Suchergebnisse

AbstractA requirement for performing robust genetic and statistical analyses on twins is correctly assigned zygosities. In order to increase the power to detect small risk factors of disease, zygosity testing should also be amenable for high throughput screening. In this study we validate and implement the use of a panel of 50 single nucleotide polymorphisms (SNPs) for reliable high throughput zygosity testing and compare it to a panel of 16 short tandem repeats (STRs). We genotyped both genomic (gDNA) and whole genome amplified DNA (WGA DNA), ending up with 47 SNP and 11 STR markers fulfilling our quality criteria. Out of 99 studied twin pairs, 2 were assigned a different zygosity using SNP and STR data as compared to self reported zygosity in a questionnaire. We also performed a sensitivity analysis based on simulated data where we evaluated the effects of genotyping error, shifts in allele frequencies and missing data on the qualitative zygosity assignments. The frequency of false positives was less than 0.01 when assuming a 1% genotyping error, a decrease of 10% of the observed minor allele frequency compared to the actual values and up to 10 missing markers. The SNP markers were also successfully genotyped on both gDNA and WGA DNA from whole blood, saliva and filter paper. In conclusion, we validate a robust panel of 47 highly multiplexed SNPs that provide reliable and high quality data on a range of different DNA templates.

Principality of Asturias Regional Government (Spain)[IDI/2018/000159]; Instituto de Salud Carlos III (RTICC-Spain).

Despite major advances in the knowledge of the molecular basis of renal cell carcinoma, prognosis is still defined using clinical and pathological parameters. Moreover, no valid predictive biomarkers exist to help us selecting the best treatment for each patient. With these premises, we aimed to analyse the expression and to determine the prognostic and predictive value of 64 key single nucleotide polymorphisms in 18 genes related with angiogenesis or metabolism of antiangiogenics in two cohorts of patients with localized and advanced renal cell cancer treated at our institution. The presence of the selected single nucleotide polymorphisms was correlated with clinical features, disease free survival, overall survival and response rate. In patients with localized renal cell cancer, 5 of these polymorphisms in 3 genes involved in angiogenesis predicted for worse disease free survival (VEGFR2: rs10013228; PDGFRA: rs2228230) or shorter overall survival (VEGFR2: rs10013228; VEGFR3: rs6877011, rs307826) (p < 0.05). Rs2071559 in VEGFR2 showed a protective effect (p = 0.01). In the advanced setting, 5 SNPs determined inferior overall survival (IL8: rs2227543, PRKAR1B: rs9800958, PDGFRB: rs2302273; p = 0.05) or worse response rate (VEGFA: rs699947, rs3025010 p ≤ 0.01)). Additionally 1 single nucleotide polymorphism in VEGFB predicted for better response rate rs594942 (p = 0.03). Genetic analysis of renal cell carcinoma patients might provide valuable prognostic/predictive information. A set of SNPs in genes critical to angiogenesis and metabolism of antiangiogenics drugs seem to determine post-surgical outcomes and treatment response in our series. ; This work was supported by a grant of the Andalusian Government through the program "Convocatoria Consejería de Salud y Bienestar Social 2012". Project number PI-0427-2012. ; Peer reviewed

Abstract
Several genetic loci in chromosomes 11 and 15 have recently been associated with non-syndromic autism spectrum disorder (ASD) in populations from North America and Europe. The aim of the present study was to investigate whether such an association exists in a Latvian population. Ninety-five patients with ASD in the age range 3–20 years (mean age 8 years, SD 3.18) participated in the study. The control group consisted of 161 healthy, non-related individuals without ASD randomly selected from the Latvian Genome Database. Four single nucleotide polymorphisms (SNPs) — rs11212733, SNP rs1394119, rs2421826, rs1454985 — were genotyped by the TaqMan method. Allele frequency differences between ASD patients and control subjects were compared for each SNP using a standard chi-square test with Bonferroni correction. The level of statistical significance was set at 0.05 for nominal association. Only the genetic marker rs11212733, localised on the long arm of chromosome 11 in locus 22.3, was found to be strongly associated with the ASD patient group (χ2 6.982, Padjusted 0.033, odds ratio 1.625). Our data demonstrating a significant relationship between the SNP rs11212733 and the development of ASD in a Latvian population suggest that it is not a population-specific relationship. Thus, future studies focusing on the DDX10 gene and related genetic loci are needed.

Genetic and environmental factors are believed to have a key role in the development and pathogenesis of autoimmune thyroid diseases (AITD). This study aimed to investigate the association between two CTLA-4 gene single nucleotide polymorphisms (SNPs) CT60/rs3087243 and CT61/rs11571319 with autoimmune thyroiditis in a sample of Iraqi patients. Seventy-five patients (67 females, 8 males) and eighty-eight subjects (79 females and 9 males) matched in age, gender, and ethnicity as a control group. Thyroid autoantibodies were present in females more than in males with a total positivity of anti-TPO of 92% and anti-TG positivity of57.3 %. Thyroid evaluation tests including T3, T4, and TSH were abnormal only in patients not receiving L-thyroxine treatment for autoimmune hypothyroidism, while patients on L-treatment and control subjects had normal results of these tests. CTLA-4 genotype frequencies were consistent with Hardy-Weinberg equilibrium (HWE) with no significant differences (p > 0.05) between the genotypes of patients and the control group. Analysis of CTLA-4 genotype and allele frequencies in patients and controls indicated the lack of significant differences among these frequencies except for allele G of rs3087243 which was associated significantly (P= 0.032) with the disease with OR of 1.62, while allele A can have a protective effect with OR of 0.66. Alleles of rs11571319 showed no significant ifferences despite the decreased frequency of G allele (83.33vs.87.5 %) and increased frequency of A allele (16.66vs.12.5%) in patients compared to controls. In conclusion, G allele of rs3087243 can be considered a risk factor for autoimmune hypothyroidism while noassociation was found regarding rs11571319 in the Iraqi population.

In Ukraine, about 3 million people work in hazardous and dangerous conditions. The study of hereditary specificity in development of occupational diseases is being actively conducted through molecular genetic analysis of single-n udeotide gene polymorphisms. While studying single-nucleotide gene polymorphisms of occupational diseases, many complicated bioethical questions arise regarding the confidentiality of personal data, the choice between the profession chosen and the risk to one's own health. Complicated bioethical issues that arise when studying single-nudeotide gene polymorphisms of occupational diseases need to be actively discussed, not only by physicians, occupational pathologists, employers, scientists, but also by politicians and lawyers, taking into account ethical and social norms and implications.

Toll-like receptors (TLRs) play a key role in innate immune response activation against viruses. TLR7, one of the TLRs family, is potentially important in controlling viral infection and the production of vaccines against the virus. The wide spectrum of discrepancy in response to antiviral drugs among different populations which is emerged by some pandemics like COVID-19 might be due to their different TLR7 single nucleotide polymorphisms (SNPs). The present study aimed to investigate the consequences of 401 non-synonymous missense SNPs (nsSNPs) within TLR7 on its protein structure, stability, and function by using specific bioinformatics tools. Seven bioinformatics tools were used to investigate 401 TLR7 nsSNPs from the dbSNP database. The results showed that the six variations, rs1171508003 (R262H), rs35160120 (F580S), rs968155471 (H587Q), rs202028806 (Y871D), rs1331496205 (W933S), and rs181600414 (R1004W), were found to be extremely deleterious by all of the employed bioinformatics tools. All six variations showed an impact on the protein's structure, function, and stability. Among them, Y871D (rs202028806) and R1004W (rs181600414) were revealed as the most damaging nsSNPs. This study suggested that the predicted six damaging variants of TLR7 could indirectly or directly destabilize the structure of protein and deviate its function to some extent.

Single-nucleotide polymorphisms (SNPs) are useful markers for biodiversity assessment, linkage analysis, traceability and paternity testing. To date, there are no available SNPs for goat in the NCBI dbSNP database and only a few are reported in the literature. Within the European Union Econogene project, we characterized 27 SNPs in goats using a targeted-gene approach. Polymorphisms were identified in a panel of 16 unrelated individuals belonging to eight different goat breeds selected throughout Europe. Genotypes of 30 goats from each of the eight breeds were determined for all the SNPs characterized and diversity measures were estimated. The caprine SNPs described will be a useful complement to the available genome markers. ; EU Commission Econogene contract QLK5-CT-2001–02461

There is substantial evidence suggesting a role for hormone-regulated kallikrein-related peptidases (KLKs) in carcinogenesis and tumour metastasis. KLKs are considered to have potential as prognostic biomarkers for hormone dependent cancers, particularly ovarian cancer. The purpose of this study was to evaluate the association between Kallikrein-related peptidase 3 (KLK3) gene single nucleotide polymorphisms (SNPs) located in hormone response elements and ovarian cancer survival. DNA samples were analyzed from 304 Australian women diagnosed with epithelial ovarian cancer. The KLK3 rs266882 and rs11084033 SNPs were genotyped by the Sequenom iPLEX Mass Array platform. Hazard ratios (HR) and 95% confidence intervals (CI) were estimated using Cox regression models. An association was observed with ovarian cancer survival for homozygote carriers of the rare allele of rs11084033 (adjusted HR 2.12, 95% CI 1.08–4.15). This finding is consistent with bioinformatic analysis predicting the rs11084033 rare allele to be responsible for the loss of a confirmed androgen response element, and with published expression data suggesting that aggressive ovarian cancers show decreased KLK3 tumor expression. The rs11084033 has potential prognostic significance in ovarian cancer. However, this finding requires replication, and further investigation regarding the functional significance of rs11084033 and correlated SNPs.

[Background and Purpose] The E3 ubiquitin ligase MDM2 (murine double minute 2) is the main negative regulator of the p53 protein—a key player in neuronal apoptosis after ischemia. A functional single-nucleotide polymorphism in the human MDM2 gene promoter (rs2279744) regulates MDM2 protein expression. We investigated whether the MDM2 SNP309, by controlling p53-mediated apoptosis, determines functional outcome after stroke. ; [Methods] Primary cortical neurons were subjected to oxygen and glucose deprivation. Mice were subjected to ischemic (transient middle cerebral artery occlusion) or hemorrhagic (collagenase injection) stroke models. Protein and mRNA levels of MDM2 and p53 were measured in both neuronal and brain extracts. The interaction of MDM2 with p53 was disrupted by neuronal treatment with nutlin-3a. siRNA was used to knockdown MDM2 expression. We analyzed the link between the MDM2 SNP309 and functional outcome, measured by the modified Rankin Scale scores, in 2 independent hospital-based stroke cohorts: ischemic stroke cohort (408 patients) and intracerebral hemorrhage cohort (128 patients). ; [Results] Experimental stroke and oxygen and glucose deprivation induced the expression of MDM2 in the brain and neurons, respectively. Moreover, oxygen and glucose deprivation promoted MDM2 binding with p53 in neurons. Disruption of the MDM2-p53 interaction with nutlin-3a, or MDM2 knockdown by siRNA, triggered p53 accumulation, which increased neuronal susceptibility to oxygen and glucose deprivation-induced apoptosis. Finally, we showed that patients harboring the G allele in the MDM2 promoter had higher MDM2 protein levels and showed better functional outcome after stroke than those harboring the T/T genotype. The T/T genotype was also associated with large infarct volume in ischemic stroke and increased lesion volume in patients with intracerebral hemorrhage. ; [Conclusions] Our results reveal a novel role for the MDM2-p53 interaction in neuronal apoptosis after ischemia and show that the MDM2 SNP309 determines the functional outcome of patients after stroke. ; This work was funded by Instituto de Salud Carlos III (PI15/00473, RD16/0019/0018, and RD16/0019/0001), European Regional Development Fund, Ministerio de Economía y Competitividad (SAF2016-78114-R), European Union's Horizon 2020 Research and Innovation Programme (Grant Agreement 686009), and Junta de Castilla y León (IES007P17). Drs Rodríguez (RD16/0019/0018), Delgado-Esteban (CP0014/00010), and Sobrino (CPII17/00027) are supported by Instituto de Salud Carlos III. ; Peer reviewed