Variable Number Tandem Repeat Genotype Research Articles

Abstract C055: Unraveling pancreatic cancer susceptibility at 5p15.33: Functional characterization of a novel VNTR element

Abstract Genome-wide association studies (GWAS) have identified independent signals at 5p15.33 across numerous cancers, with protective alleles for one cancer often conferring risk for another. Many of these associations are thought to act via allele-specific alterations in the cis- regulation of target genes. Transcriptomic analyses in multiple tissue types implicate two plausible target genes: TERT and CLPTM1L. However, the mechanisms linking cancer susceptibility alleles to their presumed target genes, along with the observed antagonistic pleiotropy between different cancers remain elusive. With this in mind, we employed a comprehensive approach, integrating statistical fine-mapping of GWAS summary statistics with massively parallel reporter assays (MPRA) and a densely tiled CRISPRi screen performed across eight cell lines, representative of four distinct cancers associated with 5p15.33 alleles – pancreatic, melanoma, lung, and bladder cancer. Integrative screening identified up to 30 variants across multiple signals in the locus with putative allele-specific transcriptional activity. Furthermore, a variable number tandem repeat (VNTR) in intron 9 of CLPTM1L emerged as a potent transcriptional enhancer in CRISPRi screening. Leveraging PacBio sequencing, VNTR alleles of European ancestry samples from the 1000 Genomes Project were genotyped and found to be highly polymorphic, with longer VNTRs linked to the haplotype tagged by rs31490-A (risk increasing for pancreatic cancer). Subsequent imputation into a pancreatic cancer GWAS of 9,040 cases and 12,496 controls revealed an association between longer VNTRs and risk of pancreatic cancer (OR for VNTR in the 75th percentile = 1.17, 95% CI = 1.13-1.22, P = 2.21x10-12). The significance of the association for the lead SNP rs31490 after conditioning on the VNTR genotype dropped to P= 2.20x10-5, suggesting that VNTR alleles merit consideration as part of the credible variant set for pancreatic cancer. Targeted CRISPRi assays suggested VNTR-mediated cis-regulation of both TERT and CLPTM1L in PANC-1 and MIA PaCa-2 pancreatic cancer cell lines, while dual luciferase reporter assays in the same cell lines revealed that VNTR enhancer activity is mediated by Hippo pathway transcription factors. In ongoing experiments, we aim to expand on luciferase reporter assays and DNA-protein binding assays in relevant cell lines with the aim of not only deciphering how longer VNTRs differentially exert their transcriptional effects compared to shorter alleles but also characterizing the divergent directions of effect between different cancer types. These findings underscore the proposition that pancreatic cancer susceptibility at the 5p15.33 locus may be mediated by both SNPs and an uncharted class of variants, yet to be characterized in the post-GWAS landscape. Citation Format: Aidan O'Brien, Hyunkyung Kong, Minal Patel, Katelyn E Connelly, Mai Xu, Irene Collins, Jun Zhong, Jason Hoskins, Michelle Ho, Brenen Papenburg, Mark M Iles, Matthew H Law, Maria-Teresa Landi, Rachael Stolzenber- Solomon, Brian M Wolpin, Alison P Klein, Nick Orr, Stephen J Chanock, Sara Lindström, Marc-Henri Stern, Ludmila Prokunina-Olsson, Jieyon Choi, Kevin M Brown, Laufey T Amundadottir. Unraveling pancreatic cancer susceptibility at 5p15.33: Functional characterization of a novel VNTR element [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr C055.

The influence of PER3 VNTR genotypes on the age of onset in a group of bipolar I disorder patients: an exploratory study

BackgroundPER3 is a circadian gene that contains a variable number of tandem repeats (VNTR) which codifies for three genotypes: 4/4; 4/5; and 5/5 and is involved in non-visual response to light, a critical process associated with bipolar disorder onset. Benedetti et al. (Neurosci Lett 445(2):184–7) related this VNTR with bipolar disorder age of onset and linked genotype 5/5 with an earlier onset. In this study, we aimed to investigate these associations of PER3 VNTR genotypes with age of onset in a homogenous sample of German patients with bipolar I disorder through Kaplan-Meier curves.Methods45 patients were enrolled and divided into three groups according to PER3 VNTR genotypes. Recognizing common biological features, we built a combined group of -5 allele carriers (4/5 + 5/5). As a primary outcome, Kaplan-Meier analysis was conducted to delineate the three genotypes’ influence on age of onset. The secondary Kaplan-Meier analysis aimed to evaluate the relation between the 4/4 homozygotes group and the combined group (4/5 + 5/5) with age of onset. Finally, we proceeded to compare groups through a Log Rank Test and performed an analysis of covariance (ANCOVA).ResultsThe Kaplan-Meier analysis with three separate genotypes didn’t replicate the findings of Benedetti’s study. The analysis comparing genotype 4/4 with the combined group showed the influence of PER3 VNTR variants on the age of onset and relates genotype 4/4 to an earlier onset. ANCOVA between the combined and the 4/4 genotype groups, correlated genotype 4/4 with an increased number of depressive episodes.ConclusionThis study showed no significant effect of PER3 VNTR genotypes on the age of onset and in linking genotype 5/5 with an earlier onset age. Contrasting results may arise from intrinsic differences between the two studies but also shed light on hypothetically different levels of functioning of PER3 VNTR genotypes in the context of bipolar pathology. Further studies will require bigger and more homogeneous clinical samples.

Association of NLRP3 and IL-4 VNTR polymorphisms and genetic susceptibility to preeclampsia: A case-control study

IntroductionAbnormalities in the maternal immune system and insufficient gestational immune tolerance may significantly contribute to the development of preeclampsia (PE). The NLR family pyrin domain containing 3 (NLRP3) functions as a pattern recognition receptor that identifies pathogen-associated molecular patterns. Interleukin-4 (IL-4) is a potent anti-inflammatory cytokine that modulates the immune response. Therefore, this study aims to elucidate the impact of NLRP3 and IL-4 variable number of tandem repeats (VNTR) polymorphisms on susceptibility to PE. Materials and MethodsA total of 1,018 patients with PE and 1,007 normal pregnant women were recruited as the case group and the control group, respectively. Peripheral blood DNA was extracted, and NLRP3 and IL-4 VNTR polymorphisms were genotyped using polymerase chain reaction and gel electrophoresis. Genotypes and allele frequencies of pregnant women were assessed in both cohorts. ResultsThe NLRP3 VNTR 9–7 genotype in the PE group was significantly lower than that in the control group, but 9 and 14 allele frequencies were significantly higher in patients with PE. Individuals with IL-4 VNTR genotypes 1–2 had a lower risk of PE than controls, and the IL-4 VNTR 2 allele frequency was significantly lower in patients with PE. ConclusionsThis study, the first of its kind in the literature, evaluates the impact of NLRP3 VNTR and IL-4 VNTR polymorphisms on PE, revealing a significant correlation with PE susceptibility. This investigation contributes to understanding the pathogenesis of PE and provides a reference point for developing strategies to prevent and treat the disease in the future.

Association of the neonatal Fc receptor promoter variable number of tandem repeat polymorphism with immunoglobulin response in patients with chronic inflammatory demyelinating polyneuropathy.

Chronic inflammatory demyelinating polyneuropathy (CIDP) is an autoimmune disease with humoral and cellular autoimmunity causing demyelination of peripheral nerves, commonly treated with intravenous immunoglobulins (IVIg). The neonatal Fc receptor (FcRn), encoded by the FCGRT gene, prevents the degradation of immunoglobulin G (IgG) by recycling circulating IgG. A variable number of tandem repeat (VNTR) polymorphism in the promoter region of the FCGRT gene is associated with different expression levels of mRNA and protein. Thus, patients with genotypes associated with relatively low FcRn expression may show a poorer treatment response to IVIg due to increased IVIg degradation. VNTR genotypes were analyzed in 144 patients with CIDP. Patients' clinical data, including neurological scores and treatment data, were collected as part of the Immune-Mediated Neuropathies Biobank registry. Most patients (n = 124, 86%) were VNTR 3/3 homozygotes, and 20 patients (14%) were VNTR 2/3 heterozygotes. Both VNTR 3/3 and VNTR 2/3 genotype groups showed no difference in clinical disability and immunoglobulin dosage. However, patients with a VNTR 2 allele were more likely to receive subcutaneous immunoglobulins (SCIg) than patients homozygous for the VNTR 3 allele (25% vs. 9.7%, p = 0.02) and were more likely to receive second-line therapy (75% vs. 54%, p = 0.05). The VNTR 2/3 genotype is associated with the administration of SCIg, possibly reflecting a greater benefit from SCIg due to more constant immunoglobulin levels without lower IVIg levels between the treatment circles. Also, the greater need for second-line treatment in VNTR 2/3 patients could be an indirect sign of a lower response to immunoglobulins.

CSF biomarker analysis of ABCA7 mutation carriers suggests altered APP processing and reduced inflammatory response

BackgroundThe Alzheimer’s disease (AD) risk gene ABCA7 has suggested functions in lipid metabolism and the immune system. Rare premature termination codon (PTC) mutations and an expansion of a variable number of tandem repeats (VNTR) polymorphism in the gene, both likely cause a lower ABCA7 expression and hereby increased risk for AD. However, the exact mechanism of action remains unclear. By studying CSF biomarkers reflecting different types of AD-related pathological processes, we aim to get a better insight in those processes and establish a biomarker profile of mutation carriers.MethodsThe study population consisted of 229 AD patients for whom CSF was available and ABCA7 sequencing and VNTR genotyping had been performed. This included 28 PTC mutation and 16 pathogenic expansion carriers. CSF levels of Aβ1–42, Aβ1–40, P-tau181, T-tau, sAPPα, sAPPβ, YKL-40, and hFABP were determined using ELISA and Meso Scale Discovery assays. We compared differences in levels of these biomarkers and the Aβ ratio between AD patients with or without an ABCA7 PTC mutation or expansion using linear regression on INT-transformed data with APOE-status, age and sex as covariates.ResultsCarriers of ABCA7 expansion mutations had significantly lower Aβ1–42 levels (P = 0.022) compared with non-carrier patients. The effect of the presence of ABCA7 mutations on CSF levels was especially pronounced in APOE ε4-negative carriers. In addition, VNTR expansion carriers had reduced Aβ1–40 (P = 0.023), sAPPα (P = 0.047), sAPPβ (P = 0.016), and YKL-40 (P = 0.0036) levels.ConclusionsOur results are suggestive for an effect on APP processing by repeat expansions given the changes in the amyloid-related CSF biomarkers that were found in carriers. The decrease in YKL-40 levels in expansion carriers moreover suggests that these patients potentially have a reduced inflammatory response to AD damage. Moreover, our findings suggest the existence of a mechanism, independent of lowered expression, affecting neuropathology in expansion carriers.

ABCA7‐reducing mutation carriers have reduced CSF amyloid biomarker levels, suggestive of increased amyloid deposition

AbstractBackgroundThe Alzheimer’s disease (AD) risk gene ABCA7 has suggested functions in lipid metabolism and the immune system. Rare premature termination codon (PTC) mutations and an expansion of a variable number of tandem repeats (VNTR) polymorphism in the gene, both likely cause a lower ABCA7 expression and hereby increased risk for AD. However, the exact mechanism‐of‐action remains unclear. By studying CSF biomarkers reflecting different types of AD‐related pathological processes, we aim to get a better insight in those processes and establish a biomarker profile of mutation carriers.MethodThe study population consisted of 228 AD patients (27 PTC mutation and 16 pathogenic expansion carriers) for whom CSF was available and ABCA7 sequencing and VNTR genotyping had been performed. CSF levels of amyloid β (Aβ) 40 and 42, sAPP‐α and ‐β, YKL‐40 and hFABP were determined using ELISA and Meso Scale Discovery assays. We compared differences in levels of these biomarkers AD patients with or without an ABCA7 PTC mutation or expansion, and further stratified on APOE e4 status.ResultCarriers of ABCA7 mutations/expansions had significantly lower Aβ42 levels (p= 0.0031) and amyloid ratio (p=0.020) compared to non‐carrier patients, and were threefold more likely to have abnormal Aβ42 values. The effect on amyloid biomarkers remained significant when considering PTC mutations or VNTR expansions separately. APOE e4 carriers had significantly lower Aβ42 (p=0.0013) and amyloid ratio (p<0.001) compared to non‐APOE e4 carriers. When combined, both APOE e4 allele and ABCA7 carrier status influenced amyloid ratio and Aβ42 levels. Remarkably, within non‐APOE e4 carriers, ABCA7 mutation/expansion carriers did have significantly reduced Aβ42 levels (mean=540 pg/mL) compared to ABCA7 non‐carriers (812 pg/mL; p=0.0051), attaining lower levels as e4 carriers (612 pg/mL). Finally, in carriers of the pathogenic expansion we observed lower YKL40 levels (p=0.011), suggesting reduced neuroinflammation.ConclusionOur results highlight that carriers of ABCA7 PTC mutations and repeat expansions show more pronounced abnormalities in CSF amyloid beta markers than non‐carrier patients, especially in non‐APOE e4 carriers. Expansion carriers also had a decrease in neuroinflammation marker YKL40. Our results suggest that reduced ABCA7 expression leads to increase in amyloid pathology and potentially a reduced inflammatory response to damage.

Dim light melatonin onset following simulated eastward travel is earlier in young males genotyped as PER35/5 than PER34/4

ABSTRACT Inter-individual variability exists in recovery from jetlag following travel across time zones. Part of this variation may be due to genetic differences at the variable number tandem repeat (VNTR) polymorphism of the PERIOD3 (PER3) gene as this polymorphism has been associated with chronotype and sleep, as well as sensitivity to blue light on melatonin suppression. To test this hypothesis we conducted a laboratory-based study to compare re-entrainment in males genotyped as PER34/4 (n = 8) and PER35/5 (n = 8) following simulated eastward travel across six time zones. The recovery strategy included morning blue-enriched light exposure and appropriately-timed meals during the first 24 h after simulated travel. Dim light melatonin onset (DLMO), sleep characteristics, perceived sleepiness levels (Stanford Sleepiness Scale), and resting metabolic parameters were measured during constant routine periods before and after simulated travel. While DLMO time was similar between the two groups prior to simulated eastward travel (p = .223), it was earlier in the PER35/5 group (17h23 (17h15; 17h37)) than the PER34/4 group (18h05 (17h53; 18h12)) afterwards (p = .046). During resynchronisation, perceived sleepiness and metabolic parameters were similar to pre-travel in both groups but sleep was more disturbed in the PER35/5 group (total sleep time: p = .008, sleep efficiency: p = .008, wake after sleep onset: p = .023). The PER3 VNTR genotype may influence the efficacy of re-entrainment following trans-meridian travel when blue-enriched light exposure is incorporated into the recovery strategy on the first day following travel.

Validation and comparative analysis of kogene mycobacterial interspersed repetitive unit-variable number of tandem repeat typing kit and its application on clinically isolated mycobacterium tuberculosis samples from national tuberculosis hospital, Republic of Korea.

Tuberculosis (TB) remains a serious public health burden in Korea. Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeat (MIRU-VNTR) is preferred for epidemiological TB investigation. Until recently, the difficulty lies in epidemiological TB investigation due to the absence of commercialized MIRU-VNTR in Korea. Here, we have evaluated the newly designed MIRU-VNTR kit by Kogenebiotech, Korea. A total of 200 samples, where 100 are Mycobacrerium tuberculosis (M. tuberculosis), and the other 100 are non-M. tuberculosis, were used. Initially, the Kogenebiotech MIRU-VNTR typing kit (KoMIRU) was compared with Multilocus Variable Number Tandem Repeat Genotyping of M. tuberculosis typing kit (MVNTR) by Philip Supply for validation purpose. Then, Limit of Detection for DNA copies was optimized. Finally, KoMIRU and Genoscreen MIRU-VNTR typing kit (GeMIRU) were tested and comparatively analyzed for its specificity and sensitivity. The study showed that the KoMIRU has slightly higher discriminatory power over MVNTR, 100% versus 97.5%. In comparative analysis, the KoMIRU has shown comparable capability as GeMIRU, showing 100% for sensitivity and specificity with a 95% CI value of 96.38 to 100.00%. Also, no discrepancies were observed on discriminated lineage strains between KoMIRU and GeMIRU. Out of 100, 84 were identified as Beijing strains, and remains were identified as NEW-1 (n = 8), Uganda (n = 6), East African Indian (EAI) (n = 6), Turkey (n = 2), and Haarlem (n = 1). In this study, KoMIRU has shown a comparable capability to GeMIRU. Furthermore, previous researches had suggested an association between lineage strains and drug resistance; hence, the implementation of KoMIRU can help in TB control and prevention.

Homozygosity of short VNTR lengths in the CEL gene may confer susceptibility to idiopathic chronic pancreatitis

ObjectiveThe carboxyl-ester lipase (CEL) gene contains a variable number of tandem repeats (VNTR) region. It remains unclear whether the number of repeats in the CEL VNTR is related to the risk of pancreatic diseases. The aim of this study was to investigate whether CEL VNTR length is associated with idiopathic chronic pancreatitis (ICP), alcoholic chronic pancreatitis (ACP), or pancreatic cancer in a cohort of Chinese patients. MethodsCEL VNTRs were genotyped in patients diagnosed with ICP (n = 771), ACP (n = 222), or pancreatic cancer (n = 263), and in healthy controls (n = 927). CEL VNTR lengths were determined using a screening method combining PCR and DNA fragment analysis. ResultsOverall, the CEL VNTR lengths ranged from 5 to 22 repeats, with the 16-repeat allele (‘normal’ size, N) accounting for 73.82% of all observed alleles. The VNTR allele frequencies and genotype distributions were not significantly different between healthy controls and patients with ACP or pancreatic cancer. For the ICP group, allele frequencies did not differ significantly from the controls, while the frequency of the SS genotype (homozygosity for 5–15 repeats) was significantly higher in the patients (4.67%) than in the controls (1.94%) (p = 0.0014; OR = 2.47; 95% CI = 1.39–4.39). ConclusionsThere were no associations between the CEL VNTR length and ACP or pancreatic cancer. However, homozygosity for short VNTR lengths may confer susceptibility to ICP.

Association of occupational stress, period circadian regulator 3 (PER3) gene polymorphism and their interaction with poor sleep quality.

Occupational stress is associated with sleep quality among workers and the human variable number tandem repeat (VNTR) polymorphism of the period circadian regulator 3 (PER3) gene relates to sleep-wake regulation. The main aims of the present study were to examine the effects of PER3 VNTR genotypes, occupational stress, and their interactions on sleep quality. A cross-sectional study was conducted and 729 workers were recruited in Sichuan. Sleep quality were assessed using the Pittsburgh Sleep Quality Index. Occupational stress was measured using the Generic Job Stress Questionnaire. PER3 genotypes were determined with polymerase chain reaction. High and medium occupational stress were linked to a higher risk of poor sleep quality than low levels. Unconditional logistic regression indicated that PER3 genotype was significantly associated with sleep quality, and an increased risk of poor sleep of >1.5-times was observed in those with the allele 5 compared to allele 4. The 5/5 genotype was associated with both sleep latency and sleep duration. Crossover analysis showed an occupational stress×PER3 interaction. Compared to subjects with both low and medium occupational stress and 4/4+4/5 genotype, those with both high occupational stress and 5/5 genotype had a higher risk of poor sleep quality. Stratified logistic analyses found that compared with low and medium occupational stress, high occupational stress increased the risk of poor sleep by more than five-times in 5/5 genotype carriers. Occupational stress and PER3 genotype had both separate and combined effects on poor sleep quality of workers. The results suggest that occupational stress may increase the risk of poor sleep quality through interaction with the PER3 gene polymorphism.

ENOS and VEGF Variants Might Increase the Risk of Pancreatic Cancer

Background: Endothelial nitric oxide synthase (eNOS) is essential in chronic inflammation and carcinogenesis. The association between variants in vascular endothelial growth factor (VEGF) and several cancers still remains uncertain. We studied whether there is a relation between eNOS/VEGF variants and risk of pancreatic cancer (PC). Materials and Methods: This prospective case-control study included 76 PC patients (28 women and 48 men) and 100 healthy controls. Blood samples from all participants were genotyped for eNOS variable number tandem repeat (VNTR) and VEGF insertion/deletion (I/D) variants by PCR. Results: There was a significant difference between groups for the eNOS intron 4 VNTR genotype distributions (p = 0.01). eNOS 4a/4b and 4b/4b genotypes were higher in patients with PC group compared to controls while eNOS 4a/4b genotype was more prevalent in control group than in patient group. Significant differences were observed between groups for the VEGF I/D variant genotype and allele frequencies (p < 0.00, and p < 0.00). VEGF I/D variant I/I genotype and I allele increased in patient group than controls. A statistically significant association was observed when the patients were compared with the controls according to D/D + D/I versus D/D (p < 0.00, OR: 0.094, 95% CI: 0.03–0.22). Conclusions: We provided evidence that eNOS VNTR and VEGF I/D variants might influence the development of PC.

VNTR2/VNTR3 genotype in the FCGRT gene is associated with reduced effectiveness of intravenous immunoglobulin in patients with myasthenia gravis

Background:Intravenous immunoglobulin (IVIG) has been commonly used to treat myasthenia gravis exacerbation, but is still ineffective in nearly 30% of patients. A variable number of tandem repeat (VNTR) polymorphism in the FCGRT gene has been found to reduce the efficiency of IgG biologics. However, whether the polymorphism influences the efficacy of IVIG in generalized myasthenia gravis (MG) patients with exacerbations remains unknown.Methods:The distribution of VNTR genotypes was analyzed in 334 patients with MG. Varied VNTR alleles were determined by capillary electrophoresis and confirmed by Sanger sequencing. Information of endogenous IgG levels were collected in patients without previous immunotherapy (n = 26). Medical records of patients who received IVIG therapy were retrospectively analyzed for therapeutic outcomes of IVIG treatment (n = 61). Patients whose Activities of Daily Living scores decreased by 2 or more points on day 14 were considered responders to the treatment.Results:The VNTR3/3 and VNTR2/3 genotypes were detected in 96.7% (323/334) and 3.4% (11/334) patients, respectively. Patients with VNTR2/3 heterozygosity had lower endogenous IgG levels than those with VNTR3/3 homozygosity (9.81 ± 2.61 g/L versus 12.41 ± 2.45g/L, p = 0.016). The response rate of IVIG therapy was 78.7% (48/61). All responders and nine non-responders were VNTR3/3 homozygotes, whereas all the patients with VNTR2/3 genotypes were non-responders (n = 4). In patients who took IVIG treatments, endogenous IgG levels were significantly lower in non-responders compared with responders (12.93 ± 2.24 g/L versus 8.85 ± 2.69 g/L, p = 0.006), especially in VNTR2/3 heterozygotes (7.86 ± 1.78 g/L, p = 0.001).Conclusion:The VNTR2/3 genotype could influence endogenous IgG levels and serve as a predictive marker for poor responses to IVIG in MG patients.

Genotyping of Mycobacterium tuberculosis in Liaoning with variable number of tandem repeats method

Objective To explore the genotype distribution and transmission patterns of 81 Mycobacterium tuberculosis (MTB) clinical isolates from Liaoning province with the variable number tandem repeats (VNTR). Methods The 81 strains were isolated from each city of the province in 2018, the p-nitrobenzoic acid (PNB) was used to identify the flora, so as to distinguish Mycobacterium tuberculosis complex from non-tuberculous mycobacteria. The solid ratio method was used to conduct drug susceptibility tests on four first-line anti-tuberculosis drugs using Roche's medium. Based on PCR, the standard 24 sites were detected and analyzed, and the Beijing genotype was identified by the RD105 gene deletion method. Microsoft Excel software was used for polymorphism analysis, and website ( https://www.miru-vntrplus.org/MIRU/index ) was used to get the VNTR genotyping results, the locus polymorphism and clustering rate at the same time was calculated. SPSS 23.0 software was used for statistical description of data, and χ 2 test carried out on count data or drug resistance in each year; when the theoretical frequency is less than 5, the Fisher exact probability method is used to calculate the two-sided P value, and the test level is α=0.05. Results The clustering analysis of genotype showed that 81 strains were categorized into 3 gene clusters (genogroup I, II and III), in which 1.23% (1/81) was belong to genogroup I, 4.94% (4/81) was genogroup II, and 93.83% (76/81), one of the largest group of genes for III group. The clustering rate was 4.94% (4/81) and the least estimated proportion of the recent infection rate was 2.47% (2/81). The polymorphism of 5 in 24 VNTR loci was better, 3 loci was acceptable, the remaining 16 loci was less polymorphic. Conclusion The drug resistant Mycobacterium tuberculosis shows obvious gene polymorphisms in Liaoning province and Beijing genotype is the predominant prevalent strain (III group). 摘要 ：目的了解辽宁省81例结核分枝杆菌多位点数目可变串联重复序列分析(variable number of tandem repeats. VNTR)的基因多态性及近期传播情况。 方法 对2018年辽宁省内送至辽宁省疾病预防控制中心实验室的菌株进行传 代后米用对硝基苯甲酸(p-nitrobenzok: acid, PNB)培养基进行菌群鉴定, 以区分结核分枝杆菌复合体和非结核分枝杆 菌。采用固体比例法利用罗氏培养基对4种一线抗结核药物进行药敏实验。以PCR为基础对标准24位点进行检测分 析, 利用RD105基因缺失法鉴定北京基因型。利用Microsoft Excel软件进行多态性分析, 利用 https://www.miru-vntrplus.org/MIRU/index 网站得到VNT R基因分型结果, 同时进行位点多态性和成簇率的计算。采用SPSS 23.0软件进行数据的 统计描述 , 对计数资料或各年度耐药情况进行 χ 2 检验；当理论频数<5时 , 采用Fisher确切概率法计算双侧 P 值, 检验水 准α=0.05。 结果 经分析81株菌株可分为3个基因群（I、Ⅱ、Ⅲ), 菌株数分别为1(1.23%)、4(4.94%)和76(93.83%), 其中最大的基因群为Ⅲ群。成簇率为4.94%(4/81)。近期感染率最小估计值为2.47%(2/81)。24个VNTR位点中有5 个位点的多态性较好, 3个位点的多态性尚可, 16个位点的多态性较差。 结论 初步证实辽宁省耐药结核分枝杆菌菌 株存在明显的基因多态性, 其主要流行型为北京基因型（Ⅲ群）。

VIM-Positive Pseudomonas aeruginosa Sink Colonization Dynamics in Patient Rooms of a Dutch Tertiary-Care Hospital

Background: In hospitals, Verona integron-encoded metallo-β-lactamase (VIM)–positive Pseudomonas aeruginosa (VPPA) frequently colonize sink drains. Sink use has been shown to disperse VPPA to other surfaces surrounding sinks, creating a potential transmission source. Objective: Because VPPA have been isolated from sinks and patients within our hospital, we analyzed colonization dynamics in 2 sinks identified as VPPA hot spots between 2012 and 2018. Methods: One sink was in an intensive care unit (ICU) patient room and the other was in a gastrointestinal surgery (GIS) patient room. ICU patients were screened for VPPA on admission, at discharge, and weekly during hospitalization. GIS patients were screened for VPPA only on clinical indication. In this study, patient and sink isolates were typed at 8 loci using multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA). Results: Overall, 19 sink isolates from the ICU room were included. In 2013, VPPA isolates with identical VNTR genotypes (“clone B,” VNTR nos. 2-4-8-4-4-5-10-[-2]) were found in the wash basin, aerator, drain, and siphon. The drain plug was replaced in August 2013, but B was isolated from the drain 1 month later. Every year between 2014 and 2018, clone B and other closely related genotypes were recovered from this drain. In 2018, clone B was also found on the wash basin and counter. No positive patients were identified in this room until 2016, when a patient acquired clone B 6 days after admission. From the GIS room, 6 sink isolates and 4 patients’ isolates were included. In 2012, clone B was found on the wash basin and sink drain plug. Also, 3 VPPA-positive patients stayed in this room in 2012: at discharge, 1 patient was colonized by “clone A,” VNTR numbers 6-7-8-5-9-8-6-1. Furthermore, 2 other patients screened positive for clone B prior to admission in 2012, so they likely acquired VPPA elsewhere. The drain plug was replaced in 2013, and no VPPA was found again until 2017, when 2 VPPA-positive patients stayed in this room: 1 was already a carrier of clone B, and the other was a carrier of clone B 1 day after admission. No positive sink cultures were found until January 2018, when closely related B isolates were recovered from the wash basin, drain, and drain plug. Conclusions: Between 2013 and 2018, clone B persisted in the ICU room sink. In the GIS room sink, clone B may have disappeared after 2012, but it was reintroduced by known carriers. However, few patients became colonized after being admitted to these rooms, even when VPPA were discovered on surfaces outside the sink drain (ie, the wash basin and counter).Funding: NoneDisclosures: None

Monitoring vaccinated cattle for induction and longevity of persistent tick-transmissible infection: Implications for wider deployment of live vaccination against East Coast fever in Tanzania.

The infection and treatment (ITM) procedure remains the only available method of immunization against Theileria parva infection. One constraint to deployment is the perception that the carrier state induced by ITM could result in enhanced disease problems. More than one million cattle have been ITM vaccinated in pastoralist systems in Tanzania over the last 2 decades. We present the results of a longitudinal study of six groups of cattle in Maasai villages in northern Tanzania exposed to natural tick challenge for between 2weeks and 14years post-vaccination. The p104 nested PCR revealed a higher frequency of T.parva carriers among vaccinates (30%) compared with controls (8%) (OR=4.89, p=.000), with the highest frequency of carriers found in calves vaccinated 6months previously, although carrier state was also detected in cattle vaccinated >10years prior to the study. Variable number tandem repeat genotype analysis revealed 6 MS7 alleles with sizes ranging from 150bp to 500bp, but only two alleles were detected in cattle vaccinated >4years earlier, relative to five alleles detected in recently vaccinated cattle and controls. In terms of heterozygosity, diversity was maximal in calves vaccinated within the last 2weeks (h=0.776) but lowest in cattle vaccinated 4years earlier (h=0.375). The analysis suggested close genetic relatedness of parasites in vaccinated and unvaccinated groups and up to 96% of variation was within rather than between the groups. These results confirm that ITM leads to a long-term T.parva carrier state in cattle and the detection of vaccine component VNTR in co-grazing unvaccinated cattle suggests potential vaccine transmission by ticks. However, vaccination stocks did not totally replace local genotypes, at least in cattle populations. These findings should mitigate concerns that ITM modifies T.parva field populations in a way that enhances disease in the medium term.

Serological and molecular characterization of Leptospira kirschneri serogroup Grippotyphosa isolated from bovine in Brazil

Leptospirosis is a zoonotic disease caused by a bacterium of the genus Leptospira that affects domestic animals, including cattle. Despite of this importance in livestock, little is known about the epidemiology of leptospirosis in cattle in Brazil and other tropical countries. In this context, the objective of this study was to perform the culture of urine and kidney (n = 372 animals) of slaughtered bovines of Minas Gerais state (Brazil), in order to obtain pure cultures of Leptospira strains and carry out its characterization by serological (microscopic agglutination test) and molecular techniques (rrs, secY sequencing and variable-number tandem-repeat genotyping). One strain, named UFU 02, was obtained from a male bovine without apparent alterations in ante-mortem examination. The strain was characterized belonging to species Leptospira kirschneri and serogroup Grippotyphosa. The serogroup Grippotyphosa is most often described in wild species, suggesting a link between domestic and wild cycles/environments. Considering the importance of the country in livestock breeding, the knowledge about leptospiral strains could help to control the disease in the herds.

Parsing out the role of dopamine D4 receptor gene (DRD4) on alcohol-related phenotypes: A meta-analysis and systematic review.

Genetics account for moderate variation of individual differences in developing alcohol use disorder (AUD), but it is unclear which genetic variations contribute to AUD risk. One candidate gene investigated due to its association with AUD is the dopamine D4 receptor gene (DRD4), which contains a 48-base pair variable number tandem repeat (VNTR) in exon 3 of its coding region. To date, no quantitative synthesis of the published literature on the effects of DRD4 VNTR variation on alcohol-related phenotypes has been conducted. MEDLINE, Embase, Web of Science, and PsycInfo were searched for studies that reported on alcohol craving, alcohol consumption, severity of AUD, and case-control (AUD versus no diagnosis of AUD) studies in DRD4L (seven repeats or more) carriers compared with DRD4S (six repeats or less) homozygotes. Random-effects meta-analysis was used for all analyses. A pooled sample size of 655 to 13,360 of 28 studies were included. Compared with DRD4S homozygotes, DRD4L carriers had increased number of drinking days (SMD: 0.205; 95% CI: 0.008 to 0.402), binge drinking days (SMD: 0.217; 95% CI: 0.0532 to 0.380), and severity of AUD (SMD: 0.143; 95% CI: 0.028to0.259). There was no difference between DRD4 VNTR genotypes on drinks per drinking day, largest number of drinks per day/occasion, and case-control analysis. It was not possible to conduct a meta-analysis of the craving data, but a systematic review of this literature found mixed results on DRD4 VNTR genotype effect. The present meta-analysis suggests DRD4 VNTR variation may be a risk factor for problematic alcohol use. Our findings are limited, however, by the absence of ancestry data from studies included in our analysis, precluding our ability to adjust for population stratification. Due to the likelihood of type I error in candidate gene approaches, our work highlights the critical need for studies with larger and more inclusive samples that account for sex and genetic ancestry to fully understand this relationship.

Structural Asymmetry in the Frontal and Temporal Lobes Is Associated with PCSK6 VNTR Polymorphism.

The nodal cascade influences the development of bodily asymmetries in humans and other vertebrates. The gene PCSK6 has shown a regulatory function during left-right axis formation and is therefore thought to influence bodily left-right asymmetries. However, it is not clear if variation in this gene is also associated with structural asymmetries in the brain. We genotyped an intronic 33bp PCSK6 variable number tandem repeat (VNTR) polymorphism that has been associated with handedness in a cohort of healthy adults. We acquired T1-weighted structural MRI images of 320 participants and defined cortical surface and thickness for each HCP region. The results demonstrate a significant association between PCSK6 VNTR genotypes and gray matter asymmetry in the superior temporal sulcus, which is involved in voice perception. Heterozygous individuals who carry a short (≤ 6 repeats) and a long (≥ 9 repeats) PCSK6 VNTR allele show stronger rightward asymmetry. Further associations were evident in the dorsolateral prefrontal cortex. Here, individuals homozygous for short alleles show a more pronounced asymmetry. This shows that PCSK6, a gene that has been implicated in the ontogenesis of bodily asymmetries by regulating the nodal cascade, is also relevant for structural asymmetries in the human brain.

Variants in the BACH2 and CLEC16A gene might be associated with susceptibility to insulin-triggered type1 diabetes.

Aim/IntroductionInsulin administration was found to trigger type 1 diabetes in six Japanese type 2 diabetes patients with type 1 diabetes high‐risk human leukocyte antigen class II and the class I allele of the insulin gene variable number tandem repeat genotype. The objective of the present study was to assess the contribution of non‐human leukocyte antigen single‐nucleotide polymorphisms (SNPs) to the risk of developing insulin‐triggered type 1 diabetes.Materials and MethodsWe genotyped 13 type 1 diabetes susceptible SNPs in six patients and compared them with those in Japanese controls (Hap Map3‐JPT). The SNPs that showed statistically significant results were further analyzed using non‐diabetic control participants and participants with type 2 diabetes at the Ehime University Hospital.ResultsThe risk allele frequency of BACH2 rs3757247 in the six patients was significantly more frequent than that in 86 Japanese controls (P = 0.038). No significant difference in the allele frequency was observed in the other SNPs. This result was confirmed by the findings that the risk allele frequency of BACH2 in the six patients was significantly higher than that in the non‐diabetic control participants (n = 179) and type 2 diabetes with or without insulin treatment (n = 154 or n = 152; P = 0.035, 0.034 or 0.037, respectively). Despite being statistically not significant, the six patients were all homozygous for the CLEC16A rs12708716 risk allele and five were homozygous for the CLEC16A rs2903692 risk allele.ConclusionsIn addition to type 1 diabetes high‐risk human leukocyte antigen class II and the class I allele of the insulin gene variable number tandem repeat genotype, the possibility that the risk variants of BACH2 and CLEC16A could contribute to the development of insulin‐triggered type 1 diabetes cannot be excluded.

Mycobacterium avium in Community and Household Water, Suburban Philadelphia, Pennsylvania, USA, 2010-2012.

Attention to environmental sources of Mycobacterium avium complex (MAC) infection is a vital component of disease prevention and control. We investigated MAC colonization of household plumbing in suburban Philadelphia, Pennsylvania, USA. We used variable-number tandem-repeat genotyping and whole-genome sequencing with core genome single-nucleotide variant analysis to compare M. avium from household plumbing biofilms with M. avium isolates from patient respiratory specimens. M. avium was recovered from 30 (81.1%) of 37 households, including 19 (90.5%) of 21 M. avium patient households. For 11 (52.4%) of 21 patients with M. avium disease, isolates recovered from their respiratory and household samples were of the same genotype. Within the same community, 18 (85.7%) of 21 M. avium respiratory isolates genotypically matched household plumbing isolates. Six predominant genotypes were recovered across multiple households and respiratory specimens. M. avium colonizing municipal water and household plumbing may be a substantial source of MAC pulmonary infection.