Minor Single Nucleotide Polymorphisms Research Articles

Impact of Single Nucleotide Polymorphisms of the Promoter of the TNF Gene on Adalimumab Treatment Responses in Hidradenitis Suppurativa

Background: Results of randomized clinical trials show great variation in response to treatment with adalimumab (ADA) in hidradenitis suppurativa (HS). This varied response may be associated with genetic polymorphisms. Objectives: The aim of the study was to study the association between carriage of single nucleotide polymorphisms (SNPs) in the promoter of the tumor necrosis factor (TNF) gene and their response to ADA. Methods: Patients with moderate to severe HS who received ADA treatment for at least 12 weeks were enrolled. SNPs were analyzed with PCR-restriction fragment length polymorphism. Hidradenitis Suppurativa Clinical Response (HiSCR) score, International Hidradenitis Suppurativa Severity Scoring System 4 (IHS4) score, inflammatory lesion (AN) count, and draining tunnel (dT) count were collected at weeks 0, 12, 24, 36, and 48. Results: HiSCR response after 12 weeks of ADA treatment was 71.8% among carriers of the common GGG haplotype and 50.0% among carriers of minor frequency SNP haplotypes (p: 0.031; odds ratio: 0.39). This significant difference persisted until week 36. Carriers of minor frequency SNP haplotypes also had a lower relative decrease of the AN count at weeks 12 and 24; the dT count and IHS4 were not statistically different between the two groups. Conclusions: Carriage of at least one minor frequency SNP haplotype of the promoter of the TNF gene is associated with a decreased response to ADA. This association may have an impact on treatment decision-making.

Fine-scale genomic tracking of Ross River virus using nanopore sequencing

BackgroundRoss River virus (RRV) is Australia’s most common and widespread mosquito-transmitted arbovirus and is of significant public health concern. With increasing anthropogenic impacts on wildlife and mosquito populations, it is important that we understand how RRV circulates in its endemic hotspots to determine where public health efforts should be directed. Current surveillance methods are effective in locating the virus but do not provide data on the circulation of the virus and its strains within the environment. This study examined the ability to identify single nucleotide polymorphisms (SNPs) within the variable E2/E3 region by generating full-length haplotypes from a range of mosquito trap-derived samples.MethodsA novel tiled primer amplification workflow for amplifying RRV was developed with analysis using Oxford Nanopore Technology’s MinION and a custom ARTIC/InterARTIC bioinformatic protocol. By creating a range of amplicons across the whole genome, fine-scale SNP analysis was enabled by specifically targeting the variable region that was amplified as a single fragment and established haplotypes that informed spatial-temporal variation of RRV in the study site in Victoria.ResultsA bioinformatic and laboratory pipeline was successfully designed and implemented on mosquito whole trap homogenates. Resulting data showed that genotyping could be conducted in real time and that whole trap consensus of the viruses (with major SNPs) could be determined in a timely manner. Minor variants were successfully detected from the variable E2/E3 region of RRV, which allowed haplotype determination within complex mosquito homogenate samples.ConclusionsThe novel bioinformatic and wet laboratory methods developed here will enable fast detection and characterisation of RRV isolates. The concepts presented in this body of work are transferable to other viruses that exist as quasispecies in samples. The ability to detect minor SNPs, and thus haplotype strains, is critically important for understanding the epidemiology of viruses their natural environment.Graphical

Association of Fatty Acid Desaturase 1 rs174547 Polymorphism with the Composition of Long-Chain Polyunsaturated Fatty Acids in Serum Glycerophospholipids during Pregnancy.

The increase in fetal requirements of long-chain polyunsaturated fatty acids (LCPUFAs) during pregnancy alters maternal fatty acid metabolism, and therefore, fatty acid desaturase (FADS) gene polymorphisms may change blood fatty acid composition or concentration differently during pregnancy. We investigated the relationship between a FADS1 single-nucleotide polymorphism (SNP) and maternal serum LCPUFA levels in Japanese pregnant women during the first and third trimesters and at delivery. Two hundred and fifty-three pregnant women were included, and fatty acid compositions of glycerophospholipids in serum (weight %) and the FADS1 SNP rs174547 (T/C) were analyzed. LCPUFAs, including arachidonic acid (ARA) and docosahexaenoic acid (DHA), significantly decreased from the first to the third trimester of pregnancy. Furthermore, DHA significantly decreased from the third trimester of pregnancy to delivery. At all gestational stages, linoleic acid (LA) and α-linolenic acid were significantly higher with the number of minor FADS1 SNP alleles, whereas γ-linolenic acid and ARA and the ARA/LA ratio were significantly lower. DHA was significantly lower with the number of minor FADS1 SNP alleles only in the third trimester and at delivery, suggesting that genotype effects become more obvious as pregnancy progresses.

Exploring Machine Learning Algorithms to Unveil Genomic Regions Associated With Resistance to Southern Root-Knot Nematode in Soybeans.

Southern root-knot nematode [SRKN, Meloidogyne incognita (Kofold & White) Chitwood] is a plant-parasitic nematode challenging to control due to its short life cycle, a wide range of hosts, and limited management options, of which genetic resistance is the main option to efficiently control the damage caused by SRKN. To date, a major quantitative trait locus (QTL) mapped on chromosome (Chr.) 10 plays an essential role in resistance to SRKN in soybean varieties. The confidence of discovered trait-loci associations by traditional methods is often limited by the assumptions of individual single nucleotide polymorphisms (SNPs) always acting independently as well as the phenotype following a Gaussian distribution. Therefore, the objective of this study was to conduct machine learning (ML)-based genome-wide association studies (GWAS) utilizing Random Forest (RF) and Support Vector Machine (SVM) algorithms to unveil novel regions of the soybean genome associated with resistance to SRKN. A total of 717 breeding lines derived from 330 unique bi-parental populations were genotyped with the Illumina Infinium BARCSoySNP6K BeadChip and phenotyped for SRKN resistance in a greenhouse. A GWAS pipeline involving a supervised feature dimension reduction based on Variable Importance in Projection (VIP) and SNP detection based on classification accuracy was proposed. Minor effect SNPs were detected by the proposed ML-GWAS methodology but not identified using Bayesian-information and linkage-disequilibrium Iteratively Nested Keyway (BLINK), Fixed and Random Model Circulating Probability Unification (FarmCPU), and Enriched Compressed Mixed Linear Model (ECMLM) models. Besides the genomic region on Chr. 10 that can explain most of SRKN resistance variance, additional minor effects SNPs were also identified on Chrs. 10 and 11. The findings in this study demonstrated that overfitting in GWAS may lead to lower prediction accuracy, and the detection of significant SNPs based on classification accuracy limited false-positive associations. The expansion of the basis of the genetic resistance to SRKN can potentially reduce the selection pressure over the major QTL on Chr. 10 and achieve higher levels of resistance.

Novel single nucleotide polymorphisms in the bovine leukemia virus genome are associated with proviral load and affect the expression profile of viral non-coding transcripts

Bovine leukemia virus (BLV) infects bovine B-cells and causes malignant lymphoma, resulting in severe economic losses in the livestock industry. To control the spread of BLV, several studies have attempted to clarify the molecular mechanisms of BLV pathogenesis, but the details of the mechanism are still enigmatic. Currently, viral non-coding RNAs are attracting attention as a novel player for BLV pathogenesis because these transcripts can evade the host immune response and are persistently expressed in latent infection. One of the viral non-coding RNA, AS1, is encoded in the antisense strand of the BLV genome and consists of two isoforms, AS1-L and AS1-S. Although the function of the AS1 is still unknown, the AS1 RNA might also have some roles because it keeps expressing in tumor tissues. In the present study, we identified novel single nucleotide polymorphisms (SNPs) located in the AS1 coding region and indicated that individuals infected with BLV with minor SNPs showed low proviral load. To evaluate the effect of identified SNPs, we constructed infectious clones with these SNPs and found that their introduction affected the expression profile of AS1 RNA; the amount of AS1-L isoform increased compared with the wild type, although the total amount of AS1 RNA remained unchanged. Prediction analysis also suggested that the introduction of SNPs changed the secondary structure of AS1 RNA. These results explain part of the relationship between BLV expansion in vivo and the expression profile of AS1, although further analysis is required.

Mechanism underlying the regulation of sortilin expression and its trafficking function.

This review summarizes and analyzes the updated information on the regulation of sortilin expression and its trafficking function. Evidence indicates that the expression and function of sortilin are closely regulated at four levels: DNA, messenger RNA (mRNA), protein, and trafficking function. DNA methylation, several mutations, and minor single-nucleotide polymorphisms within DNA fragments affect the expression of SORT1 gene. A few transcription factors and microRNAs modulate its transcription as well as the splicing or stability of the mRNA. Moreover, several translation factors control the synthesis of sortilin protein, and posttranslational modifications affect its degradation processes. Multiple adaptor molecules modulate the sortilin trafficking function in the anterograde or retrograde pathway. Recent advances in the regulation of sortilin expression and function, and its related mechanisms will help the ongoing research related to sortilin and promote future clinical application via sortilin intervention.

The association of HBG2, BCL11A, and HBS1L-MYB polymorphisms to thalidomide response in Chinese β-thalassemia patients

Thalidomide has been shown to reactivate fetal hemoglobin (HbF) production and reduce the need for blood transfusions in β-thalassemia patients. However, some patients show a minor response or no response to thalidomide. In view of its potential side effects, targeted prescription of thalidomide is imperative. We initially aimed to explore the relevance of HBG2 (rs7482144), BCL11A (rs11886868, rs4671393, rs766432 and rs1427407) and HBS1L-MYB (rs9399137, rs4895440 and rs4895441) single nucleotide polymorphisms (SNPs) in thalidomide response. Eight SNPs were investigated by PCR and DNA sequencing, and their roles in thalidomide response in Chinese β-thalassemia patients were assessed. Results demonstrated that minor alleles of four SNPs were associated with an increased main response risk (rs7482144: P = 0.015; rs9399137: OR = 4.911, P = 0.029; rs4895440: OR = 4.522, P = 0.040; and rs4895441: OR = 4.522, P = 0.040). For patients with non-transfusion-dependent thalassemia (NTDT), with an increase in the minor allele numbers of rs7482144 (P = 0.011), rs9399137 (P = 0.013), rs4895440 (P = 0.011) and rs4895441 (P = 0.011), Hb increments after treatment were increased significantly as well. The cumulative effects of patients carrying any combination of one or three significant minor alleles included a gradually increased main response risk compared to those without the significant minor alleles (P = 0.040–0.018, OR = 8.556–11.000). Furthermore, Hb increments after treatment correlated with cumulative numbers of minor alleles in the four significant SNPs among patients with NTDT (P = 0.001). It was demonstrated that SNPs in HBG2 and HBS1L-MYB contributed significantly to thalidomide response in Chinese patients with β-thalassemia and that the cumulative number of minor SNP alleles may serve as good predictors of treatment response in this population.

GENE-26. HOST GENETIC VARIATIONS IN MACROPHAGE MIGRATION INHIBITOR FACTOR CONFER WORSE PROGNOSIS IN GLIOBLASTOMA

Abstract Genetic and systemic prognostic factors have been identified in glioblastoma (GBM) that correlate with survival, but patient-specific genomic risk factors that impact prognosis or response to immunotherapies have not been elucidated. GBM promotes an immune suppressive microenvironment via many mechanisms including the production of macrophage migration inhibitory factor (MIF) by GBM cancer stem cells, which activates myeloid derived suppressor cells (MDSCs). Increased circulating and intracranial MDSCs as well as intratumoral MIF expression in GBM patients portend a worse overall prognosis. Endogenous MIF expression is dependent on two genetic microsatellite loci: single nucleotide polymorphisms (SNPs) and CATT repeats within the promoter. To determine whether these genetic variations were linked to GBM development and/or prognosis, we assessed peripheral nucleated blood from 520 GBM patients for the MIF SNPs and CATT repeats. MIF microsatellite frequencies were similar between the normal population and GBM patients indicating loci variability was not a risk factor for GBM development. However, newly diagnosed IDH wild-type GBM patients with a minor allele SNP who received standard of care therapy had a 3.1 month shorter progression free survival (PFS), and a 4.3 month shorter overall survival (OS) when compared to patients with two major allele SNPs. This association was seen also with the CATT-repeat analyses. Furthermore, in a multivariate analysis for PFS that included age, sex, Karnofsky performance status, MGMT methylation status, 1p/19q co-deletion, and SNP status as covariates, only age and SNP status were independently associated with shorter PFS. Taken together, patients with variant MIF microsatellite loci experienced shorter PFS and decreased OS compared to those with the most common loci. These results are currently being validated in a separate 1700 patient cohort with the intent of understanding how MIF expression influences myeloid populations within the GBM microenvironment and then developing novel peripheral GBM screening markers for aggressiveness.

Drug-response related genetic architecture of Bangladeshi population

Many Single Nucleotide Polymorphisms (SNPs) have been discovered to be responsible for inter-individual variability in drug response. Since allelic distribution and extent of linkage disequilibrium (LD) blocks of SNPs vary among populations, frequencies of different SNP alleles associated with drug response and patterns of LD should be analyzed separately for different populations. In the present study, we listed the SNPs associated with drug response along with the responsive drugs and calculated the frequencies of the major and minor alleles in the genomes of Bangladeshi individuals. We then analyzed the genotypic data to find LD blocks, tag SNPs (tSNP), frequencies of different haplotypes and association (crossover rates) between different LD blocks of the drug response related SNPs. Among 156 non-redundant autosomal drug response related SNPs, there are nineteen LD blocks and five tSNPs in Bangladeshi population. Certain minor SNP alleles in worldwide population are present as the major ones (with frequencies ≥0.5) in Bangladeshi population. Based on the available SNP data in the 1000 genome database, these particular SNP alleles have similar distributions in other South Asian populations (Telegu and Gujrati Indian, Punjabi Pakistani and Sri Lankan Tamil).

Abstract 17134: Variation Within a Left Ventricle-Specific Hand1 Enhancer Impairs Gata Transcription Factor Binding and Disrupts Ventricular Conduction System Development

The ventricular conduction system (VCS), composed of the His bundle, the left and right bundle branches, and the Purkinje fiber network, rapidly propagates electrical impulses through the ventricles to coordinate chamber contraction. An ECG depicts VCS-mediated ventricular depolarization as the QRS interval. Disorders of the VCS may manifest as arrhythmias, and are associated with increased risk of sudden cardiac death and overall mortality. The genetic and developmental mechanisms underlying VCS dysfunction are poorly understood. Genome-wide association studies have identified multiple single nucleotide polymorphisms (SNPs) associated with VCS arrhythmias. A majority of these SNPs occur outside of coding domains, within intergenic or intronic regions. We hypothesize that such pathogenic SNPs may impact VCS development and function by altering the expression of critical genes. Two intergenic SNPs associated with QRS prolongation occur near the bHLH cardiac transcription factor HAND1 . We have identified a left ventricle (LV) enhancer, located between these two SNPs, that is necessary and sufficient for LV cis -regulatory activity. Two evolutionarily conserved GATA transcription factor consensus-binding sites within this enhancer are bound by GATA4 and necessary for cis -regulatory activity. CRISPR-mediated deletion of this enhancer dramatically reduced Hand1 expression solely within the LV. Mice homozygous for this deleted enhancer displayed dysregulated LV gene expression, morphologically abnormal His bundles and left bundle branches, and a VCS phenotype consistent with right bundle branch block. Genome-wide association analyses of human patients with QRS prolongation revealed additional, linked SNPs, one of which overlaps with a critical GATA cis -regulatory element within the LV-specific Hand1 enhancer. This SNP disrupts GATA4 binding. Ongoing studies of mice that genetically mimic these minor SNP variants will assess reduced Hand1 expression and impaired VCS function. We conclude that a LV-specific Hand1 enhancer is necessary for VCS development and a SNP associated with QRS prolongation directly influences GATA4 binding to a critical cis -regulatory element within this enhancer.

Haplotypes composed of minor frequency single nucleotide polymorphisms of the TNF gene protect from progression into sepsis: A study using the new sepsis classification

ObjectivesSeveral articles have provided conflicting results regarding the role of single nucleotide polymorphisms (SNPs) in the promoter region of the TNF gene in susceptibility to sepsis. Former articles have been based on previous definitions of sepsis. This study investigated the influence of TNF haplotypes on the development of sepsis using the new Sepsis-3 definitions. MethodsDNA was isolated from patients suffering from infection and systemic inflammatory response syndrome. Haplotyping was performed for six SNPs of TNF. The serum levels of tumour necrosis factor alpha (TNF-α) of these patients were measured using an enzyme immunosorbent assay. Patients were classified into infection and sepsis categories using the Sepsis-3 definitions. Associations between the TNF haplotypes and the clinical characteristics and serum TNF-α levels of the patients were examined. ResultsThe most common TNF haplotype h1 was composed of major alleles of the studied SNPs. Carriage of haplotypes composed of minor frequency alleles was associated with a lower risk of developing sepsis (odds ratio 0.41, 95% confidence interval 0.19–0.88, p=0.022), but this did not affect the 28-day outcome. Serum TNF-α levels were significantly higher among patients homozygous for h1 haplotypes who developed sepsis compared to infection (p=0.032); a similar result was not observed for patients carrying other haplotypes. ConclusionsHaplotypes containing minor frequency SNP alleles of TNF protect against the development of sepsis without affecting the outcome.

Fibrinogen and clot-related phenotypes determined by fibrinogen polymorphisms: Independent and IL-6-interactive associations.

Interleukin-6 (IL-6) induces the expression of fibrinogen, and polymorphic variation within the fibrinogen genes is believed to alter the magnitude of this expression. The identification of the functional relevance of individual fibrinogen single nucleotide polymorphisms (SNPs) has been hindered by the high linkage disequilibrium (LD) reported in the European fibrinogen gene locus. This study investigated two novel and 12 known fibrinogen SNPs of potential functional relevance, in 2010 Tswana individuals known to have low LD. We aimed to identify functional polymorphisms that contribute to clot-related phenotypes and total and γ’ fibrinogen concentrations independently and through their interaction with IL-6, by taking advantage of the high fibrinogen and IL-6 concentrations and the low LD reported in black South Africans. Fibrinogen was significantly associated with IL-6, thereby mediating associations of IL-6 with clot formation and structure, although attenuating the association of IL-6 with clot lysis time. None of the common European fibrinogen haplotypes was present in this study population. Putative functional fibrinogen SNPs FGB–rs7439150, rs1800789 (–1420G/A) and rs1800787 (–148C/T) were significantly associated with fibrinogen concentration and altered clot properties, with several associations significantly influenced by IL-6 concentrations. The impact of harbouring several minor fibrinogen SNP alleles on the association of IL-6 and fibrinogen concentration was cumulative, with possession of each additional minor allele showing a stronger relationship of IL-6 with fibrinogen. This was also reflected in differences in clot properties, suggesting potential clinical relevance. Therefore, when investigating the effect of fibrinogen genetics on fibrinogen concentrations and CVD outcome, the possible interactions with modulating factors and the fact that SNP effects seem to be additive should be taken into account.

Single Nucleotide Polymorphisms Associated with Pain Sensitivity After Laparoscopic Cholecystectomy.

To systematically evaluate variations in single-nucleotide polymorphisms within 13 candidate pain genes in patients differing in phenotype characteristics based on a composite measure of pain sensitivity. In a case-control study, 149 patients scheduled for laparoscopic cholecystectomy were individually categorized according to preoperative pain sensitivity and postoperative pain intensity. Cases (pain group) reported cannulation-induced pain intensity higher than 2.0, together with postoperative pain intensity of 7.0 or higher (visual analog scale [VAS] units), and controls (low-pain group) reported cannulation-induced pain intensity of 2.0 or lower, together with postoperative pain intensity lower than 4.0 (VAS units). Genotyping of exomes was performed in 32 case and 25 control patients compared with respect to variations within 13 candidate pain genes. There were no statistically significant differences in single nucleotide polymorphisms (SNPs) within the candidate genes between the case and control groups, but minor allele SNPs in the ABCB1 and COMT genes were more common in patients with higher levels of pain sensitivity and intensity. In this candidate gene study, based on a composite measure of pain sensitivity, no variations reached statistical significance after correction for multiple testing, most likely due to the large number of markers analyzed and few patients. Nevertheless, the results suggest a possible genetic contribution of single-nucleotide polymorphisms within the ABCB1 and COMT genes in individuals with higher levels of pain sensitivity.

The Common Follicle-Stimulating Hormone Receptor (FSHR) Promoter Polymorphism FSHR -29G > A Affects Androgen Production in Normal Human Small Antral Follicles.

Follicle-stimulating hormone receptors (FSHRs) are almost exclusively expressed on granulosa cells, and FSH action is probably most clearly reflected in intrafollicular hormone milieu of antral follicles. Little is known about the possible effects of the common single nucleotide polymorphism (SNP) FSHR −29G > A (rs1394205) on hormonal conditions in humsan small antral follicles (hSAFs) obtained from women in the natural menstrual cycle. This study investigated the follicle fluid (FF) concentrations of anti-Müllerian hormone, estradiol, progesterone, androstenedione, and testosterone in hSAF in relation to the different genotypes of FSHR −29G > A. FF from 362 follicles was collected in 95 women undergoing fertility preservation, who did not suffer from a disease that directly affected ovarian function. The testosterone levels of the minor A/A genotype were significantly increased compared to the A/G and the G/G genotype. Furthermore, significantly reduced androstenedione levels were observed for the G/G genotype, as compared to the A/G genotype, while the other hormones did not show statistical significant differences. In conclusion, the androgen levels of hSAF were significantly elevated in the minor SNP genotype in the FSHR promoter polymorphism FSHR −29G > A.

8q24 Polymorphisms and Diabetes Mellitus Regulate Apolipoprotein A-IV in Colorectal Carcinogenesis.

Here, we explored the genetic interactions between diabetes and oncogenic single-nucleotide polymorphisms (SNPs) that determine colorectal cancer (CRC) morbidity. 8q24 rs6983267 polymorphism analysis and cDNA microarray were performed in 107 CRCs to identify the genes associated with diabetes and the oncogenic SNP. Then clinical significance of the gene was validated in 132 CRCs. Meta-analysis of microarray data and diabetic comorbidity was performed. Of genes associated with a minor SNP allele at 8q24, diabetes, and MYC overexpression, apolipoprotein A-IV (ApoA-IV) was associated with oncogenesis and poor prognosis in CRC patients. Patients with high ApoA-IV expression showed significantly poorer prognosis by univariate and multivariate analysis. Meta-analysis revealed lipid metabolism was associated with ApoA-IV-related oncogenesis in diabetic patients. Changes in lipid metabolism associated with aberrant expression of ApoA-IV were risks for CRC oncogenesis.

Polymorphism in the TRP8 gene in Kyrgyz population: Putative association with highland adaptation

The human TRPM8 gene encodes a receptor mediating cold sensitivity, and this points to its putative role in cold adaptation. The structural variability of the TRPM8 gene for five single-nucleotide polymorphisms (SNPs) has been studied in the Kyrgyz population. The SNPs are located in the coding regions of the gene, and three of them are confined to a 20-bp segment in exon 7. The frequencies of minor SNP alleles are as follows: rs13004520 G/C = 0.06; rs28901637 A/T = 0.13; rs11562975 G/C = 0.27; rs7593557 G/A = 0.21; rs11563071 C/G = 0.12. The analyzed sample of Kyrgyz population includes 275 individuals living at different altitudes and under drastically different climatic conditions. The frequency of the minor rs11562975 allele in the highlanders (living above 3200 m ASL and higher) is lower by a factor of 1.5 than in the residents of lower regions (760–3000 m ASL; p < 0.01). This result indicates a selective role of rs11562975 in adapting to cold. A comparison of haplotype frequencies in the Kyrgyz population with Europeans, East Asians, and Africans shows a clear narrowing of genotype variation in Europeans in comparison to all the others. Probably, this phenomenon is related to a decline in the population size (bottleneck effect) during evolution. We consider the exon–intron structure of the TRPM8 gene. The epigenetic markers in the vicinity of the gene have been analyzed. Two strong binding sites for insulator ctcf proteins are present there. They are likely to be associated with chromatin conformation and alternative splicing regulation. A structural–functional characterization of genes for the TRP protein family is provided.

Polymorphism in the TRP8 gene in Kyrgyz population: putative association with highland adaptation

The human TRPM8 gene encodes a receptor mediating cold sensitivity, and this fact points to its putative role in cold adaptation. The structural variability of the TRPM8 gene for five single-nucleotide polymorphisms (SNPs) has been studied in Kyrgyz population. The SNPs are located in coding regions of the gene, and three of them are confined to a segment of 20 bp in exon 7. The frequencies of minor SNP alleles are: rs13004520 G/C = 0.06; rs28901637 А/Т = 0.13; rs11562975 G/C = 0.27; rs7593557 G/A = 0.21; rs11563071 С/G = 0.12. The analyzed sample of Kyrgyz population includes 275 individuals living at different altitudes and under drastically different climatic conditions. The frequency of the minor rs11562975 allele in highlanders (living above 2 800 m A. S. L.) is one-third lower than in residents of lower regions (760–2 800 m A. S. L.; p &lt; 0.01). This result presumes a selective role of rs11562975 in cold adaptation. Comparison of haplotype frequencies in Kyrgyz people with Europeans, East Asians, and Africans shows a clear narrowing of genotype variation in Europeans in comparison to all others. Probably, this phenomenon is related to a population size decline (bottleneck effect) during the evolution. We consider the exon– intron structure of the TRPM8 gene. Epigenetic markers in the vicinity of the gene have been analyzed. Two strong binding sites for insulator ctcf proteins are present there. They are likely to be associated with chromatin conformation and alternative splicing regulation. A structure–functional characterization of genes for the TRP protein family is provided.

Factors associated with sustained virological response in 24‐week telaprevir‐based triple therapy for chronic hepatitis C genotype 1b patients with the IL28B minor genotype

Single nucleotide polymorphisms (SNP) near the interleukin-28B (IL28B) gene affect the outcome of 24-week telaprevir-based triple therapy with telaprevir, pegylated interferon-α and ribavirin for chronic hepatitis C virus (HCV) genotype 1b patients. We aimed to identify factors associated with treatment outcomes in patients with the unfavorable minor IL28B SNP genotype, who have poor response to combination therapy. Pretreatment and on-treatment factors associated with sustained virological response (SVR) for 24-week telaprevir-based triple therapy were analyzed using multiple logistic regression analysis in 106 HCV genotype 1b patients with the minor IL28B SNP rs8099917 genotype (non-TT). Of the 106 non-TT patients, 62 (58.5%) achieved SVR. Of the 44 remaining patients, 22 experienced relapse, 13 experienced viral breakthrough and nine were non-responders. Pretreatment factors such as treatment-naïve/prior treatment response (P = 0.0041), high fasting serum low-density lipoprotein cholesterol (LDL-C) concentration (P = 0.0068) and low serum HCV RNA levels (P = 0.0088) were significantly and independently associated with SVR. On-treatment factors such as achievement of rapid virological response (RVR) were significantly and independently associated with SVR (P = 0.0001). For both pre- and on-treatment factors, treatment-naïve/prior treatment response (P = 0.0018), low pretreatment serum fasting LDL-C (P = 0.0062) and achieving RVR (P = 0.0021) were significantly and independently associated with SVR. In HCV genotype 1b patients with the minor IL28B SNP rs8099917 genotype, evaluating prior treatment response and achieving RVR and pretreatment serum fasting LDL-C concentrations were useful for predicting SVR achievement after 24-week telaprevir-based triple therapy.

Functional Differences Exist between TNFα Promoters Encoding the Common −237G SNP and the Rarer HLA-B*5701-Linked A Variant

A large body of functional and epidemiological evidence have previously illustrated the impact of specific MHC class I subtypes on clinical outcome during HIV-1 infection, and these observations have recently been re-iterated in genome wide association studies (GWAS). Yet because of the complexities surrounding GWAS-based approaches and the lack of knowledge relating to the identity of rarer single nucleotide polymorphism (SNP) variants, it has proved difficult to discover independent causal variants associated with favourable immune control. This is especially true of the candidate variants within the HLA region where many of the recently proposed disease influencing SNPs appear to reflect linkage with ‘protective’ MHC class I alleles. Yet causal MHC-linked SNPs may exist but remain overlooked owing to the complexities associated with their identification. Here we focus on the ancestral TNFα promoter −237A variant (rs361525), shown historically to be in complete linkage disequilibrium with the ‘protective’ HLA-B*5701 allele. Many of the ancestral SNPs within the extended TNFα promoter have been associated with both autoimmune conditions and disease outcomes, however, the direct role of these variants on TNFα expression remains controversial. Yet, because of the important role played by TNFα in HIV-1 infection, and given the proximity of the −237 SNP to the core promoter, its location within a putative repressor region previously characterized in mice, and its disruption of a methylation-susceptible CpG dinucleotide motif, we chose to carefully evaluate its impact on TNFα production. Using a variety of approaches we now demonstrate that carriage of the A SNP is associated with lower TNFα production, via a mechanism not readily explained by promoter methylation nor the binding of transcription factors or repressors. We propose that the −237A variant could represent a minor causal SNP that additionally contributes to the HLA-B*5701-mediated ‘protective’ effect during HIV-1 infection.

Association between the synovial expression of cyclic citrullinated peptide and susceptibility variants of HLA-DRB1 shared epitope alleles and PADI 4 gene single nucleotide polymorphisms in patients with rheumatoid arthritis

To analyze the association between the synovial expression of cyclic citrullinated peptide (CCP) and susceptibility variants of HLA-DRB1 shared epitope (SE) alleles and/or peptidylarginine deiminase 4 (PADI4) gene single nucleotide polymorphisms (SNP) in patients with rheumatoid arthritis (RA). From October 2008 to December 2011, 53 RA patients and 42 controls were enrolled. The expression of CCP in RA synovial tissues was detected by immunohistochemical assay with 6×His tagged anti-CCP single chain fragment V (ScFv) antibodies generated by pHEN2 phagemid recombinant antibodies display system. PADI4 SNP was genotyped by reverse transcription cDNA sequencing and heterozygote was DNA haplotype was mapped by TA clone sequencing. HLA-DRB1 SE alleles were analyzed by sequence specific primer-polymerase chain reaction (SSP-PCR). The prevalence of synovial CCP expression was significantly different between RA group and the control (76.9% and 11.4% respectively, P < 0.01). The frequencies of 2 SNPs (PADI4_89 G+ and PADI4_104 T+) varied significantly between the groups(P < 0.05). Compared with the major haplotypes, only these two minor alleles were associated with the increased RA susceptibility (OR = 3.67 and 2.53, P < 0.05). SE+ alleles was strongly associated with RA susceptibility (OR = 5.57, P < 0.01). The synovial expression of CCP in RA was strongly associated with SE+ alleles, only 2 minor SNPs (PADI4_89 G+ and PADI4_104T+) and the combination. Serum anti-CCP titers were significantly associated with SE+ alleles, PADI4_104T+, SE+/PADI4_89 G+ and SE+/PADI4_104T+ haplotype. The synovial expression of CCP and the generation of anti-CCP antibodies are strongly associated with SE alleles and/or certain PADI4 gene SNP in RA.