA methyltransferase complex for N6-methyladenosine modification and plays a critical role in various human diseases. However, whether single nucleotide polymorphisms (SNPs) of the WTAP gene predispose to endometriosis risk remains to be investigated. Methods: We genotyped three WTAP polymorphisms in 473 ovarian endometriosis patients and 459 control participants using the Agena Bioscience MassArray iPLEX platform. The logistic regression models were utilized to assess the associations between WTAP SNPs and the risk of ovarian endometriosis. Results: In the single-locus analyses, we found that the rs1853259G variant genotypes significantly increased, while the rs7766006T variant genotypes significantly decreased the association with ovarian endometriosis risk. Combined analysis indicated that individuals with two unfavorable genotypes showed significantly higher ovarian endometriosis risk (adjusted OR = 1.71 [1.23-2.37], p = 0.001) than those with zero risk genotypes. In the stratified analysis, the risk effect of the rs1853259 AG/GG and rs7766006 GG genotypes was evident in subgroups of age ≤30, gravidity≤1, parity≤1, rASRM stage I, and the rs7766006GG genotype was associated with worse risk (adjusted OR = 1.64 [1.08-2.48], p = 0.021) in the patients with rASRM stage II + III + IV. The haplotype analysis indicated that individuals with GGG haplotypes had a higher risk of ovarian endometriosis than wild-type AGG haplotype carriers. Moreover, false positive report probability and Bayesian false discovery probability analysis validated the reliability of the significant results. The quantitative expression trait loci analysis revealed that rs1853259 and rs7766006 were correlated with the expression levels of WTAP. Conclusion: Our findings demonstrated that WTAP polymorphisms were associated with susceptibility to ovarian endometriosis among Chinese women.

Higher milk consumption is associated with a lower risk of diabetes mellitus: A case-control study.

Studies have determined that people with genetically defined lactase non-persistence have lower dairy intake that may lead to an increase risk of various non-communicable diseases. Furthermore, lactase non-persistence itself has been associated with insulin resistance. However, data on lactase non-persistence status and dairy intake in developing countries are sparse. We therefore aimed to define 1) the prevalence of lactase non-persistence among individuals with diabetes and non-diabetes in Thai population and 2) the links between lactase non-persistence, milk consumption, and risk of diabetes mellitus. We conducted a case-control study from participants of the National Health Examination Survey. DNA was isolated from the blood for LCT -13910C>T (rs4988235) polymorphism and processed using the Bio-rad c1000 touch thermal cycler and MALDI-TOF Mass Spectrometry MassARRAY Typer v4.0 (Agena Bioscience, San Diego, CA, USA) at the Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital. Cases were participants with previously diagnosed diabetes mellitus or fasting plasma glucose ≥126 mg/dL (n = 1,756) vs. the controls (n = 2,380). We included 4,136 participants, 62% female, and 98.8% were > 30 years old. Homozygous CC genotype (i.e., lactase non-persistence) was noted in 98.6% and only 1.4% carried heterozygous CT. Most (76%) consumed milk <1 portion/month. Participants with either CC or CT genotype had comparable milk consumption and the risk of diabetes mellitus. Males, older adults, and lower education had a lower chance of consuming milk at least one portion per month. Besides various baseline variables, we found that higher milk consumption was associated with a lower DM risk (P = .01). The prevalence of lactase non-persistence in Thai population is very high. A significant difference in milk consumption frequency in relation to the lactase non-persistence status was not found. However, higher milk consumption is associated with a lower risk of diabetes mellitus.

Performance of MassARRAY system for the detection of SARS-CoV-2 compared to real-time PCR.

Early identification of COVID-19 (coronavirus disease of 2019) by diagnostic tests played an important role in the isolation of infectious patients and management of this pandemic. Various methodologies and diagnostic platforms are available. The current "gold standard" for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) diagnosis is real-time reverse transcriptase-polymerase chain reaction (RT-PCR). To overcome the limitations posed by the short supply experienced early during the pandemic and to increase our capacity, we assessed the performance of the MassARRAY System (Agena Bioscience). MassARRAY System (Agena Bioscience) combines RT-PCR (reverse transcription-polymerase chain reaction) with high-throughput mass spectrometry processing. We compared the MassARRAY performance to a research-use-only E-gene/EAV (Equine Arteritis Virus) assay and RNA Virus Master PCR. Discordant results were tested with a laboratory-developed assay using the Corman etal. E-gene primers and probes. 186 patient specimens were analyzed using the MassARRAY SARS-CoV-2 Panel. The performance characteristics were as follows: the positive agreement was 85.71%, 95% CI (78.12 - 91.45), and the negative agreement was 96.67%, 95% CI (88.47 - 99.59). 19/186 (10.2%) results were found to be discordant and assessed by a different assay with the exception of 1, where the sample was not available for repeat testing. 14 out of 18 agreed with the MassARRAY after testing with the secondary assay. The overall performance after discordance testing was as follows: the positive agreement was 97.3%, 95% CI (90.58 - 99.67), and the negative agreement was 97.14%, 95% CI (91.88 - 99.41). Our study demonstrates that the MassARRAYSystem is an accurate and sensitive method for SARS-CoV-2 detection. Following the discordant agreement with an alternate RT-PCR test, the performance was found to have sensitivity, specificity, and accuracy exceeding 97%, making it a viable diagnostic tool. It can be used as an alternative method during periods when real-time RT-PCR reagent supply chains are disrupted.

GENETIC VARIATION AND PREDICTED PHENOTYPES IN CYP2C9, CYP2C19, CYP3A4, CYP3A5 AND CYP2D6 GENES AMONG 552 PATIENTS WITH UNCONTROLLED TREATED HYPERTENSION

Objective: Altered drug metabolism may be a contributing factor to uncontrolled hypertension. Beta-blockers, alpha-blockers, calcium antagonists and angiotensin receptor blockers undergo hepatic metabolism by cytochrome P450 (CYP) enzymes. Genetic variation can contribute to interindividual variation, lack of treatment response or side effects with discontinuation of treatment. We aimed to determine common CYP gene variations in patients with treated but uncontrolled hypertension and to compare the distribution with the prevalence in the overall Caucasian population. Design and method: In this national multicenter study we mapped CYP2D6, CYP2C9, CYP2C19, CYP3A4 and CYP3A5 polymorphisms in 552 patients prescribed &gt; = 2 antihypertensive agents and with systolic daytime ambulatory blood pressure (ABPM) &gt; = 135 mmHg. On the (MALDI-TOF) MassARRAY analyzer, single nucleotide variants and small insertions/deletions (indels) were investigated with the VeriDose Core Panel and CYP2D6 copy-number variation with the VeriDose CYP2D6 CNV Panel (Agena Biosciences). Each allele is associated with either normal, decreased, absent, increased or unknown enzyme function based on activity scores defined by the The Clinical Pharmacogenetics Implementation Consortium (CPIC) and describe function and phenotypes for genes (IM = Intermediate metabolizer, PM = poor metabolizer, RM = rapid metabolizer and UM = ultra-rapid metabolizer). Results: 94% of patients were Caucasian. Mean daytime ABPM was 146/84 mmHg (135-190/55-106 mmHg), median age 63 (26-86) years and 35% were female. The distributions of the predicted phenotypes (illustrated in colors in Figure) for each enzyme did not differ from that reported in Caucasian population by The Pharmacogenomics Knowledgebase (PharmGK) (gray). 11% had normal phenotype in all five enzymes whereas 49% had &gt; = 2 enzymes affected by gene variants. Conclusions: The phenotype distribution of five relevant CYP genes in patients with uncontrolled hypertension did not differ from the general Caucasian population. Dosing guidelines based on CYP2D6 genotype currently exist for metoprolol, but for other antihypertensive drugs further investigation is needed. The low proportion of patients with five normal enzymes and the high proportion with &gt; = 2 enzymes affected suggest that pharmacogenetic CYP-testing may be useful for individualizing drug treatment in patients with uncontrolled hypertension.

IRF5-TNOP3 polymorphisms are associated with elite control of HIV infection: A retrospective study.

IRF5-TNPO3polymorphisms have previously been related to immune response, and TNPO3 plays a role inhuman immunodeficiency virus(HIV)-1infection after nuclear import. Therefore, we analyzed the genetic association between IRF5-TNPO3 polymorphisms and the HIV elite control in long-term nonprogressors (LTNPs). We performed a retrospective cohort study on 183 LTNPs, who were antiretroviral therapy-naïvewith CD4+ ≥ 500 cells/mm3 , viral load ≤10 000 copies/mL, and asymptomatic over 10 years after HIV seroconversion. The primary outcome variable was HIV elite control (undetectable viral load in at least 90% of the measurements for at least 1year). Seven IRF5-TNPO3polymorphisms were genotyped using Agena Bioscience's MassARRAY platform. We found a significant association between specific IRF5-TNPO3genotypes and HIV elite control: rs2004640 TT (aOR = 2.05;p = 0.041), rs10954213 AA (aOR = 1.95;p = 0.035), rs2280714 TT (aOR = 2.02;p = 0.031), and rs10279821 CC (aOR = 2.12;p = 0.017). We also found a significant association between IRF5-TNPO3haplotype TATC composed of the favorable significant polymorphisms (rs2004640, rs10954213, rs2280714, and rs10279821) and the HIV elite control (aOR = 1.59;p = 0.048).IRF5-TNPO3rs2004640, rs10954213, rs2280714, and rs10279821 polymorphisms were related to HIV elite control in LTNPs. Our data provide new knowledge about the impact of IRF5-TNPO3polymorphisms on HIV pathogenesis to understand the phenomenon of natural HIV control.

Replication of genetic associations of chemotherapy-related cardiotoxicity in the adjuvant NSABP B-31 clinical trial.

The cardiotoxic effects of doxorubicin, trastuzumab, and other anticancer agents are well known, but molecular genetic testing is lacking for the early identification of patients at risk for therapy-related cardiac toxicity. Using the Agena Bioscience MassARRAY system, we genotyped TRPC6 rs77679196, BRINP1 rs62568637, LDB2 rs55756123, RAB22A rs707557, intergenic rs4305714, LINC01060 rs7698718, and CBR3 rs1056892 (V244M) (previously associated with either doxorubicin or trastuzumab-related cardiotoxicity in the NCCTG N9831 trial of anthracycline-based chemotherapy ± trastuzumab) in 993 patients with HER2+ early breast cancer from the NSABP B-31 trial of adjuvant anthracycline-based chemotherapy ± trastuzumab. Association analyses were performed with outcomes of congestive heart failure (N = 29) and maximum decline in left ventricular ejection fraction (LVEF) using logistic and linear regression models, respectively, under an additive model with age, baseline LVEF, and previous use of hypertensive medications as covariates. Associations of maximum decline in LVEF in the NCCTG N9831 patients did not replicate in the NSABP B-31 patients. However, TRPC6 rs77679196 and CBR3 rs1056892 were significantly associated with congestive heart failure, p < 0.05, with stronger associations observed in patients treated with chemotherapy only (no trastuzumab) or in the combined analysis of all patients relative to those patients treated with chemotherapy + trastuzumab. TRPC6 rs77679196 and CBR3 rs1056892 (V244M) are associated with doxorubicin-induced cardiac events in both NCCTG N9831 and NSABP B-31. Other variants previously associated with trastuzumab-related decline in LVEF failed to replicate between these studies.

Chronic Kidney Disease: Interaction of Adiponectin Gene Polymorphisms and Diabetes.

Adiponectin is an adipokine multipeptide hormone with insulin-sensitizing; anti-atherosclerotic; and anti-inflammatory properties. Chronic kidney disease (CKD) may be associated with low adiponectin. The adiponectin gene ADIPOQ is thought to be the only major gene responsible for plasma adiponectin levels; which are associated with diabetes and diabetic nephropathy. The purpose of this study was to investigate the association between ADIPOQ polymorphism and CKD. In addition; the combined effects of ADIPOQ polymorphism and diabetes and levels of total urinary arsenic and blood cadmium on CKD were also explored. This study included 215 CKD patients and 423 age-sex matched controls. The ADIPOQ polymorphisms were determined using the Agena Bioscience Mass ARRAY System. The levels of blood cadmium and urinary arsenic species were measured. The ADIPOQ rs182052 GA/AA genotype had a marginally lower odds ratio (OR) for CKD than the GG genotype. The OR (95% confidence interval; CI) was 16.33 (5.72-46.66) of CKD in subjects carrying the ADIPOQ rs182052 GG genotype and diabetes compared to non-diabetes subjects carrying the ADIPOQ rs182052 GA/AA genotype; the interaction term had p = 0.015; and the synergy index was 6.64 (1.81-24.36) after multivariate adjustment. A significant interaction of diabetes and ADIPOQ rs1501299 risk genotype increased the OR of CKD after multivariate adjustment with a synergy index of 0.31 (0.11-0.86) and a multiplicative interaction with p = 0.001. These results suggest that ADIPOQ rs182052 and rs1501299 risk genotypes may significantly modify the association between diabetes and CKD but not the association between total urinary arsenic and blood cadmium and CKD.

Study protocol of the HD-MED study aiming to personalize drug treatment in Huntington's disease: a longitudinal, observational study to assess medication use and efficacy in relation to pharmacogenetics.

Huntington's disease (HD) is a hereditary, neurodegenerative disorder characterized by motor, cognitive, and psychiatric symptoms. Currently, HD can only be managed symptomatically, including a large variety of prescribed drugs. Many HD patients experience negative medication effects (e.g. side effects or non-response). Pharmacogenetic (PGx) studies show how genetic variation affects both medication efficacy and toxicity and holds the potential to improve these outcomes of drug treatment. To classify the effect of the PGx profile of CYP2C19 and CYP2D6 in HD gene expansion carriers on negative medication effects of HD-related medication. Multicenter, observational study with 1-year follow-up. Adult HD gene expansion carriers who use one or more HD-related medications are eligible to participate. A detailed overview of medication use, medication efficacy, and side effects is retrospectively and prospectively collected via medication diaries, questionnaires, phone calls, and pharmacy medication verification schemes. PGx analysis on whole blood-extracted DNA is performed with Agena Bioscience VeriDose® Core Panel and long-range polymerase chain reaction copy number variation analysis. Per the study protocol-defined negative medication effects in HD gene expansion carriers with a genotype predicted poor or ultrarapid metabolizer phenotype will be compared with HD gene expansion carriers with a predicted intermediate and normal metabolizer phenotype. Frequencies will be analyzed via χ2 and logistic multivariate regression analysis. In addition, we summarize in this manuscript HD-relevant PGx prescription recommendations to improve drug therapy. The original study protocol was approved by the medical research ethics committee Leiden Den Haag Delft on 26 November 2019. HD-MED is a low-risk study that will generate personalized PGx results that can immediately be implemented in clinical practice, thus potentially improving pharmacovigilance and patients' quality of life. This study is registered in the International Clinical Trial Registry Platform under registration number NL8251, URL https://trialsearch.who.int/Trial2.aspx?TrialID=NL8251.

2001. Clinical management changes after positive multiplex gastrointestinal pathogen panel testing for evaluation of diarrhea

Abstract Background IDSA guidelines for diarrhea include pathogen-specific management. Compared to non-molecular tests, multiplex gastrointestinal pathogen panels (GIPPs) may allow for more timely and cost-effective diagnoses and care. However, this has yet to be definitively demonstrated. Our objective was to determine the impact of positive GIPP results on clinical management, including antimicrobial use. Methods We performed a retrospective study of patients with diarrhea and a positive GIPP result (xTAG Gastrointestinal Pathogen Panel, Luminex) at an academic, tertiary-care medical center from January-December 2018. We excluded immunocompromised patients (solid organ or stem cell transplant, HIV with absolute CD4 count &amp;lt; 200 cells/µL, primary immunodeficiency, and immunosuppressive medications including biologics). We collected patient and clinical data via electronic medical record review. Our primary outcome of interest was change in antimicrobial usage. Results A total of 2,333 GIPP tests were performed of which 266 (11.4%) were positive. Of 193 patients who met inclusion criteria, 34% were tested in an emergency room, 38% in outpatient clinics, and 29% on inpatient wards. Of these, 55% were men, 65% were white, and the median age was 31 years (interquartile range, IQR 5-56). The median turnaround time from GIPP collection to result was 31 hours (IQR 24-53). The most frequently identified pathogens were norovirus, Salmonella, and Campylobacter (Figure 1). In 43% of patients, results led to one or more management changes including antibiotic discontinuation (8%) and antibiotic initiation (25%). Antibiotics were most often discontinued for norovirus (Figure 1A) and started for Campylobacter (Figure 1B). Other management changes occurred in 13% of patients, including avoidance of further diagnostic testing and isolation precaution change. The median turnaround time did not differ for GIPPs that were (30 hours; IQR 22-50) or were not (32 hours; IQR 25-56) associated with management change. Conclusion Positive GIPP results can prompt changes in antimicrobial treatment in non-immunocompromised patients with diarrhea. Future efforts will evaluate the appropriateness of these management changes. Disclosures Melissa B. Miller, PhD, Abbott Molecular: Grant/Research Support|Agena Biosciences: Board Member|ArcBio: Grant/Research Support|Cepheid: Board Member|Luminex Molecular Diagnostics: Board Member|QIAGEN: Board Member|QIAGEN: Grant/Research Support|Sherlock Biosciences: Advisor/Consultant|Talis Biomedical: Board Member|Thermo Fisher: Honoraria|Werfen: Board Member.

Исследование ассоциации полиморфизма rs10508336 гена транскрипционного фактора TAF3 с риском развития заболеваний артерий нижних конечностей в российской популяции

Atherosclerosis obliterans (AO) and diabetic angiopathy (DA) are known to be peripheral artery diseases (PAD) of multifactorial origin, in which genetic and environmental factors play a synergetic role. TAF3 is one of the genes that has been found to be associated with PAD. The aim of the study: To analyze the association of the rs10508336 polymorphism of the TAF3 gene with the risk of PAD in the Russian population. Materials and methods: The study involved 1261 patients, including 642 healthy subjects and 619 PAD patients. All patients were recruited at the Vascular Surgery Division of the Kursk Regional Clinical Hospital. Isolation of genomic DNA was carried out by chloroform extraction and precipitation with ethanol. Genotyping was carried out on the basis of the Research Institute of Genetic and Molecular Epidemiology of KSMU using a MassARRAY-4 time-of-flight genomic mass spectrometer (Agena Bioscience, USA). Results: We found that polymorphism rs10508336 is associated with an increased risk of developing bilateral peripheral atherosclerosis exclusively in smokers (P&lt;0.05). The polymorphism was found to be statistically significantly associated with an increased risk of DA (OR=1.59, 95% CI 1.02-2.46, P=0.045). Furthermore, an association of the rs10508336-A allele with an increase in blood glucose levels in PAD was observed (P=0.01). Conclusion: In the Russian population, an association of the rs10508336 polymorphism of the TAF3 gene with an increased risk of AO, hyperglycemia, and diabetic angiopathy was revealed for the first time. The identified associations point out a possible relationship between carbohydrate metabolism and atherosclerotic processes in the determination of peripheral arterial diseases.

3′ Untranslated Region Variants in DEFA5 Gene Associated with Susceptibility to Iga Nephropathy in the Chinese Han Population

Aim: To evaluate the association between single-nucleotide polymorphisms in the 3' untranslated region of the DEFA5 gene and IgA nephropathy (IgAN) risk, the authors performed an association study in the Chinese Han population. Materials & methods: The authors recruited 426 IgAN patients and 498 controls. The MassARRAY platform (Agena Bioscience, Inc., CA, USA) was used to genotype single-nucleotide polymorphisms in DEFA5. Odds ratios and 95% CIs were calculated through logistic regression analysis. Results: The authors observed that rs12716641 significantly reduced IgAN risk in the allele (odds ratio: 0.77; p =0.026) and genotype (odds ratio: 0.75; p =0.039) models. Stratification analysis revealed that several genotypes of rs12716641 played a protective role against IgAN. Conclusion: The authors' results revealed that single-nucleotide polymorphisms in the 3' untranslated region of DEFA5 were associated with IgAN risk.

Rs420137, rs386360 and rs7763726 polymorphisms in fibronectin type III domain containing 1 are associated with susceptibility to coronary heart disease: Analysis in the Han population.

BackgroundNumerous genetic studies have shown that genes are related to the pathogenesis of coronary heart disease (CHD). The main aim of this study was to confirm whether fibronectin type III domain containing 1 (FNDC1) polymorphisms correlate with the risk of CHD.MethodsIn this study, in order to assess the association between three FNDC1 single nucleotide polymorphisms (SNPs) and the risk of CHD, we conducted a case-control study involving 630 patients with CHD and 568 healthy controls using Agena MassARRAY (Agena Bioscience, San Diego, CA, USA). Genotype distribution in case and control groups was analyzed by Chi square test. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated by logistic regression models adjusted for age, sex, smoking, and alcohol consumption to assess the correlation between SNPs and CHD risk.ResultsOur results indicated that FNDC1-rs420137, -rs386360, and -rs7763726 played important roles in enhancing the risk of CHD. Subgroup analysis revealed that rs420137 increased the susceptibility to CHD in males, smokers, and patients aged ≤62 years. Rs360 had an increased risk of CHD in males, patients at aged ≤62 years, smokers, and non-drinkers. Furthermore, the association of rs7763726 with increased CHD risk was also observed in males, patients aged ≤62 years, smokers, and drinkers. Last but not least, these three SNPs we selected were protective factors against hypertension in CHD individuals.ConclusionOur research suggest that FNDC1-rs420137, -rs386360, and -rs7763726 variants may be regarded as novel biomarkers for predicting CHD risk and other specific mechanisms of action of CHD need to be further studied.

Mitochondrial genomic variation in dementia with Lewy bodies: association with disease risk and neuropathological measures

Dementia with Lewy bodies (DLB) is clinically diagnosed when patients develop dementia less than a year after parkinsonism onset. Age is the primary risk factor for DLB and mitochondrial health influences ageing through effective oxidative phosphorylation (OXPHOS). Patterns of stable polymorphisms in the mitochondrial genome (mtDNA) alter OXPHOS efficiency and define individuals to specific mtDNA haplogroups. This study investigates if mtDNA haplogroup background affects clinical DLB risk and neuropathological disease severity. 360 clinical DLB cases, 446 neuropathologically confirmed Lewy body disease (LBD) cases with a high likelihood of having DLB (LBD-hDLB), and 910 neurologically normal controls had European mtDNA haplogroups defined using Agena Biosciences MassARRAY iPlex technology. 39 unique mtDNA variants were genotyped and mtDNA haplogroups were assigned to mitochondrial phylogeny. Striatal dopaminergic degeneration, neuronal loss, and Lewy body counts were also assessed in different brain regions in LBD-hDLB cases. Logistic regression models adjusted for age and sex were used to assess associations between mtDNA haplogroups and risk of DLB or LBD-hDLB versus controls in a case-control analysis. Additional appropriate regression models, adjusted for age at death and sex, assessed associations of haplogroups with each different neuropathological outcome measure. No mtDNA haplogroups were significantly associated with DLB or LBD-hDLB risk after Bonferroni correction.Haplogroup H suggests a nominally significant reduced risk of DLB (OR=0.61, P=0.006) but no association of LBD-hDLB (OR=0.87, P=0.34). The haplogroup H observation in DLB was consistent after additionally adjusting for the number of APOE ε4 alleles (OR=0.59, P=0.004). Haplogroup H also showed a suggestive association with reduced ventrolateral substantia nigra neuronal loss (OR=0.44, P=0.033). Mitochondrial haplogroup H may be protective against DLB risk and neuronal loss in substantia nigra regions in LBD-hDLB cases but further validation is warranted.

Novel KEL allele associated with loss of Kpb identified in a white blood donor.

The importance of identifying variant alleles among blood donors is significant to the safety of transfusion for recipients. Molecular methods have become more prominent in the routine process of antigen typing donor units. Some variant antigens cannot be detected using only serologic methods. Molecular testing allows the determination of nucleotide sequences that are used to predict a phenotype. Antigens of the Kell blood group system are known for being highly immunogenic and causing adverse reactions upon antibody formation. A female white blood donor who typed Kp(b-) using serologic methods on multiple donations since 2005 was the subject of a typing discrepancy investigation. Routine genotyping using a commercial genotyping kit (HemoID DQS Panel; Agena Bioscience, San Diego, CA) predicted the donor to type Kp(a+b+). Investigation of the discrepancy between these two results identified a rare single nucleotide variant in the KEL gene at nucleotide position c.948G>T that alters amino acid residue 316 from tryptophan (Trp) to cysteine (Cys). After discovery of the novel allele, adsorption and elution studies were performed to see if there was weakened Kpb expression. The elution studies yielded negative results, which indicated that Kpb is not expressed. The KEL transcripts expressed by the donor were determined using cDNA analysis, and the predicted amino acid sequence of the novel allele was modeled to investigate the impact of the amino acid sequence on the structure of the KEL polypeptide. Both SWISS-MODEL and Robetta software were used to evaluate the impact of the p.Trp316Cys on the three-dimensional protein structure. There was no conformational change noted with SWISS-MODEL, whereas the Robetta software showed a significant conformational change compared with the normal Kp(b+) reference sequence. Because the donor is homozygous for variants associated with k and Jsb expression, it was not possible to determine whether the novel allele is associated with loss of Kpb only or loss of all Kell antigens.

Study of LHCGR gene variants in a sample of colombian women with polycystic ovarian syndrome: A pilot study

PurposeTo evaluate the association between polymorphisms of the LHCGR gene and PCOS in a sample from Colombian women. MethodsWe included 49 Colombian women with PCOS and 49 healthy women. Genotype distributions between groups were compared, and phenotype-genotype association analysis was performed in the PCOS group. Identification of five SNP’s in the LHCGR gene was carried out through the iPLEX and MassARRAY system (Agena Bioscience). ResultsOur results showed that the rs7371084 variant was negatively associated with PCOS under the codominant, dominant, and overdominant models. Women with the TC + TT genotypes in rs2293275 had shorter menstrual cycles (p = 0.026), and women with the CT + CC genotypes in rs6732721 showed a decrease in the number of antral follicles (p = 0.038).Within the endocrine parameters, we identified associations between GA + GG genotypes in rs13405728 and CT + CC genotypes in rs6732721, and the decrease in LH levels (p = 0.013; p = 0.04, respectively). Women with TC + TT genotypes in rs2293275 had increased DHEAS (p = 0.047) and androstenedione (p = 0.045) levels. Regarding metabolic parameters, we identified associations between GA + GG genotypes in rs13405728 and CT + CC genotypes in rs6732721, and an increase in fasting glucose levels (p = 0.028; p = 0.017, respectively). ConclusionWe found that the rs7371084 variant was negatively associated with PCOS. Also, we identify associations between combined genotypes of the LHCGR gene and the phenotypic traits of PCOS, such as shorter menstrual cycle length, fewer follicles, lower LH levels, and increased DHEAS, androstenedione, and fasting glucose levels. The results of this pilot study provide a basis to clarify the genetics and pathophysiology of PCOS in the Colombian population. Future large-scale studies are recommended for this population.

A common epigenetic clock from childhood to old age

Forensic age estimation is a DNA intelligence tool that forms an important part of Forensic DNA Phenotyping. Criminal cases with no suspects or with unsuccessful matches in searches on DNA databases; human identification analyses in mass disasters; anthropological studies or legal disputes; all benefit from age estimation to gain investigative leads. Several age prediction models have been developed to date based on DNA methylation. Although different DNA methylation technologies as well as diverse statistical methods have been proposed, most of them are based on blood samples and mainly restricted to adult age ranges. In the current study, we present an extended age prediction model based on 895 evenly distributed Spanish DNA blood samples from 2 to 104 years old. DNA methylation levels were detected using Agena Bioscience EpiTYPER® technology for a total of seven CpG sites located at seven genomic regions: ELOVL2, ASPA, PDE4C, FHL2, CCDC102B, MIR29B2CHG and chr16:85395429 (GRCh38). The accuracy of the age prediction system was tested by comparing three statistical methods: quantile regression (QR), quantile regression neural network (QRNN) and quantile regression support vector machine (QRSVM). The most accurate predictions were obtained when using QRNN or QRSVM (mean absolute prediction error, MAE of ± 3.36 and ± 3.41, respectively). Validation of the models with an independent Spanish testing set (N = 152) provided similar accuracies for both methods (MAE: ± 3.32 and ± 3.45, respectively). The main advantage of using quantile regression statistical tools lies in obtaining age-dependent prediction intervals, fitting the error to the estimated age. An additional analysis of dimensionality reduction shows a direct correlation of increased error and a reduction of correct classifications as the training sample size is reduced. Results indicated that a minimum sample size of six samples per year-of-age covered by the training set is recommended to efficiently capture the most inter-individual variability..