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PubMed2026

Targeted variant analysis of feline mediastinal lymphoma using MassARRAY and clinical associations.

Lymphoma is the most commonly diagnosed cancer in cats. This study used the Agena MassARRAY to genotype 40 variants across 17 genes in feline mediastinal lymphoma. These variants have previously been identified in tumors, including T- and B-cell lymphomas, acute and chronic lymphocytic leukemias, and mast cell tumors, in humans, dogs, and cats, using various methods. They were selected based on high prevalence reported in prior oncology studies, potential relevance to targeted therapy, and suitability for multiplex PCR amplification. Pleural fluid samples were collected from 76 cats with mediastinal lymphoma, including 69 domestic shorthairs, two Persians, two Siamese, two Wichienmaat, and one Scottish Fold. The most prevalent variants were found in the BCL2, KIT, STAT3, and ZEB1 genes. Specifically, BCL2 c.83275986G > A and c.83275992G > T were present in 71.1% and 57.9%, respectively. In cats with variant-positive in KIT c.163965724C > CT significantly reduced (11 days) compared to wild-type cats (94 days) (p < 0.001). In cats with variant-positive in STAT3 c.42942437C > CA, resulted in shorter median survival compared to wild-type cats (18 days vs. 77 days, p = 0.006). The findings suggest that the variant panel could be useful for the genomic landscape of feline mediastinal lymphoma and warrant further validation.

Animals↗

PubMed2025

A MGMT Enhancer Variant is Associated with Glioma Susceptibility and Progression.

The O6-methylguanine-DNA methyltransferase (MGMT) plays a significant role in the pathogenesis and progression of glioma. Numerous enhancer variants, including those within the MGMT gene region and adjacent gene regions, have been found to be associated with cancer development and progression. We investigated the significance of enhancer variants located in the intergenic spacer far from the MGMT gene in relation to glioma susceptibility and progression. We recruited 402 glioma patients and 654 controls for this investigation using Sequenom MassARRAY genotyping. We identified a significantly elevated risk of glioma among carriers with the rs11016629 TG genotype compared to those with the GG genotype (OR = 1.41, 95% CI 1.03-1.93; P = 0.034). Subgroup analyses revealed that rs11016629 was significantly associated with glioma risk in subjects with WHO grade IV tumor (OR = 1.59, 95% CI 1.07-2.38; P = 0.023) and high-grade glioma (OR = 1.57, 95% CI 1.11-2.21; P = 0.011). Patients who underwent gross total resection with TG/TT genotypes exhibited a 2.66-fold higher risk of disease progression than GG carriers (HR = 2.66, 95% CI 1.23-5.79; P = 0.014). The study demonstrates that a MGMT enhancer variant rs11016629 contributes to both glioma susceptibility and progression.

Humans↗

PubMed2025

Newborn screening for common genetic variants associated with permanent hearing loss: Implementation in Ontario and review of the first 3 years.

PURPOSE: Early hearing detection and intervention (EHDI) programs using audiometric screening techniques alone have a limited ability to detect noncongenital childhood permanent hearing loss (PHL). In 2019, Ontario launched universal newborn screening (NBS) for PHL risk factors, including congenital cytomegalovirus and 22 common variants in GJB2 and SLC26A4. Here, we describe our experience in screening for genetic risk factors. METHODS: Ontario newborns who participated in universal newborn hearing screening (UNHS) were offered risk factor screening using dried blood spots (DBS) collected for conventional newborn screening. The screening was conducted using a custom MassArray assay, and positive results were confirmed by Sanger sequencing or polymerase chain reaction. Diagnostic audiological assessments were performed for all screen-positive infants. RESULTS: Of the 412,424 infants screened, 93 had 2 variants in GJB2 or SLC26A4. Of these, 72 had confirmed PHL, 20 had normal hearing, and 1 declined follow-up. Thirteen infants with PHL (1 in 31,724; 11.8% of screen positives) were not identified through audiometric testing as they passed (3) or missed (10) the screening. Importantly, among infants who ultimately received cochlear implants, the detection of genetic etiology through NBS led to an accelerated time to diagnosis, assessment, and intervention. CONCLUSION: Genetic screening has strengthened UNHS and care for infants with or at risk of PHL in Ontario. This study is a step toward the broader inclusion of genomic testing in NBS.

Humans↗

PubMed2025

LncRNA C5orf64 polymorphisms (rs12518552 and rs2950218) decreases pulmonary tuberculosis susceptibility.

BACKGROUND: Pulmonary tuberculosis (PTB) remains a significant global health issue, with genetic factors playing a crucial role in susceptibility. Long noncoding RNA (lncRNA) C5orf64 has been implicated in immune responses and cancer, but its association with PTB risk has not been fully explored. METHODS: Genomic DNA was extracted from peripheral blood samples of 955 participants (474 PTB cases and 481 controls). Rs12518552 and rs2950218 in C5orf64 were genotyped using the Agena MassARRAY system. Logistic regression analysis was performed to assess the association between these polymorphisms and PTB risk. Stratified analysis was conducted to evaluate the influence of age, gender, and smoking status. RESULTS: Rs12518552-G (OR = 0.82, p = 0.034) and rs2950218-T (OR = 0.77, p = 0.012) were associated with a reduced PTB risk. Stratified analysis revealed that rs12518552 was associated with a protective effect against PTB in individuals over 40 years old (OR = 0.73, p = 0.024), females (OR = 0.77, p = 0.034), and non-smokers (OR = 0.78, p = 0.040), and rs2950218 was also associated with a reduced PTB risk in individuals over 40 years old (OR = 0.73, p = 0.040), females (OR = 0.72, p = 0.046), and non-smokers (OR = 0.72, p = 0.011). CONCLUSION: C5orf64 polymorphisms, particularly rs12518552 and rs2950218, are associated with a reduced risk of PTB. These findings suggest that C5orf64 polymorphisms contribute to genetic susceptibility to PTB, with implications for PTB targeted screening and personalized therapeutic strategies.

Humans↗

PubMed2025

Association of AGER genetic variants with chronic obstructive pulmonary disease susceptibility in Southern Chinese Han populations.

OBJECTIVE: Chronic obstructive pulmonary disease (COPD) remains a leading cause of disability and mortality among elderly populations. Studies indicate that AGER plays a critical regulatory role in the pathogenesis of respiratory disorders. However, the genetic variations in AGER to COPD susceptibility remain incompletely understood. This study employs a case-control design to investigate associations between AGER genetic variants and COPD risk in the Southern Chinese Han population. METHODS: This study enrolled 270 COPD patients and 271 healthy controls. AGER single-nucleotide polymorphisms (SNPs) were analysed using the MassARRAY iPLEX platform. Logistic regression models evaluated associations between AGER polymorphisms and COPD susceptibility, with false discovery rate (FDR) correction applied to mitigate multiple testing errors. SNP-SNP interactions were investigated through multifactor dimensionality reduction (MDR) analysis. Expression quantitative trait locus (eQTL) data from the GTEx database were further analysed to assess regulatory relationships between SNPs and AGER gene expression levels. RESULTS: This study showed that rs3134941 (G allele, OR = 0.21, 95% CI = 0.10-0.41, p (FDR) = 0.001) and rs3131300 (G allele, OR = 0.32, 95% CI = 0.20-0.49, p (FDR) = 0.0001) were significantly associated with a reduced susceptibility to COPD. MDR indicated that rs3131300 was the optimal predictive model for COPD risk. Additionally, initial mechanistic investigations utilizing the GTEx database identify rs3134941 (C > G) and rs3131300 (A > G) as significant expression quantitative trait loci for AGER mRNA in cell-cultured fibroblasts and whole blood. CONCLUSION: Our study demonstrated that AGER genetic variants might play a protective role in the progression of COPD.

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PubMed2024

Evidence for a relationship between genetic polymorphisms of the L-DOPA transporter LAT2/4F2hc and risk of hypertension in the context of chronic kidney disease.

BACKGROUND: Chronic kidney disease (CKD) and hypertension are chronic diseases affecting a large portion of the population frequently coexistent and interdependent. The inability to produce/use adequate renal dopamine may contribute to the development of hypertension and renal dysfunction. The heterodimeric amino acid transporter LAT2/4F2hc (SLC7A8/SLC3A2 genes) promotes the uptake of L-DOPA, the natural precursor of dopamine. We examined the plausibility that SLC7A8/SLC3A2 gene polymorphisms may contribute to hypertensive CKD by affecting the L-DOPA uptake. METHODS: 421 subjects (203 men and 218 women, mean age of 78.9 ± 9.6 years) were recruited and divided in four groups according to presence/absence of CKD, defined as reduced estimated glomerular filtration rate (eGFR < 60 ml/min/m2) calculated using the creatinine-based Berlin Initiative Study-1 (BIS1) equation, and to presence/absence of hypertension (systolic blood pressure ≥ 140 and/or diastolic blood pressure ≥ 90 mmHg). Subjects were analysed for selected SNPs spanning the SLC7A8 and SLC3A2 loci by Sequenom MassARRAY iPLEX platform. RESULTS: The most significant SNP at the SLC3A2 (4F2hc) locus was rs2282477-T/C, with carriers of the C-allele having a lower chance to develop hypertension among CKD affected individuals [OR = 0.33 (CI 0.14-0.82); p = 0.016]. A similar association with hypertensive CKD was found for the SLC7A8 (LAT2) rs3783436-T/C, whose C-allele resulted associated with decreased risk of hypertension among subjects affected by CKD [OR = 0.56 (95% CI 0.35-0.90; p = 0.017]. The two variants were predicted to be potentially functional. CONCLUSIONS: The association between SLC3A2 and SLC7A8 variants to hypertension development in patients with renal failure could be linked to changes in L-DOPA uptake and consequently dopamine synthesis. Although the associations do not survive correction for Bonferroni multiple testing, and additional research is needed, our study opens new avenues for future basic and translational research in the field of hypertensive CKD.

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PubMed2025

The association between rs2228226 and postoperative clinical outcomes in gastric adenocarcinoma: a retrospective study.

BACKGROUND: This study aims to investigate the differences in postoperative prognosis associated with the single nucleotide polymorphism (SNP) rs2228226 (G > C) in gastric adenocarcinoma (GAC) patients. METHODS: This study enrolled 661 patients with locally advanced (pT4a) GAC after surgery. DNA was extracted from their tissues and genotyped for rs2228226 using a MassARRAY Analyzer. Based on the patients' clinical and pathological information, a multifactorial Cox regression analysis was performed to assess the correlation between rs2228226 and the clinical prognosis of pT4a GAC patients. Survival differences among patients who received postoperative chemotherapy were also examined according to rs2228226. RESULTS: After excluding patients with distant metastasis, loss to follow-up, and those not meeting the inclusion criteria, a total of 463 patients with complete data were included. The rs2228226 genotype distribution was as follows: C/C = 57 (12.3%), G/C = 200 (43.2%), and G/G = 206 (44.5%). Patients with the C/C genotype had significantly shorter disease-free survival (DFS = 12 months) and overall survival (OS = 27 months) compared to those with the G/C or G/G genotype (DFS = 19 months, log-rank P = 0.003; OS = 35 months, log-rank P = 0.002). Further analysis of patients receiving chemotherapy identified the C/C genotype, advanced age, lymph node metastasis, degree of differentiation, and failure to achieve R0 resection as independent risk factors for tumor recurrence and metastasis (P < 0.05). The C/C genotype, lymph node metastasis, and tumor recurrence and metastasis were independent risk factors for mortality (P < 0.05). CONCLUSIONS: In pT4a GAC patients undergoing postoperative chemotherapy, the C/C genotype at rs2228226 is an independent risk factor for tumor recurrence, metastasis, and death. The rs2228226 (G > C) polymorphism may serve as a potential biomarker for predicting prognosis after chemotherapy in GAC.

Humans↗

PubMed2025

ABO exon polymorphisms are related to ischemic stroke in a Chinese Han population.

BACKGROUND: Recent research have underscored the relation of ABO blood group system to cerebrovascular disorders predisposition. The present investigation endeavors to delve into the relationship between ABO polymorphisms and ischemic stroke (IS) risk. METHODS: A cohort of 646 IS patients and 649 matched healthy controls was recruited. Genotyping of five SNPs within ABO were conducted by Agena MassARRAY platform. Logistic regression models were employed to estimate odds ratios (ORs) and 95% confidence intervals (CIs). Additionally, SNP-SNP interaction was assessed by multifactor dimensionality reduction (MDR) method. Furthermore, Analysis of Variance (ANOVA) was utilized to explore the association between genotypes and blood lipid profiles. RESULTS: The study identified an elevated IS risk associated with rs8176740 and rs8176720 in the overall population. Notably, ABO rs8176720 emerged as the most informative single-locus model for IS susceptibility. These variants were related to an elevated IS risk, specifically in female subjects, the subgroup aged > 64 years, non-smokers, drinkers or non-drinkers. Moreover, rs8176749 and rs8176745 were associated with red blood cell count levels and total bilirubin levels. CONCLUSION: This study firstly demonstrated the association of ABO rs8176740 and rs8176720 with IS incidence, which increased the understanding regarding the effect of ABO on IS pathogenesis.

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