Allele Frequencies Of Variants Research Articles

Assessing Genetic Variants in Matched Biocompartments From Patients With Serous Ovarian Cancer.

The clinical use of molecular tumor profiling (MTP) is expanding and there is an increasing use of MTP data to manage patient care. At the University of Colorado, 18 patients were diagnosed with primary serous ovarian cancer between 9/2015 and 6/2019 and consented for banking and analysis of tumor, ascites and plasma. All 18 patients had tumor and plasma samples that were sent for MTP, and 13 of 18 patients additionally had ascites collected and sent for MTP. 50-gene panel testing and BRCA testing were performed on primary tumor. BRCA genetic variants were more likely to be identified in plasma as compared to ascites or tumor, though not statistically significant (P = 0.17). Co-occurring genetic variants between plasma and ascites were less common in comparison to co-occurring variants between tumor and plasma or tumor and ascites, though not statistically significant (P = 0.68). Variants in KDR (VEGFR2) and TP53 were most likely to be conserved across all 3 biocompartments. Mutant allele frequencies (MAF) of individual genetic variants varied across biocompartments, though tended to be highest in the tumor, followed by ascites.

A decade of molecular diagnosis of Mucolipidosis II and III in Brazil: a pooled analysis of 32 patients

Abstract GlcNAc-1-phosphotransferase is a hexameric complex formed by subunits α, β, and γ, where the first two are encoded by the GNPTAB gene and the third by the GNPTG gene. Pathogenic variants identified in the GNPTAB gene cause the diseases Mucolipidosis II and III alpha/beta, which are severe and characterized by an overflow of lysosomal hydrolases into the extracellular environment, and their absence in lysosomal compartments causes an accumulation of non-degraded macromolecules. Methodology: a retrospective study that included 32 unrelated Brazilian patients with a clinical and genetic diagnosis of Mucolipidosis II/III alpha/beta. The regional frequency of the altered alleles was determined. Results: The patients were from all regions of Brazil. The most prevalent variants were c.3503_3504del, associated with the severe form of the disease, and c.1208T>C, associated with the milder form. Variant c.3503_3504del is the most frequently found in the Midwest, Northeast, and Southeast regions of Brazil. In the South, 42.8% of the alleles present the c.1196C>T variant. Conclusions: From the perspective of all patients diagnosed with Mucolipidosis II/III in Brazil, it is possible to conclude that different regions present allelic frequencies of specific pathogenic variants, which can be explained by the occurrence of a founding effect or high inbreeding rates.

Estimation of polymorphisms in the drug-metabolizing enzyme, cytochrome P450 2C19 gene in six major ethnicities of Pakistan

ABSTRACT Interindividual differences in cytochrome P450 (CYP) 2C19 activity may result in variations in the therapeutic response to drugs metabolized by this enzyme. Differences at gene level may translate into protein level with consequent impairment of the enzyme activity. As a result patients with such genetic differences might experience undesirable effects or no effect at all. The aim of the present study was to find out the prevalence of allelic and genotype frequencies of low activity variants of CYP2C19 genes in healthy individuals from six distinct ethnicities of Pakistan. Blood sample was taken from healthy volunteers following informed consent. Isolation of the DNA was followed by the PCR amplification and restriction fragment length polymorphism. Selected samples were sequenced by Sanger sequencing. The frequency of major alleles was 84.93% for CYP2C19*2 and 91.85% for CYP2C19*3, while minor allele was present at 15.06% for CYP2C19*2 and 8.14% for CYP2C19*3. For CYP2C19*2, the frequency of *1*1 genotype was 75.80%, *1*2 was 18.27%, and *2*2 was 5.92% whereas for CYP2C19*3, The frequency of *1*1 genotype was 84.19%, *1*3 was 15.30%, and *3*3 was 0.49% in the Pakistani population. A substantial variation in genotype and allelic frequencies was observed in various ethnicities. Our study demonstrates that a significant Pakistani population has at least one minor allele, which indicates a large number of patients potentially being affected by these variations. Especially, a significant genotype frequency of PM suggests implication for the treatment response and severity/frequency of adverse effects in patients receiving drugs metabolized by CYP2C19.

Prevalence of OCT1 (rs628031) genetic polymorphism in south Indian population

Genetic polymorphism is defined as the presence of a heterozygous deoxyribose nucleic acid (DNA) variant in greater than 1% of the population. Genetic polymorphism integrates genetic information in clinical decision-making. High polymorphism of organic cation transporters (OCT) transport genes may represent a significant portion of the variation in the pharmacokinetics and pharmacodynamics of substrate drugs transported by OCT1. The scarcity of research and the difference of effect in the genetic variability of the rs628031 polymorphism in various groups provide compelling reasons to perform the study. The purpose of this study is to find the prevalence of rs628031 polymorphism in the South Indian population. The phenol-chloroform technique was used to extract DNA from 48 healthy individuals in the research. Polymerase chain reaction was used to amplify the acquired DNA samples. After digestion with a tailored restriction enzyme, restriction fragment length polymorphism was utilized to discover genetic polymorphisms. The minor allele frequency of rs628031 was 0.67, indicating its deviation with the Hardy–Weinberg principle. The frequency of variant alleles discovered in this study was comparable to that seen in the Javanese population. The study's major findings provide the groundwork for future pharmacogenetic investigations in this group, as well as contribute to a better understanding of the role of the rs628031 polymorphism in drug response and benefit in developing a customized treatment regimen with improved efficacy and safety.

APOE Variants in an Iberian Alzheimer Cohort Detected through an Optimized Sanger Sequencing Protocol.

The primary genetic risk factor for late onset Alzheimer’s disease (LOAD) is the APOE4 allele of Apolipoprotein E (APOE) gene. The three most common variants of APOE are determined by single nucleotide polymorphisms (SNPs) rs429358 and rs7412. Our aim was to estimate allele and genotype frequencies of APOE variants in an Iberian cohort, thus helping to understand differences in APOE-related LOAD risk observed across populations. We analyzed saliva or buccal swab samples from 229 LOAD patients and 89 healthy elderly controls (≥68 years old) from Northern Portugal and Castile and León region, Spain. The genotyping was performed by Sanger sequencing, optimized to overcome GC content drawbacks. Results obtained in our Iberian LOAD and control cohorts are in line with previous large meta-analyses on APOE frequencies in Caucasian populations; however, we found differences in allele frequencies between our Portuguese and Spanish subgroups of AD patients. Moreover, when comparing studies from Iberian and other Caucasian cohorts, differences in APOE2 and APOE4 frequencies and subsequent different APOE-related LOAD risks must be clarified. These results show the importance of studying genetic variation at the APOE gene in different populations (including analyses at a regional level) to increase our knowledge about its clinical significance.

A Transparent Approach to Calculate Detection Rate and Residual Risk for Carrier Screening

Carrier screening involves detection of carrier status for genes associated with recessive conditions. A negative carrier screening test result bears a nonzero residual risk (RR) for the individual to have an affected child. The RR depends on the prevalence of specific conditions and the detection rate (DR) of the test itself. Herein, we provide a detailed approach for calculating DR and RR. DR was calculated on the basis of the sum of disease allele frequencies (DAFs) of pathogenic variants found in published literature. As a proof of concept, DAF data for cystic fibrosis were compared with society guidelines. The DAF data calculated by this method were consistent with the published cystic fibrosis guideline. In addition, we compared DAF for four genes (ABCC8, ASPA, GAA, and MMUT) across three laboratories, and outlined the likely reasons for discrepancies between these laboratories. The utility of carrier screening is to support couples with information while making reproductive choices. Accurate development of DR and RR is therefore critical. The method described herein provides an unbiased and transparent process to collect, calculate, and report these data.

Pharmacogenetic considerations in the treatment of co-infections with HIV/AIDS, tuberculosis and malaria in Congolese populations of Central Africa

BackgroundHIV-infection, tuberculosis and malaria are the big three communicable diseases that plague sub-Saharan Africa. If these diseases occur as co-morbidities they require polypharmacy, which may lead to severe drug–drug-gene interactions and variation in adverse drug reactions, but also in treatment outcomes. Polymorphisms in genes encoding drug-metabolizing enzymes are the major cause of these variations, but such polymorphisms may support the prediction of drug efficacy and toxicity. There is little information on allele frequencies of pharmacogenetic variants of enzymes involved in the metabolism of drugs used to treat HIV-infection, TB and malaria in the Republic of Congo (ROC). The aim of this study was therefore to investigate the occurrence and allele frequencies of 32 pharmacogenetic variants localized in absorption distribution, metabolism and excretion (ADME) and non-ADME genes and to compare the frequencies with population data of Africans and non-Africans derived from the 1000 Genomes Project. ResultsWe found significant differences in the allele frequencies of many of the variants when comparing the findings from ROC with those of non-African populations. On the other hand, only a few variants showed significant differences in their allele frequencies when comparing ROC with other African populations. In addition, considerable differences in the allele frequencies of the pharmacogenetic variants among the African populations were observed. ConclusionsThe findings contribute to the understanding of pharmacogenetic variants involved in the metabolism of drugs used to treat HIV-infection, TB and malaria in ROC and their diversity in different populations. Such knowledge helps to predict drug efficacy, toxicity and ADRs and to inform individual and population-based decisions.

Inclusion of variants discovered from diverse populations improves polygenic risk score transferability.

SummaryThe majority of polygenic risk scores (PRSs) have been developed and optimized in individuals of European ancestry and may have limited generalizability across other ancestral populations. Understanding aspects of PRSs that contribute to this issue and determining solutions is complicated by disease-specific genetic architecture and limited knowledge of sharing of causal variants and effect sizes across populations. Motivated by these challenges, we undertook a simulation study to assess the relationship between ancestry and the potential bias in PRSs developed in European ancestry populations. Our simulations show that the magnitude of this bias increases with increasing divergence from European ancestry, and this is attributed to population differences in linkage disequilibrium and allele frequencies of European-discovered variants, likely as a result of genetic drift. Importantly, we find that including into the PRS variants discovered in African ancestry individuals has the potential to achieve unbiased estimates of genetic risk across global populations and admixed individuals. We confirm our simulation findings in an analysis of hemoglobin A1c (HbA1c), asthma, and prostate cancer in the UK Biobank. Given the demonstrated improvement in PRS prediction accuracy, recruiting larger diverse cohorts will be crucial—and potentially even necessary—for enabling accurate and equitable genetic risk prediction across populations.

Natural selection on sleep duration in Drosophila melanogaster

Sleep is ubiquitous across animal species, but why it persists is not well understood. Here we observe natural selection act on Drosophila sleep by relaxing bi-directional artificial selection for extreme sleep duration for 62 generations. When artificial selection was suspended, sleep increased in populations previously selected for short sleep. Likewise, sleep decreased in populations previously selected for long sleep when artificial selection was relaxed. We measured the corresponding changes in the allele frequencies of genomic variants responding to artificial selection. The allele frequencies of these variants reversed course in response to relaxed selection, and for short sleepers, the changes exceeded allele frequency changes that would be expected under random genetic drift. These observations suggest that the variants are causal polymorphisms for sleep duration responding to natural selection pressure. These polymorphisms may therefore pinpoint the most important regions of the genome maintaining variation in sleep duration.

Abstract 14781: Computational Prediction of Protein Subdomain Stability as a Novel Approach to Cardiac Myosin Binding ProteinC Variant Adjudication and Clinical Risk Stratification in Hypertrophic Cardiomyopathy

Introduction: Patients with HCM and a pathogenic sarcomere variant have a higher risk of adverse clinical outcomes compared to those without a sarcomere gene variant. Pathogenic truncating variants in MYBPC3 (encoding cardiac myosin binding protein C, MYBP-C) cause loss-of-function and are the most common genetic cause of HCM. However, a substantial number of patients carry missense variants in MYBPC3 that cannot be clearly classified as either pathogenic or benign. Interpretation of these variants of uncertain significance (VUS) remain a significant challenge. Hypothesis: We hypothesize that a structural-based algorithm, STRUM, which estimates the effect of missense variants on subdomain protein folding, will enable clinical risk stratification of patients with HCM and a MYBPC3 VUS. Methods and Results: Among the 7,963 patients in the multi-center Sarcomeric Human Cardiomyopathy Registry (SHaRe), 19 unique missense pathogenic variants and 120 missense VUSs in MYBPC3 were identified. Within SHaRe and GnomAD, 110 benign missense variants (allele frequency > 4e-05) were identified. Following structural modeling of each MyBP-C domain, variants were predicted to cause subdomain misfolding if ΔΔG < = -1.2 kcal/mol (STRUM+). 93% of benign variants were predicted to be STRUM (-). Time-event analysis for an overall composite clinical endpoint [defined as the first occurrence of ventricular arrhythmia, heart failure, all-cause mortality, atrial fibrillation (AF), or stroke] demonstrated that patients carrying a STRUM+ MYBPC3 VUS exhibited a higher rate of adverse events compared to those with a STRUM- VUS (Hazard Ratio=2.29, P=0.0282). Of the 120 missense VUSs, 34 (28%) were STRUM+. In silico saturation mutagenesis of MYBPC3 identified 4,943/23,427 (21%) missense variants predicted to cause subdomain misfolding. Conclusions: STRUM is capable of clinically risk stratifying HCM patients with a MYBPC3 VUSs . These findings support the routine use of STRUM in variant interpretation algorithms and clinical decision making.

Evaluation of the individual detoxification potential in the firefighters and rescuers of emercom of Russia

Relevance. Professional activities of firefighters and rescuers are usually associated with aggressive chemical exposure with increased physical exertion and psychological stress. Therefore, for professional selection and monitoring the health status of firefighters and rescuers of EMERCOM of Russia it is necessary to evaluate the activity of cytochrome P450 isoenzymes that are directly involved in detoxification pathways in the liver.Intention. To evaluate the activity of the CYP3A4 enzyme by phenotyping methods and to establish the frequency of allelic variants of the gene of this enzyme (rs2740574 and rs4987161 polymorphisms) in firefighters and rescuers of EMERCOM of Russia for targeted treatment, rehabilitation and prevention.Methodology. Polymorphisms (rs2740574 and rs4987161) of the CYP3A4 gene and also CYP3A4 activity by the ratio of 6-β-hydroxycortisol / cortisol in the urine were determined during routine periodical medical examination of 64 rescuers and firefighters of rescue units of EMERCOM of Russia. The average age of examined persons was (29.8 ± 5.5) years; 30 of them are rescuers of the North-West Regional Search and Rescue Squad and 34 are firefighters of the territorial fire departments of St. Petersburg.Results and Discussion. According to the results of genotyping of rs2740574 polymorphism of the CYP3A4 gene, EMERCOM employees were divided into 2 groups depending on the presence or absence of a minor allele: “poor” and “rapid” metabolizers (9.4% and 80.6%, respectively). According to the results of genotyping of the rs4987161 polymorphism of the CYP3A4 gene, the examined were classified as “rapid” metabolizers, because patients with a minor allele were not identified. Depending on the ratio of 6-β-hydroxycortisol / cortisol in the urine, the activity level of CYP3A4 was “normal” in 67 %, “poor” in 13 % and “rapid” in 20 % of cases. The ratio of 6-β-hydroxycortisol / cortisol in the urine tended to increase with an increase in work experience and age. No relationship between the studied polymorphic variants of the CYP3A4 gene and the established enzyme activity was observed.Conclusion. Genotyping methods made it possible to identify allelic variants of the CYP3A4 gene that could affect the functionality of the enzyme; however, no association of the studied polymorphisms with enzyme activity was found. In such cases, in the absence of informative genetic markers, it is recommended to evaluate the enzyme activity by phenotyping methods.

Burden of Rare Variants in the OTOG Gene in Familial Meniere's Disease.

Meniere's disease (MD) is a rare inner ear disorder characterized by sensorineural hearing loss, episodic vertigo, and tinnitus. Familial MD has been reported in 6 to 9% of sporadic cases, and few genes including FAM136A, DTNA, PRKCB, SEMA3D, and DPT have been involved in single families, suggesting genetic heterogeneity. In this study, the authors recruited 46 families with MD to search for relevant candidate genes for hearing loss in familial MD. Exome sequencing data from MD patients were analyzed to search for rare variants in hearing loss genes in a case-control study. A total of 109 patients with MD (73 familial cases and 36 early-onset sporadic patients) diagnosed according to the diagnostic criteria defined by the Barany Society were recruited in 11 hospitals. The allelic frequencies of rare variants in hearing loss genes were calculated in individuals with familial MD. A single rare variant analysis and a gene burden analysis (GBA) were conducted in the dataset selecting 1 patient from each family. Allelic frequencies from European and Spanish reference datasets were used as controls. A total of 5136 single-nucleotide variants in hearing loss genes were considered for single rare variant analysis in familial MD cases, but only 1 heterozygous likely pathogenic variant in the OTOG gene (rs552304627) was found in 2 unrelated families. The gene burden analysis found an enrichment of rare missense variants in the OTOG gene in familial MD. So, 15 of 46 families (33%) showed at least 1 rare missense variant in the OTOG gene, suggesting a key role in familial MD. The authors found an enrichment of multiplex rare missense variants in the OTOG gene in familial MD. This finding supports OTOG as a relevant gene in familial MD and set the groundwork for genetic testing in MD.

Association of Collagen Gene (COL4A3) rs55703767 Variant With Response to Riboflavin/Ultraviolet A-Induced Collagen Cross-Linking in Female Patients With Keratoconus.

To investigate for the first time the association of collagen COL4A3 (rs55703767), COL5A1 (rs7044529), and COL4A4 (rs2229813) variants with response to corneal collagen cross-linking (CXL) with riboflavin and ultraviolet A in patients with keratoconus (KC). A total of 147 eligible patients with KC were genotyped for the specified collagen variants using real-time TaqMan-based polymerase chain reaction. Adjusted odds ratio (OR) with 95% confidence interval (CI) was applied to assess the strength of the association with response to CXL for a decrease in maximum keratometry and/or an increase in corneal thickness. Eighty-two patients (55.8%) had post-CXL successful outcomes. The overall analysis revealed that minor allele frequencies of COL4A3, COL5A1, and COL4A4 variants were 0.22, 0.22, and 0.38, respectively. The G/T genotype of the COL4A3 variant was more prevalent in the successful group (43%) compared with the failure group (23%) (P < 0.001). COL4A3 (rs55703767) was associated with a good response under heterozygote (OR: 2.19, 95% CI, 1.04-4.59, P < 0.001) and overdominant (OR: 2.59, 95% CI, 1.25-5.38, P = 0.008) models. By contrast, COL5A1 and COL4A4 variants were not associated with the effective response after CXL treatment. Interestingly, stratification analysis by sex revealed that CXL was more successful in female patients with KC under heterozygote (OR: 4.71, 95% CI, 1.74-12.75), dominant (OR: 3.16, 95% CI, 1.29-7.78), and overdominant (OR: 5.18, 95% CI, 1.92-13.95) models for COL4A3 (rs55703767) variant. The COL4A3 (rs55703767) variant, among other study variants, could be implicated in CXL riboflavin/ultraviolet A treatment response in patients with KC in the study population. Large-scale replication and follow-up studies in different ethnic groups are warranted.

Phenotypic and genetic spectrum of isolated macrodactyly: somatic mosaicism of PIK3CA and AKT1 oncogenic variants

BackgroundIsolated macrodactyly is a severe congenital hand anomaly with functional and physiological impact. Known causative genes include PIK3CA, AKT1 and PTEN. The aim of this study is to gain insights into the genetics basis of isolated macrodactyly.ResultsWe enrolled 24 patients with isolated macrodactyly. Four of them were diagnosed with Proteus syndrome based on skin presentations characteristic to this disease.Targeted next-generation sequencing was performed using patients’ blood and affected tissues. Overall, 20 patients carry mosaic PIK3CA pathogenic variants, i.e. p.His1047Arg (N = 7), p.Glu542Lys (N = 6), p.Glu545Lys (N = 2), p.His1047Leu (N = 2), p.Glu453Lys (N = 1), p.Gln546Lys (N = 1) and p.His1047Tyr (N = 1). Four patients who met the diagnostic criteria of Proteus syndrome carry mosaic AKT1 p.Glu17Lys variant. Variant allele frequencies of these mosaic variants obtained through next-generation sequencing range from 10 to 33%. In genotype–phenotype correlation analysis of patients with PIK3CA variant, we found that patients with the macrodactyly of the lower limbs tend to carry PIK3CA variants located in the helical domain (P = 0.005).ConclusionsMosaic PIK3CA and AKT1 variants can be found in all of our samples with isolated macrodactyly. Insights into phenotypic and genetic spectrum of isolated macrodactyly may be helpful in perusing a more precise and effective management of isolated macrodactyly.

The value of the MTHFR polymorphisms in pathogenesis of nontraumatic necrosis of femoral head

Introduction. Among the etiological factors of non-traumatic avascular necrosis of the femoral head are the following: the prolonged use of corticosteroids, alcohol abuse, systemic lupus erythematosus, sickle cell anemia, the Legg Calve Perthes disease, ionizing radiation, cytotoxic agents, etc. At the same time necrosis of the femoral head might occur in the absence of the above factors (idiopathic necrosis). The reasons for idiopathic avascular necrosis could be a mechanical obstacle to the flow of blood, thrombotic occlusion of vessels, extravascular compression.&#x0D; The purpose of this study is to examine the role of C677T gene mutation of the MTHFR gene in the development of non-traumatic avascular necrosis of the femoral head.&#x0D; Materials and methods. During this study there was a comparative analysis of the frequency of the C677T gene allelic variants conducted in 41 patients with a verified diagnosis of non-traumatic avascular necrosis (main group) and 320 healthy individuals (control group). The survey program included the study of polymorphisms of MTHFR C677T gene by PCR.&#x0D; Results. Differences in the frequency of occurrence of C allele of C677T gene MTHFR in the heterozygous state in case of non-traumatic avascular necrosis and in its absence were not statistically significant (51.2% against 37.2% respectively, 2 = 3.014, p = 0.083). The genotype TT (T in the homozygous state) of the C677T MTHFR gene was detected in 19.5% of the main group patients. A similar index in the control group was two times lower and amounted to 9.0 percent, the differences between groups statistically significant, 2 = 4.314, p = 0.038.&#x0D; Conclusion. The study showed the importance of having the T C677T MTHFR gene in the pathogenesis of non-traumatic avascular necrosis of the femoral head. The data obtained and the analysis of the current literature suggests that this polymorphism is one of genetic predictors of non-traumatic avascular necrosis of the femoral head and other cardiovascular diseases as well.

Роль полиморфных маркеров гена IL10 в патогенезе сахарного диабета 1-го типа

Сахарный диабет типа 1 (СД1) представляет собой многофакторное заболевание, которое характеризуется аутоиммунной природой. Важным фактором в патогенезе СД1 является генетическая предрасположенность, характеризующаяся наличием функциональных однонуклеотидных замен (SNP) в генах цитокинов, ответственных за воспаление. Предполагают, что длительное хроническое воспаление приводит к необратимому разрушению β-клеток поджелудочной железы и может быть объяснено наличием функциональных полиморфных маркеров в генах-антагонистах. Цель исследования - изучение частоты аллельных вариантов ряда полиморфных маркеров гена IL10 при СД1 у жителей Москвы и Московской области. Методика. В работу включено 366 больных СД 1 типа и 526 здоровых индивидов русского происхождения. Группу больных составили пациенты с наличием сахарного диабета 1 типа различной манифестации с общей медианой 41±5 лет. Обе группы выравнены по полу и возрасту. Определение генотипов полиморфных маркеров rs1800896, rs1800872 и rs3024505 гена IL10 проводилось с помощью ПЦР «в реальном времени» на амплификаторе «Real-time CFX96 Touch» (Bio-Rad, США) с использованием готовой смеси для ПЦР qPCRmix-HS (Евроген, Россия) и уникальных праймеров и зондов. Результаты. В результате проведенного исследования выявлена статистически значимая ассоциация полиморфного маркера rs1800896 гена IL10 с повышенным риском развития СД1 (χ2=15.52, OR=1.48, CI95%=1.23-1.79, р=0,0004). Заключение. Полученные результаты дополняют информацию о механизмах возникновения СД типа 1. Внедрение в практику анализа полиморфных вариантов гена IL10 позволит выявить предрасположенность к развитию этого заболевания, его прогрессированию у пациентов с аутоиммунными заболеваниями и у лиц, находящихся в группе риска. Type 1 diabetes mellitus (T1DM) is a multifactorial disease of an autoimmune origin. An important factor in the pathogenesis of T1DM is genetic predisposition characterized by the presence of functional single-nucleotide polymorphisms (SNPs) in the cytokine genes contributing to inflammation. Long-standing, chronic inflammation is considered to result in irreversible destruction of all pancreatic b-cells and may be due to the presence of functional polymorphic markers in genes of inflammation antagonists, such as the interleukin 10 (IL10) gene. Aim. The aim of this study was to determine the frequency of allelic variants in a number of IL10 gene polymorphic markers in residents of Moscow and the Moscow Region with T1DM. Methods. The study includes 366 patients with T1DM with different manifestations and a median duration of 41+5 years and 526 healthy individuals. The groups were gender- and age-matched. Genotypes of the rs1800896, rs1800872, and rs3024505 polymorphic markers of the IL10 gene were determined with real-time PCR on a Real-Time CFX96 Touch amplifier (Bio-Rad, USA) with a qPCRmix-HS ready-mixed PCR kit (Eurogen, Russia) and unique primers and probes. Results. The rs1800896 polymorphic marker of the IL10 gene statistically significantly correlated with increased risk of T1DM (χ2=15.52, OR=1.48, CI95%=1.23-1.79, р=0.0004). Conclusion. The study results complement the information about T1DM mechanisms of origin and pathogenesis. Implementation in practice of the methods for analyzing polymorphic variants of the IL10 gene will allow revealing a predisposition to this disease and/or its progression in patients with autoimmune diseases or in people at risk.

The identified clinical features of Parkinson's disease in homo-, heterozygous and digenic variants of PINK1

To investigate the prevalence and genotype-phenotype correlations of phosphatase and tensin homolog induced putative kinase 1 (PINK1) variants in Parkinson's disease (PD) patients, we analyzed 1700 patients (842 familial PD and 858 sporadic PD patients from Japanese origin). We screened the entire exon and exon-intron boundaries of PINK1 using Sanger sequencing and target sequencing by Ion torrent system. We identified 30 patients with heterozygous variants, 3 with homozygous variants, and 3 with digenic variants of PINK1-PRKN. Patients with homozygous variants presented a significantly younger age at onset than those with heterozygous variants. The allele frequency of heterozygous variants in patients with age at onset at 50 years and younger with familial PD and sporadic PD showed no differences. [123I]meta-iodobenzylguanidine (MIBG) myocardial scintigraphy indicated that half of patients harboring PINK1 heterozygous variants showed a decreased heart to mediastinum ratio (12/23). Our findings emphasize the importance of PINK1 variants for the onset of PD in patients with age at onset at 50 years and younger and the broad spectrum of clinical symptoms in patients with PINK1 variants.

Bacterial antigen translocation and age as BMI-independent contributing factors on systemic inflammation in NAFLD patients.

Low-grade systemic inflammation is a crucial landmark in NAFLD favouring disease progression and comorbidities. We evaluated the input of circulating bacterial antigens on systemic markers of inflammation in NAFLD patients. Multicenter cross-sectional study including consecutive patients with biopsy-proven NAFLD. Demographic, metabolic and fibrosis-related variables were collected. Circulating bacterial antigens were quantified in blood. Toll-like receptor SNPs were genotyped. Serum cytokine levels were evaluated. Peripheral blood mononuclear cell response to bacterial antigens was evaluated in vitro. Three hundred and fifteen patients from five Spanish hospitals were distributed by BMI. At least, one bacterial antigenic type was found in 66 patients with BMI < 30 (63.4%) and 163 patients with BMI > 30 (77.3%) (P = .014). HOMA-IR was significantly higher in the presence of circulating antigens among patients with BMI < 30. NASH and significant fibrosis in non-obese patients were more frequent in the presence of at least two circulating antigenic types. Allelic frequencies of TLR variants were similar to controls and did not affect clinical or laboratory parameters. Pro-inflammatory cytokines were significantly increased in patients with bacterial antigens, regardless of BMI. TLR gene and protein expression levels were significantly increased in PBMCs from patients with bacterial antigens. Antigen concentrations independently influenced TNF-α and IL-6, in both BMI subgroups of patients. Age independently influenced TNF-α and IL-6 in non-obese patients, and TNF-α in obese patients. Serum circulating bacterial antigens as well as age were BMI-independent factors related to increased systemic inflammation in NAFLD and provides insight on the multifaceted sources of inflammation in these patients.

Genomic analysis of 21 patients with corneal neuralgia after refractive surgery.

Refractive surgery, specifically laser-assisted in situ keratomileusis and photorefractive keratectomy, are widely applied procedures to treat myopia, hyperopia, and astigmatism. After surgery, a subgroup of cases suffers from persistent and intractable pain of obscure etiology, thought to be neuropathic. We aimed to investigate the contribution of genomic factors in the pathogenesis of these patients with corneal neuralgia. We enrolled 21 cases (6 males and 15 females) from 20 unrelated families, who reported persistent pain (>3 months), after refractive surgery (20 laser-assisted in situ keratomileusis and 1 photorefractive keratectomy patients). Whole-exome sequencing and gene-based association test were performed. Whole-exome sequencing demonstrated low-frequency variants (allele frequency < 0.05) in electrogenisome-related ion channels and cornea-expressed collagens, most frequently in SCN10A (5 cases), SCN9A (4 cases), TRPV1 (4 cases), CACNA1H and CACNA2D2 (5 cases each), COL5A1 (6 cases), COL6A3 (5 cases), and COL4A2 (4 cases). Two variants, p.K655R of SCN9A and p.Q85R of TRPV1, were previously characterized as gain-of-function. Gene-based association test assessing "damaging" missense variants against gnomAD exome database (non-Finnish European or global), identified a gene, SLC9A3R1, with statistically significant effect (odds ratio = 17.09 or 17.04; Bonferroni-corrected P-value < 0.05). These findings in a small patient cohort did not identify a common gene/variant among most of these cases, as found in other disorders, for example small-fiber neuropathy. Further studies of these candidate genes/variants might enhance understanding of the role of genetic factors in the pathogenesis of corneal neuralgia.

Pharmacogenomics of anticancer drugs: Personalising the choice and dose to manage drug response.

The field of pharmacogenomics has made great strides in oncology over the last 20 years and indeed a significant number of pre-emptive genetic tests are now routinely undertaken prior to anticancer drug administration. Many of these gene-drug interactions are the fruits of candidate gene and genome-wide association studies, which have largely focused on common genetic variants (allele frequency>1%). Examples where there is clinical utility include genotyping or phenotyping for G6PD to prevent rasburicase-induced RBC haemolysis, and TPMT to prevent thiopurine-induced bone marrow suppression. Other associations such as CYP2D6 status in determining the efficacy of tamoxifen are more controversial because of contradictory evidence from different sources, which has led to variability in the implementation of testing. As genomic technology becomes ever cheaper and more accessible, we must look to the additional data our genome can provide to explain interindividual variability in anticancer drug response. Clearly genes do not act on their own and it is therefore important to investigate genetic factors in conjunction with clinical factors, interacting concomitant drug therapies and other factors such as the microbiome, which can all affect drug disposition. Taking account of all of these factors, in conjunction with the somatic genome, is more likely to provide better predictive accuracy in determining anticancer drug response, both efficacy and safety. This review summarises the existing knowledge related to the pharmacogenomics of anticancer drugs and discusses areas of opportunity for further advances in personalisation of therapy in order to improve both drug safety and efficacy.