Haplotype Effects Research Articles

BDNF Levels According to Variations in the CACNA1C Gene: Sex-Based Disparity.

The CACNA1C gene encodes the pore-forming alpha-1c subunit of L-type voltage-gated calcium channels. The calcium influx through these channels regulates the transcription of the brain-derived neurotrophic factor (BDNF). Polymorphisms in this gene have been consistently associated with psychiatric disorders, and alterations in BDNF levels are a possible biological mechanism to explain such associations. Here, we sought to investigate the effect of the CACNA1C rs1006737 and rs4765913 polymorphisms and their haplotypes on serum BDNF concentration. We further aim to investigate the regulatory function of these SNPs and the ones linked to them. The study enrolled 641 young adults (362 women and 279 men) in a cross-sectional population-based survey. Linear regression was used to test the effects of polymorphisms and haplotypes on BDNF levels adjusted for potential confounders. Moreover, regulatory putative functional roles were assessed using in silico approach. BDNF levels were not associated with CACNA1C polymorphisms/haplotype in the total sample. When the sample was stratified by sex, checking the effect of polymorphisms on men and women separately, the A-allele of rs4765913 was associated with lower BDNF levels in women compared with the TT genotype (p = 0.010). The AA (rs1006737-rs4765913) haplotype was associated with BDNF levels in opposite directions regarding sex, with lower levels of BDNF in women (p = 0.040) compared to those without this haplotype, while with higher levels in men (p = 0.027). These findings were supported by the presence of regulatory marks only on the male fetal brain. Our results suggest that the BDNF levels regulation may be a potential mechanism underpinning the association between CACNA1C and psychiatric disorders, with a differential role in women and men.

Two novel InDels within the promoter of SIRT1 are associated with growth traits in chickens

ABSTRACT 1. The objectives of the present study were to elucidate the relationship between novel variations of the SIRT1 gene and chicken growth traits. In total, 1,429 chickens, including six breeds and a Gushi ×Anka F2 resource population, were genotyped using PCR-RFLP. 2. Two novel InDels (c.-1552_-1553insCG and c.-450_-451delCG) in the promoter of the chicken SIRT1 gene were identified. An association study showed that c.-1552_-1553insCG was significantly correlated with growth traits and serum lipid indicators. 3. The insertion genotype was most highly associated with body weight at day old, two- and four-week-old chickens, and with shank circumference at four and eight weeks of age. The wild type genotype at this site was most highly associated with serum lipid indicators. 4. In contrast, c.-450_-451delCG was significantly correlated with muscle fibre diameter. The SIRT1 gene expression in chickens with different InDel genotypes was analysed and was significantly higher with heterozygous genotypes at both sites in muscle and fat tissue, relative to expression in chickens with the corresponding homozygous genotypes. 5. The effects of different haplotypes on SIRT1 promoter activity showed that promoter activity depends on haplotype, with haplotype HapII exhibiting the highest activity. 6. It was concluded that the SIRT1 gene is associated with chicken growth traits and that the two InDels influence SIRT1 promoter activity in chickens.

РОЛЬ ПОЛИМОРФНЫХ ЛОКУСОВ ГЕНОВ МОНОАМИНЕРГИЧЕСКИХ СИСТЕМ В ФОРМИРОВАНИИ АГРЕССИВНОСТИ У ЗДОРОВЫХ ИНДИВИДОВ

Aggressive behavior is an integral part of the human psyche. However, environmental risk factors, mental illness and somatic diseases can cause increased aggression, which represents the biological basis of antisocial behavior in a human society. An important role in the development of aggressive behavior belongs to the hereditary factors, that are probably related to abnormal functioning of neurotransmitter systems in the brain. However, the underlying genetic mechanisms remain unclear. The present study aimed to assess the main effects of monoaminergic systems gene polymorphisms (serotonergic - SLC6A4 , HTR2A , HTR1B, dopaminergic - DRD4 , MAOB ) together with haplotypic and gene-environmental effects on individual differences in aggression level in 642 mentally healthy individuals with sex and ethnicity inclusion as covariates. Aggression level was assessed using the Russian version of the Buss-Perry Aggression Questionnaire. The genotyping of the SLC6A4 ( 5-HTTLPR and rs1042173 ), HTR2A ( rs7322347 ), HTR1B ( rs13212041 ), DRD4 ( rs1800955 ), MAOB ( rs6651806 ) gene polymorphisms was conducted via polymerase chain reaction (real time and restriction fragment length polymorphism analysis). Statistical analysis included multiple linear/logistic regression (PLINK v. 1.9). The correction for multiple testing was conducted by the FDR procedure (False Discovery Rate). Statistical analysis revealed the association of SLC6A4 5-HTTLPR S -allele with an increased aggression level in men (pFDR = 0.022) and in Udmurts (pFDR = 0.009). In addition, we revealed that paternal care significantly affected association of SLC6A4 rs1042173 and aggression level (p = 0.001). The study demonstrated environmental, genderand ethnicity-specific role of the SLC6A4 gene in individual differences in aggression level in mentally healthy individuals.

Ancestry‐specific intronic variants on the APOE ɛ4 haplotype influence enhancer activity and interaction with APOE promoter

The risk for late-onset Alzheimer disease (AD) in APOEε4 carriers differs between ancestral groups, where APOEε4's odds ratio for AD risk is lower in African (AFR) homozygous carriers than in non-Hispanic White (NHW) or Japanese (JPT) carriers (odds ratio ∼2-5 vs >15). Local ancestry (LA) analyses in APOEε4 carrier populations have shown the protective effect in AFR relative to EUR/JPT is due to noncoding factors lying in the LA surrounding APOEε4. Thus, regulatory differences between risk and protective LA haplotypes are most likely involved in the differential risk effect seen for APOEε4 on different backgrounds.We identified 56 significant sequence differences between AFR and EUR/JPT APOEε4 haplotypes from the 1000 genomes in the immediate topologically associated domain surrounding APOE. We performed two different Massively Parallel Reporter Assay (MPRA) designs; one assessing small haplotype (∼900bp) effects and one based upon single variant effects. We supplemented these results with single fragment luciferase reporter assays. All assays were performed in at least duplicate in HMC3 (microglia), U118 (astrocytes) and SH-SY5Y (neurons) cell lines. Additionally, we integrated chromatin interaction information from promoter capture C chromatin conformation assays in the same cell types.We identified a region in the first introns of TOMM40 with increased EUR/JPT enhancer activity, supported by both MPRA analyses and APOE promoter interaction in astrocytes and microglia. Two additional regions with differential enhancer activity in neurons, but no promoter interaction, were identified; downstream of APOE and in PVRL2 introns upstream of APOE presenting with higher EUR or higher JPT haplotype variant enhancer activity compared to AFR, respectively.Our results indicate several areas of differential regulation in this LA region on APOEε4 haplotypes dependent on cell type. As APOE is mostly expressed in glial cells, the data in TOMM40 introns points to this region as having the biggest impact on APOE expression in our study and thus highly supports the involvement of this region in the differential risk effects seen for APOEε4. Follow-up of the identified regulatory regions is currently ongoing using in-house iPSC derived cell lines.

Phenotypic and DNA Marker-Assisted Characterization of Russian Potato Cultivars for Resistance to Potato Cyst Nematodes

Potato is one of the most important food crops in the world and also in the Russian Federation. Among harmful organisms reducing potato yield potential, the potato cyst nematodes (PCN) are considered to be ones of the most damaging pests. Information on PCN resistant cultivars is important for potato breeding and production. Russian potato cultivars are characterized in the state-bio-test program for resistance to only one PCN species Globodera rostochiensis and one pathotype Ro1 which is reported to be present in the country. This study aimed to find domestic cultivars with multiple resistances to different PCN species and different pathotypes using phenotyping coupled with molecular marker analysis due to the risk of the occasional introduction of new pests. The phenotypic response was determined by the inoculation of plants with pathotypes Ro5 of G. rostochiensis and Pa3 of G. pallida. The obtained results were supplemented by the state-bio-test data on resistance to Ro1 of G. rostochiensis. Nine of 26 Russian cultivars were resistant both to Ro5 and Ro1 pathotypes and two cultivars possess multiple resistances to both PCN species. Most tested molecular markers associated with the Gpa2, GpaVvrn, GpaVsspl, Grp1 loci showed discrepancies with phenotyping. However, a predictive haplotype and epistatic effect were detected.

Heterozygous NUDT15 Gene Polymorphism Would Not Associate with the Severity of 6-Mercaptopurine Side Effects in Early Intensification Therapy for Childhood Acute Lymphoblastic Leukemia

BackgroundIn the treatment of childhood acute lymphoblastic leukemia (ALL), 6-mercaptopurine (6-MP) is essential for early intensification and maintenance therapy. Recently, it has been reported that a gene polymorphism of nucleoside diphosphate-linked moiety X-type motif 15 (NUDT15) rs116855232 is associated with the 6-MP induced severe myelotoxicity. Since the NUDT15 rs116855232 polymorphism is relatively common in East Asian and Hispanic populations, it is important to evaluate the association between the polymorphism and 6-MP for determining the dose of effective therapy and avoiding the side effect in Japan. However, there are few reports on the association between NUDT15 polymorphisms and the therapeutic efficacy or side effects of 6-MP in the early intensification; most previous reports focused on the maintenance therapy so far. The purpose of this study is to clarify the association between NUDT15 polymorphism and the actual treatment status with 6-MP or its side effects, therefore to contribute to the effective and safe treatment of childhood ALL in Japan.MethodsTwenty-four patients with ALL who received early intensification therapy according to the JPLSG ALL-B12 or JPLSG ALL-T11 protocol at the Department of Pediatrics, Hokkaido University Hospital, between April 2013 and May 2021 were included in the study. We retrospectively collected the clinical and laboratory data from the clinical records. And we also performed the sequence analysis of the exon 1 and 3 in NUDT15 geneResultsGenetic analysis of NUDT15 showed no nucleotide changes other than rs116855232. Twenty patients were CC (wild-type), 4 patients were CT (heterozygous-variant), and 0 patients were TT (homozygous-variant). Of the 4 patients with heterozygous-variant, one patient received a reduced dose of 6-MP because of early onset myelotoxicity during early intensification therapy. In this patient, the total dose of 6-MP was 70% of the standard dose. All the 24 patients showed myelotoxicity and hepatotoxicity during early intensification therapy. Correlations between NUDT15 haplotype and side effects as myelotoxicity and hepatotoxicity were not significant.DiscussionIn the heterozygous-variant of NUDT15 rs116855232, the incidence and degree of myelotoxicity and hepatotoxicity during early intensification therapy did not differ from the wild-type. The international consortium (Clinical Pharmacogenetics Implementation Consortium Guideline, 2018) recommends that the dose of 6-MP should be reduced to 10mg/m2/day in patients with homozygous variant of NUDT15, however, the reduction of the starting dose of 6-MP in those with heterozygous variant is not recommended. Of note, these recommendations were made based on the data in the maintenance therapy. Our study suggests that the reduction of the starting dose may not be necessary in children with heterozygous variant. The NUDT15 rs116855232 polymorphism is common in Japan, with 10% of heterozygotes and 1.1% of homozygotes. In future study, a larger study on the association between NUDT15 polymorphism and treatment outcome including side effects in the early intensification is needed in East Asia to confirm the results of our study. DisclosuresNo relevant conflicts of interest to declare.

Assessment the effect of vitamin D supplementation on plasma vitamin D levels, inflammation, and oxidative stress biomarkers based on vitamin D receptor genetic variation in breast cancer survivors: a protocol for clinical trial

BackgroundBoth human genes and environmental exposures, due to complex interplay, play important role in the cancer etiology. Vitamin D is associated with a reduced risk of incidence and mortality of several human cancers. This study will aim to investigate the possible effects of individual polymorphisms in vitamin D receptor (VDR) as well as effects of VDR haplotypes on response to vitamin D supplementation in breast cancer survivors.MethodsThis is an interventional study in which the effects of vitamin D supplementation on plasma vitamin D levels, inflammatory and antioxidant biomarkers and factors associated with cell proliferation, differentiation, damage, and apoptosis will be investigated stratified by variations in VDR genotype. The present study will be conducted on breast cancer survivors referred to the Shohadaye Tajrish hospital and its associated clinics. One hundred ninety-eight breast cancer survivors will receive 4000 IU of vitamin D3 daily for 12 weeks. VDR Fok1, ApaI, TaqI, BsmI, and Cdx-2 genotype will be determined at the end of the study and responses to vitamin D supplements (inflammatory, antioxidant, cell proliferation, differentiation, damage, and apoptosis biomarkers) will be compared between the three subgroups of each VDR polymorphism as well as different VDR haplotype categories.DiscussionGenetic variation is a fundamental factor influencing individuals’ divergent responses to diet, nutritional status, metabolic response, and diet-related health disorders. Furthermore, studies of gene and environment interactions will provide a precise and accurate assessments of individuals’ dietary requirements by considering both the genetic and environmental aspects simultaneously. The results of the current study, to some extent, will highlight the discrepancies existing in the findings of different studies regarding vitamin D, VDR, and cancer by considering both the genetic and environmental aspects simultaneously. If responses to vitamin D supplementation could be modified by VDR SNPs, determining the distribution of VDR polymorphisms in both breast cancer survivors and healthy populations will provide a new insight into the vitamin D requirements of individuals to prevent cancer and its related mortality based on their genotypes.Trial registration This trial has been registered on Iranian Registry of Clinical Trials (IRCT) under the identification code: IRCT2017091736244N1, registration date: 2017-11-10, http://www.irct.ir/trial/27153

Novel SNPs and haplotypes identified in the CD4 gene and their influence on deregressed MACE EBV indexes of milk-related traits in Simmental breed.

Cluster of differentiation 4 (CD4) is the accessory protein non-covalently bound to the T cell receptor that recognizes an invariant region of MHC class II on antigen presenting cells. Its cytoplasmic tail, physically associated with a protein tyrosine kinase, is important in the activation of helper/inducer T lymphocytes. In Bos taurus, CD4 gene is located on chromosome 5 from which two isoforms are transcribed, with a different number of amino acids due to splicing of exon 7 and variation in the reading frame. The aim of this study was to investigate the sequence of the entire CD4 gene in Simmental sires to evaluate the effects of genomic variants on the indexes of the bulls for milk, fat and protein yields, as well as somatic cell score. The associations among genomic variants and indexes were analysed using the Allele and GLM procedures of SAS 9.4. The analysis indicated that only four of the thirty-one identified SNPs influenced the considered traits. Identified variants insist on coding zones and intronic sequences, where we revealed the presence of sites for transcription factors. To evaluate the existence of haplotypic effects, combinations among the four genomic variants (SNP 3, SNP 8, SNP 11 and SNP 19) were investigated. Six different haplotypic alleles were identified, but only four of them were frequent enough to allow for an evaluation of any haplotypic effect (at least six copies in the examined sample): Hap1, Hap2, Hap3 and Hap6. The analysis of associations between the selected haplotypes in the CD4 gene with milk related indexes showed that bulls with Hap2 (T-A-C-C) had better indexes for milk and protein yields (P < 0.05), whereas the presence of the Hap1 haplotype (A-G-A-T) caused a significant decrease of the index for protein yield (P < 0.05). Frequencies of the two alleles Hap1 and Hap2 (9 and 36% respectively) make them of interest for their possible inclusion in breeding schemes and support the hypothesis of considering this gene as a candidate for the improvement of milk-related traits in the Simmental breed.

Taurine and Indicine Haplotype Representation in Advanced Generation Individuals From Three American Breeds.

Development of the American Breeds of beef cattle began in the 1920s as breeders and U. S. Experiment Station researchers began to create Bos taurus taurus × Bos taurus indicus hybrids using Brahman as the B. t. indicus source. By 1954, U.S. Breed Associations had been formed for Brangus (5/8 Angus × 3/8 Brahman), Beefmaster (½ Brahman × ¼ Shorthorn × ¼ Hereford), and Santa Gertrudis (5/8 Shorthorn × 3/8 Brahman). While these breeds were developed using mating designs expected to create base generation animals with the required genome contributions from progenitor breeds, each association has now registered advanced generation animals in which selection or drift may have caused the realized genome compositions to differ from initial expected proportions. The availability of high-density SNP genotypes for 9,161 Brangus, 3,762 Beefmaster, and 1,942 Santa Gertrudis animals allowed us to compare the realized genomic architectures of breed members to the base generation expectations. We used RFMix to estimate local ancestry and identify genomic regions in which the proportion of Brahman ancestry differed significantly from a priori expectations. For all three breeds, lower than expected levels of Brahman composition were found genome-wide, particularly in early-generation animals where we demonstrate that selection on beef production traits was likely responsible for the taurine enrichment. Using a proxy for generation number, we also contrasted the genomes of early- and advanced-generation animals and found that the indicine composition of the genome has increased with generation number likely due to selection on adaptive traits. Many of the most-highly differentiated genomic regions were breed specific, suggesting that differences in breeding objectives and selection intensities exist between the breeds. Global ancestry estimation is commonly performed in admixed animals to control for stratification in association studies. However, local ancestry estimation provides the opportunity to investigate the evolution of specific chromosomal segments and estimate haplotype effects on trait variation in admixed individuals. Investigating the genomic architecture of the American Breeds not only allows the estimation of indicine and taurine genome proportions genome-wide, but also the locations within the genome where either taurine or indicine alleles confer a selective advantage.

Remote-Sensing-Combined Haplotype Analysis Using Multi-Parental Advanced Generation Inter-Cross Lines Reveals Phenology QTLs for Canopy Height in Rice.

High-throughput phenotyping systems with unmanned aerial vehicles (UAVs) enable observation of crop lines in the field. In this study, we show the ability of time-course monitoring of canopy height (CH) to identify quantitative trait loci (QTLs) and to characterise their pleiotropic effect on various traits. We generated a digital surface model from low-altitude UAV-captured colour digital images and investigated CH data of rice multi-parental advanced generation inter-cross (MAGIC) lines from tillering and heading to maturation. Genome-wide association studies (GWASs) using the CH data and haplotype information of the MAGIC lines revealed 11 QTLs for CH. Each QTL showed haplotype effects on different features of CH such as stage-specificity and constancy. Haplotype analysis revealed relationships at the QTL level between CH and, vegetation fraction and leaf colour [derived from UAV red–green–blue (RGB) data], and CH and yield-related traits. Noticeably, haplotypes with canopy lowering effects at qCH1-4, qCH2, and qCH10-2 increased the ratio of panicle weight to leaf and stem weight, suggesting biomass allocation to grain yield or others through growth regulation of CH. Allele mining using gene information with eight founders of the MAGIC lines revealed the possibility that qCH1-4 contains multiple alleles of semi-dwarf 1 (sd1), the IR-8 allele of which significantly contributed to the “green revolution” in rice. This use of remote-sensing-derived phenotyping data into genetics using the MAGIC lines gives insight into how rice plants grow, develop, and produce grains in phenology and provides information on effective haplotypes for breeding with ideal plant architecture and grain yield.

Effect of genetic polymorphisms and haplotypes on the efficacy and safety of postoperative analgesia with ketoprofen in patients with coronary artery disease after cardiac surgery

Abstract Background Most cardiac surgeries are associated with post-sternotomy pain syndrome. Pain causes elevation of blood pressure, heart rate and may be associated with hemodynamic instability, respiratory infections, and other postoperative complications. Non-steroidal anti-inflammatory drugs (NSAIDs) are among the most commonly used analgesics in cardiac surgery. The majority of NSAIDs are metabolized by cytochrome P-450. The mechanism of action of NSAIDs is associated with blocking of prostaglandin-endoperoxide synthase (PTGS). Individual variabilities and gene polymorphisms may affect ketoprofen exposure, efficacy and safety. Purpose Evaluation of the influence of CYP2C9 - CYP2D6 and PTGS-2 rs20417 – PTGS-1 rs12353214 haplotypes on the efficacy and safety of postoperative analgesia with ketoprofen in patients with coronary artery disease after cardiac surgery. Methods The study included 90 patients. Pain intensity assessment was measured by the Numeric Rating Scale (NRS). Dyspeptic symptoms were evaluated using the Gastrointestinal Symptom Rating Scale (GSRS). Acute kidney injury was determined by Kidney Disease Improving Global Outcomes criteria. Genotyping of polymorphisms CYP2C9*3 (1075A&amp;gt;C) rs1057910, CYP2D6*4 (1846G&amp;gt;A) rs3892097, PTGS-2 (G&amp;gt;C) rs20417, PTGS-1 (C&amp;gt;T) rs12353214 was performed. Results The study revealed the following haplotypes: (1) CYP2C9*3 rs1057910 (AA) – CYP2D6*4 rs3892097 (GG), (2) CYP2C9*3 rs1057910 (AC) – CYP2D6*4 rs3892097 (GA), (3) PTGS-2 rs20417 (GG) – PTGS-1 rs12353214 (CT), (4) PTGS-2 rs20417 (CC) – PTGS-1 rs12353214 (CC). Pain intensity by the NRS score was significantly higher in patients with AA-GG haplotype compared to AC-GA haplotype for CYP2C9*3 - CYP2D6*4: 7,13±2,14 and 5±1,52 (p=0,009); 7,06±1,99 and 4,86±1,57 (p=0,007); 4,96±1,83 and 3,29±1,79 (p=0,04); 4,57±1,66 and 2,86±1,57 (p=0,02), on days 1, 2, 3 and 5 in the postoperative period, respectively. There were no significant differences in pain intensity by the NRS in patients with PTGS-2 rs20417 – PTGS-1 rs12353214 haplotypes. Also there were no significant differences in GSRS score and acute kidney injury frequency in patients with AA-GG and AC-GA haplotypes for CYP2C9*3 – CYP2D6*4 and GG-CT and CC-CC haplotypes for PTGS-2 rs20417 – PTGS-1 rs12353214. Conclusion CYP2C9*3 - CYP2D6*4 haplotypes affect efficacy of postoperative analgesia with ketoprofen in patients with coronary artery disease after cardiac surgery. Further studies are needed to develop genotype-guided postoperative pain management. Funding Acknowledgement Type of funding sources: Public grant(s) – National budget only. Main funding source(s): This study was financially supported by RF President's grant for scientific schools, project No. NSh 2698.2020.7 Pain intensity by NRSDyspepsia symptoms by GSRS

Analysis of association between MALAT1 haplotype and the severity of normal-tension glaucoma (NTG).

MALAT1, which is disorderly expressed in the growth, invasion, migration and cancer cell apoptosis, was shown to be associated with normal‐tension glaucoma (NTG), a type of optic neuropathy. The haplotype in MALAT1 affects its expression and is correlated with human diseases like normal‐tension glaucoma (NTG). However, the underlying detailed mechanism remains unclear. In this study, we aimed to analyse the association between MALAT1 haplotype and the severity of NTG in a molecular level. Quantitative real‐time PCR, ELISA and luciferase assays were performed to establish the underlying signalling pathways. RNFL thickness, RA and C/D ratio were calculated for NTG patients. Accordingly, GGGT haplotype was demonstrated to be associated with a decreased risk of NTG. The MALAT1 level in serum of NTG patients carrying GGGT haplotype was significantly decreased compared with NTG patients carrying other haplotypes, along with elevated miR‐1 expression and diminished IL‐6 expression. NTG patients carrying GGGT haplotype had thicker RNFL and RA, but a smaller C/D ratio. Sequence analysis found potential target sites of miR‐1 on MALAT1 and IL‐6, and luciferase assay confirmed the inhibitory effect of miR‐1 on MALAT1 and IL‐6 expression. Meanwhile, MALAT1 also down‐regulated miR‐1 expression and consequently up‐regulated IL‐6 expression. This study presented evidence for a regulatory network containing MALAT1, miR‐1 and IL‐6, and further demonstrated the effect of MALAT1 haplotype on the risk and severity of NTG.

The Effect of Renalase rs2576178 and rs10887800 Polymorphisms on Ischemic Stroke Susceptibility in Young Patients (

Background Ischemic stroke (IS) is the most common form of cerebrovascular accident which its precise etiology remains mysterious. Renalase is a catecholamine-degrading enzyme playing a major role in blood pressure control. Recent studies show the effect of renalase activity on various diseases like IS. In the current study, we examined the possible effects of renalase gene (RNLS) rs2576178 and rs10887800 variants at the 5′-flanking and intron 6 regions on IS, respectively. Methods One hundred and fifty-four IS patients younger than 50 years and 165 age- and sex-matched controls were recruited in the study. For genotyping of rs2576178 and rs10887800 variants, the PCR-RFLP method was used. Results The RNLS rs10887800 AG genotype was more repeated in IS patients, but the difference was marginally nonsignificant (P = 0.054). This variant was associated with IS in the overdominant model, and the AG genotype is associated with a1.6-fold increased risk of IS compared to AA+ GG genotypes (OR = 1.6, 95% CI: 1-2.5, P = 0.033). No relationship was observed between RNLS rs2576178 polymorphism and IS in all genetic models. The findings of the haplotype and combination effects of rs10887800 and rs2576178 variants on IS showed no significant association. The in silico analysis showed no effect of rs2576178 and rs10887800 polymorphisms in the RNA structure, but the alteration of RNA sequence in rs2576178 results in the lack of a MBNL1 protein binding site. ConclusionsRNLS rs10887800 but not rs2576178 polymorphism was associated with IS susceptibility in the overdominant model (AG vs AA+ GG genotypes).

Novel insight into linkage disequilibrium and additive effect of GBP1 and GBP5 SNP haplotypes associated with porcine reproductive and respiratory syndrome virus susceptibility in Korean native pigs.

Novel insight into linkage disequilibrium and additive effect of GBP1 and GBP5 SNP haplotypes associated with porcine reproductive and respiratory syndrome virus susceptibility in Korean native pigs.

A Functional Variant of CXCL16 Is Associated With Predisposition to Sepsis and MODS in Trauma Patients: Genetic Association Studies.

PurposeCXC chemokines are mediators which mediate immune cells migration to sites of inflammation and injury. Chemokine C-X-C motif ligand 16 (CXCL16) plays an important role in the occurrence and development of sepsis through leukocyte chemotaxis, leukocyte adhesion and endotoxin clearance. In this study, we selected a set of tagging single nucleotide polymorphisms (tag SNPs) in the CXCL16 gene and investigated their clinical relevance to the development of sepsis and multiple organ dysfunction syndrome (MODS) in patients with major trauma in three independent Chinese Han populations.MethodsA total of 1,620 major trauma patients were enrolled in this study. Among these patients, 920 came from Chongqing in western China, 350 came from Zhejiang Province in eastern China, and 350 came from Guizhou Province in southwestern China. The improved multiplex ligation detection reaction (iMLDR) method was employed in the genotyping and genetic association analyses to determine the associations between CXCL16 haplotypes and sepsis morbidity rate and higher MOD scores in three cohorts.ResultsOnly CXCL16 T123V181 haplotype was associated with an increased risk for sepsis morbidity and higher MOD scores in the three cohorts (OR = 1.89, P = 0.001 for the Chongqing cohort; OR = 1.76, P = 0.004 for the Zhejiang cohort; OR = 1.55, P = 0.012 for the Guizhou cohort). The effect of T123V181 haplotype on the chemotaxis, migration and endotoxin clearance of immune cells were further observed. Protein modeling analysis showed that T123 and V181 might alter the structure of the CXCL16 active center. Thus it enhanced the chemotaxis and adhesion ability of immunocytes.ConclusionWe demonstrate the mechanism of CXCL16 T123V181 haplotype which regulates the sepsis morbidity rate and thus provide a new biomarker for early diagnosis of sepsis and MODS.Clinical Trial Registrationwww.ClinicalTrials.gov, identifier NCT01713205 (https://www.clinicaltrials.gov/ct2/results?cond=&term=+NCT01713205&cntry=&state=&city=&dist=).

Three-way interaction effects of early life stress, positive parenting and FKBP5 in the development of depressive symptoms in a general population

FKBP5 gene–environment interaction (cG × E) studies have shown diverse results, some indicating significant interaction effects between the gene and environmental stressors on depression, while others lack such results. Moreover, FKBP5 has a potential role in the diathesis stress and differential susceptibility theorem. The aim of the present study was to evaluate whether a cG × E interaction effect of FKBP5 single-nucleotide polymorphisms (SNPs) or haplotype and early life stress (ELS) on depressive symptoms among young adults was moderated by a positive parenting style (PASCQpos), through the frameworks of the diathesis stress and differential susceptibility theorem. Data were obtained from the Survey of Adolescent Life in Västmanland Cohort Study, including 1006 participants and their guardians. Data were collected during 2012, when the participants were 13 and 15 years old (Wave I: DNA), 2015, when participants were 16 and 18 years old (Wave II: PASCQpos, depressive symptomology and ELS) and 2018, when participants were 19 and 21 years old (Wave III: depressive symptomology). Significant three-way interactions were found for the FKBP5 SNPs rs1360780, rs4713916, rs7748266 and rs9394309, moderated by ELS and PASCQpos, on depressive symptoms among young adults. Diathesis stress patterns of interaction were observed for the FKBP5 SNPs rs1360780, rs4713916 and rs9394309, and differential susceptibility patterns of interaction were observed for the FKBP5 SNP rs7748266. Findings emphasize the possible role of FKBP5 in the development of depressive symptoms among young adults and contribute to the understanding of possible differential susceptibility effects of FKBP5.

Gene Polymorphisms of the Renin-Angiotensin System and Bleeding Complications of Warfarin: Genetic-Based Machine Learning Models.

This study aimed to investigate the effects of genetic variants and haplotypes in the renin–angiotensin system (RAS) on the risk of warfarin-induced bleeding complications at therapeutic international normalized ratios (INRs). Four single nucleotide polymorphisms (SNPs) of AGT, two SNPs of REN, three SNPs of ACE, four SNPs of AGTR1, and one SNP of AGTR2, in addition to VKORC1 and CYP2C9 variants, were investigated. We utilized logistic regression and several machine learning methods for bleeding prediction. The study included 142 patients, among whom 21 experienced bleeding complications. We identified a haplotype, H2 (TCG), carrying three single nucleotide polymorphisms (SNPs) of ACE (rs1800764, rs4341, and rs4353), which showed a significant relation with bleeding complications. After adjusting covariates, patients with H2/H2 experienced a 0.12-fold (95% CI 0.02–0.99) higher risk of bleeding complications than the others. In addition, G allele carriers of AGT rs5050 and A allele carriers of AGTR1 rs2640543 had 5.0- (95% CI 1.8–14.1) and 3.2-fold (95% CI 1.1–8.9) increased risk of bleeding complications compared with the TT genotype and GG genotype carriers, respectively. The AUROC values (mean, 95% CI) across 10 random iterations using five-fold cross-validated multivariate logistic regression, elastic net, random forest, support vector machine (SVM)–linear kernel, and SVM–radial kernel models were 0.732 (0.694–0.771), 0.741 (0.612–0.870), 0.723 (0.589–0.857), 0.673 (0.517–0.828), and 0.680 (0.528–0.832), respectively. The highest quartile group (≥75th percentile) of weighted risk score had approximately 12.0 times (95% CI 3.1–46.7) increased risk of bleeding, compared to the 25–75th percentile group, respectively. This study demonstrated that RAS-related polymorphisms, including the H2 haplotype of the ACE gene, could affect bleeding complications during warfarin treatment for patients with mechanical heart valves. Our results could be used to develop individually tailored intervention strategies to prevent warfarin-induced bleeding.

Exploring the missing heritability in subjects with hearing loss, enlarged vestibular aqueducts, and a single or no pathogenic SLC26A4 variant

Pathogenic variants in SLC26A4 have been associated with autosomal recessive hearing loss (arHL) and a unilateral or bilateral enlarged vestibular aqueduct (EVA). SLC26A4 is the second most frequently mutated gene in arHL. Despite the strong genotype–phenotype correlation, a significant part of cases remains genetically unresolved. In this study, we investigated a cohort of 28 Dutch index cases diagnosed with HL in combination with an EVA but without (M0) or with a single (M1) pathogenic variant in SLC26A4. To explore the missing heritability, we first determined the presence of the previously described EVA-associated haplotype (Caucasian EVA (CEVA)), characterized by 12 single nucleotide variants located upstream of SLC26A4. We found this haplotype and a delimited V1-CEVA haplotype to be significantly enriched in our M1 patient cohort (10/16 cases). The CEVA haplotype was also present in two M0 cases (2/12). Short- and long-read whole genome sequencing and optical genome mapping could not prioritize any of the variants present within the CEVA haplotype as the likely pathogenic defect. Short-read whole-genome sequencing of the six M1 cases without this haplotype and the two M0/CEVA cases only revealed previously overlooked or misinterpreted splice-altering SLC26A4 variants in two cases, who are now genetically explained. No deep-intronic or structural variants were identified in any of the M1 subjects. With this study, we have provided important insights that will pave the way for elucidating the missing heritability in M0 and M1 SLC26A4 cases. For pinpointing the pathogenic effect of the CEVA haplotype, additional analyses are required addressing defect(s) at the RNA, protein, or epigenetic level.

Association Analysis Revealed That TaPYL4 Genes Are Linked to Plant Growth Related Traits in Multiple Environment

Abscisic acid (ABA), one of phytohormones, plays an important regulatory role in plant growth and development. ABA receptor PYL4 (pyrabactin resistance 1-like 4) was previously detected to be involved in plant response to a variety of stresses. TaPYL4 overexpression could enhance wheat (Triticum aestivum) drought resistance. In order to further investigate TaPYL4’s role in regulating development of other major agronomic traits in wheat, genes of TaPYL4-2A, TaPYL4-2B, and TaPYL4-2D were cloned from wheat, respectively. Polymorphism analysis on TaPYL4 sequences revealed that encoding regions of the three genes were highly conserved, without any SNP (single nucleotide polymorphism) presence. However, nine SNPs and four SNPs were identified in the promoter regions of TaPYL4-2A and TaPYL4-2B, respectively. Functional molecular markers were developed based on these polymorphisms, which were then used to scan a natural population of 323 common wheat accessions for correlation analysis between genotype and the target phenotypic traits. Both TaPYL4-2A and TaPYL4-2B markers were significantly correlated with plant growth-related traits under multiple environments (well-watered, drought and heat stress treatments). The additive effects of TaPYL4-2A and TaPYL4-2B were verified by the combinational haplotype (Hap-AB1∼Hap-AB4) effects determined from field data. Cis-acting elements were analyzed in the promoters of TaPYL4-2A and TaPYL4-2B, showing that a TGA-element bound by ARFs (auxin response factors) existed only in Hap-2A-1 of TaPYL4-2A. Gene expression assays indicated that TaPYL4-2A was constitutively expressed in various tissues, with higher expression in Hap-2A-1 genotypes than in Hap-2A-2 materials. Notably, TaARF4 could act as TaPYL4-2A transcription activator in Hap-2A-1 materials, but not in Hap-2A-2 genotypes. Analysis of geographic distribution and temporal frequency of haplotypes indicated that Hap-AB1 was positively selected in wheat breeding in China. Therefore, TaPYL4-2A and TaPYL4-2B could be a valuable target gene in wheat genetic improvement to develop the ideal plant architecture.

QTL mapping in outbred tetraploid (and diploid) diallel populations.

Over the last decade, multiparental populations have become a mainstay of genetics research in diploid species. Our goal was to extend this paradigm to autotetraploids by developing software for quantitative trait locus (QTL) mapping in connected F1 populations derived from a set of shared parents. For QTL discovery, phenotypes are regressed on the dosage of parental haplotypes to estimate additive effects. Statistical properties of the model were explored by simulating half-diallel diploid and tetraploid populations with different population sizes and numbers of parents. Across scenarios, the number of progeny per parental haplotype (pph) largely determined the statistical power for QTL detection and accuracy of the estimated haplotype effects. Multiallelic QTL with heritability 0.2 were detected with 90% probability at 25 pph and genome-wide significance level 0.05, and the additive haplotype effects were estimated with over 90% accuracy. Following QTL discovery, the software enables a comparison of models with multiple QTL and nonadditive effects. To illustrate, we analyzed potato tuber shape in a half-diallel population with three tetraploid parents. A well-known QTL on chromosome 10 was detected, for which the inclusion of digenic dominance lowered the Deviance Information Criterion (DIC) by 17 points compared to the additive model. The final model also contained a minor QTL on chromosome 1, but higher-order dominance and epistatic effects were excluded based on the DIC. In terms of practical impacts, the software is already being used to select offspring based on the effect and dosage of particular haplotypes in breeding programs.