Allele Frequencies Research Articles

Dear Malaria: Deer Have Malaria! Prevalence ofPlasmodium odocoilei Infection in White-tailed deer in Pennsylvania

Abstract Background To combat antimalarial treatment resistance, better understanding of malaria pathogenesis is needed, but existing animal model have various limitations. Notably, prevailing murine models require laboratory infection of non-natural host species. In 2016, the parasite Plasmodium odocoilei was identified in white-tailed deer (Odocoileus virginianus). This was the first non-human mammalian malaria parasite identified in North America, representing a novel naturally occurring model system that allows for integrated examination of host, vector, and systems parasite biology. In addition, sickle hemoglobinopathy is exceptionally common among white-tailed deer, occurring in up to 60% of apparently healthy animals. In humans, the prevalence of sickle hemoglobinopathy in individuals with ancestry from malaria-endemic regions is due to the protective effects of sickle trait against severe malaria. Thus, the white-tailed deer-P. odocoilei system represents the only known naturally occurring model of the association between malaria parasite biology and sickle cell disease. Pennsylvania white-tailed deer have not previously been surveyed for infection. In this study, we determined P. odocoilei prevalence in a sample of 170 Pennsylvania white-tailed deer. Methods We amplified the CytB gene of P. odocoilei by nested PCR from DNA extracted from homogenized white-tailed deer tongue tissue obtained from the PennVet Wildlife Futures Program. We confirmed samples screening positive on gel electrophoresis via unprimed sequencing (Plasmidsaurus, USA) and NCBI-BLAST analysis. Results We estimate the prevalence of P. odocoilei infection in Pennsylvania white-tailed deer to be 0.6% (1 of 170 samples). Sequencing of the positive sample revealed a 621-bp sequence with close sequence identity to previous North American isolates of P. odocoilei (query cover 91-100%, percent identity 99.34-100.00%). Biobank metadata showed the positive sample originated from a roadkilled yearling male picked up at GPS coordinates (40.8423, -79.0409) on August 15, 2022. Conclusion P. odocoilei is endemic to Pennsylvania white-tailed deer. Our future directions include screening of additional samples, determination of host hemoglobin allele frequencies, detailed parasite genetic studies, and entomologic studies to elucidate vector biology. In addition, granular sample metadata collected by the PennVet Wildlife Futures Program will allow us to analyze the effects of geographic, demographic, and temporal variables on epidemiology. In sum, our survey data empowers future Pennsylvania-based studies to take advantage of the only known naturally occurring animal model of sickling and its association with protozoan infection.

DdPCR Overcomes the CRISPR-Cas13a-Based Technique for the Detection of the BRAF p.V600E Mutation in Liquid Biopsies.

The isolation of circulating tumoral DNA (ctDNA) present in the bloodstream brings about the opportunity to detect genomic aberrations from the tumor of origin. However, the low amounts of ctDNA present in liquid biopsy samples makes the development of highly sensitive techniques necessary to detect targetable mutations for the diagnosis, prognosis, and monitoring of cancer patients. Here, we employ standard genomic DNA (gDNA) and eight liquid biopsy samples from different cancer patients to examine the newly described CRISPR-Cas13a-based technology in the detection of the BRAF p.V600E actionable point mutation and appraise its diagnostic capacity with two PCR-based techniques: quantitative Real-Time PCR (qPCR) and droplet digital PCR (ddPCR). Regardless of its lower specificity compared to the qPCR and ddPCR techniques, the CRISPR-Cas13a-guided complex was able to detect inputs as low as 10 pM. Even though the PCR-based techniques have similar target limits of detection (LoDs), only the ddPCR achieved a 0.1% variant allele frequency (VAF) detection with elevated reproducibility, thus standing out as the most powerful and suitable tool for clinical diagnosis purposes. Our results also demonstrate how the CRISPR-Cas13a can detect low amounts of the target of interest, but its base-pair specificity failed in the detection of actionable point mutations at a low VAF; therefore, the ddPCR is still the most powerful and suitable technique for these purposes.

Application of a new highly multiplexed amplicon sequencing tool to evaluate Plasmodium falciparum antimalarial resistance and relatedness in individual and pooled samples from Dschang, Cameroon.

Resistance to antimalarial drugs remains a major obstacle to malaria elimination. Multiplexed, targeted amplicon sequencing is being adopted for surveilling resistance and dissecting the genetics of complex malaria infections. Moreover, genotyping of parasites and detection of molecular markers drug resistance in resource-limited regions requires open-source protocols for processing samples, using accessible reagents, and rapid methods for processing numerous samples including pooled sequencing. P lasmodium falciparum S treamlined M ultiplex A ntimalarial R esistance and R elatedness T esting ( Pf -SMARRT) is a PCR-based amplicon panel consisting of 15 amplicons targeting antimalarial resistance mutations and 9 amplicons targeting hypervariable regions. This assay uses oligonucleotide primers in two pools and a non-proprietary library and barcoding approach. We evaluated Pf -SMARRT using control mocked dried blood spots (DBS) at varying levels of parasitemia and a mixture of 3D7 and Dd2 strains at known frequencies, showing the ability to genotype at low parasite density and recall within-sample allele frequencies. We then piloted Pf -SMARRT to genotype 100 parasite isolates collected from uncomplicated malaria cases at three health facilities in Dschang, Western Cameroon. Antimalarial resistance genotyping showed high levels of sulfadoxine-pyrimethamine resistance mutations, including 31% prevalence of the DHPS A613S mutation. No K13 candidate or validated artemisinin partial resistance mutations were detected, but one low-level non-synonymous change was observed. Pf -SMARRT's hypervariable targets, used to assess complexity of infections and parasite diversity and relatedness, showed similar levels and patterns compared to molecular inversion probe (MIP) sequencing. While there was strong concordance of antimalarial resistance mutations between individual samples and pools, low-frequency variants in the pooled samples were often missed. Overall, Pf -SMARRT is a robust tool for assessing parasite relatedness and antimalarial drug resistance markers from both individual and pooled samples. Control samples support that accurate genotyping as low as 1 parasite per microliter is routinely possible. Malaria remains a critical global public health problem. Antimalarial drug resistance has repeatedly undermined control and the emergence of artemisinin partial resistance in Africa is the latest major challenge. Malaria molecular surveillance (MMS) has emerged as a powerful tool to monitor molecular markers of resistance and changes in the parasite population. Streamlined methods are needed that can be readily adopted in endemic countries. We developed P lasmodium falciparum S treamlined M ultiplex A ntimalarial R esistance and R elatedness T esting ( Pf -SMARRT), a multiplex amplicon deep sequencing approach that uses easily accessible products without proprietary steps and can be sequenced on any Illumina sequencer. We validated this tool using controls, including mocked dried blood spots, and then implemented it to evaluate resistance and parasite relatedness among 100 samples from Cameroon. The assay was able to reliably assess the within-sample allele frequency of antimalarial resistance markers and discriminate strains within and between individuals. We also evaluated a more cost-effective surveillance approach for antimalarial resistance polymorphisms using pooled samples. While within-pool frequencies of mutations were accurate in pools with higher numbers of samples, this resulted in the loss of the ability to detect variants uncommon in the pool. Overall Pf- SMARRT provides a new protocol for conducting MMS that is easily implementable in Africa.

A Dominance Hypothesis Argument for Historical Genetic Gains and the Fixation of Heterosis in Octoploid Strawberry.

Heterosis was the catalyst for the domestication of cultivated strawberry (Fragaria × ananassa), an interspecific hybrid species that originated in the 1700s. The hybrid origin was discovered because the phenotypes of spontaneous hybrids transgressed those of their parent species. The transgressions included fruit yield increases and other genetic gains in the twentieth century that sparked the global expansion of strawberry production. The importance of heterosis to the agricultural success of the hybrid species, however, has remained a mystery. Here we show that heterosis has disappeared (become fixed) among improved hybrids within a population (the California population) that has been under long-term selection for increased fruit yield, weight, and firmness. We found that the highest yielding hybrids are among the most highly inbred (59-79%), which seems counterintuitive for a highly heterozygous, outbreeder carrying heavy genetic loads. Although faint remnants of heterosis were discovered, the between-parent allele frequency differences and dispersed favorable dominant alleles necessary for heterosis have decreased nearly genome-wide within the California population. Conversely, heterosis was prevalent and significant among wide hybrids, especially for fruit count, a significant driver of genetic gains for fruit yield. We attributed the disappearance (fixation) of heterosis within the California population to increased homozygosity of favorable dominant alleles and inbreeding associated with selection, random genetic drift, and selective sweeps. Despite historical inbreeding, the highest yielding hybrids reported to-date are estimated to be heterozygous for 20,370-44,280 of 97,000-108,000 genes in the octoploid genome, the equivalent of an entire diploid genome or more.

Detection of KIT Mutations in Systemic Mastocytosis: How, When, and Why.

More than 90% of patients affected by mastocytosis are characterized by a somatic point mutation of KIT, which induces ligand-independent activation of the receptor and downstream signal triggering, ultimately leading to mast cell accumulation and survival. The most frequent mutation is KIT p.D816V, but other rarer mutations can also be found. These mutations often have a very low variant allele frequency (VAF), well below the sensitivity of common next-generation sequencing (NGS) methods used in routine diagnostic panels. Highly sensitive methods are developing for detecting mutations. This review summarizes the current indications on the recommended methods and on how to manage and interpret molecular data for the diagnosis and follow-up of patients with mastocytosis.

Genetic aspects of lactase deficiency in indigenous populations of Siberia.

The ability to metabolize lactose in adulthood is associated with the persistence of lactase enzyme activity. In European populations, lactase persistence is determined mainly by the presence of the rs4988235-T variant in the MCM6 gene, which increases the expression of the LCT gene, encoding lactase. The highest rates of lactase persistence are characteristic of Europeans, and the lowest rates are found in East Asian populations. Analysis of published data on the distribution of the hypolactasia-associated variant rs4988235-C in the populations of Central Asia and Siberia showed that the frequency of this variant increases in the northeastern direction. The frequency of this allele is 87 % in Central Asia, 90.6 % in Southern Siberia, and 92.9 % in Northeastern Siberia. Consequently, the ability of the population to metabolize lactose decreases in the same geographical direction. The analysis of paleogenomic data has shown that the higher frequency of the rs4988235-T allele in populations of Central Asia and Southern Siberia is associated with the eastward spread of ancient populations of the Eastern European steppes, starting from the Bronze Age. The results of polymorphism analysis of exons and adjacent introns of the MCM6 and LCT genes in indigenous populations of Siberia indicate the possibility that polymorphic variants may potentially be related to lactose metabolism exist in East Asian populations. In East Asian populations, including Siberian ethnic groups, a ~26.5 thousand nucleotide pairs long region of the MCM6 gene, including a combination of the rs4988285-A, rs2070069-G, rs3087353-T, and rs2070068-A alleles, was found. The rs4988285 and rs2070069 loci are located in the enhancer region that regulates the activity of the LCT gene. Analysis of paleogenomic sequences showed that the genomes of Denisovans and Neanderthals are characterized by the above combination of alleles of the MCM6 gene. Thus, the haplotype discovered appears to be archaic. It could have been inherited from a common ancestor of modern humans, Neanderthals, and Denisovans, or it could have been acquired by hybridization with Denisovans or Neanderthals. The data obtained indicate a possible functional significance of archaic variants of the MCM6 gene.

Genotype distribution and allele frequency of thioester-containing protein 1(Tep1) and its effect on development of Plasmodium oocyst in populations of Anopheles arabiensis in Ethiopia.

Thioester-containing protein 1 (TEP1) is a crucial component of mosquitoes' natural resistance to parasites. To effectively combat malaria, there is a need to better understand how TEP1 polymorphism affects phenotypic traits during infections. Therefore, the purpose of this study was to determine the Tep1 genotype frequency in malaria vector populations from south-western Ethiopia and investigate its effect on Plasmodium oocyst development in Anopheles arabiensis populations. Using standard dippers, Anopheles mosquito larvae were collected from aquatic habitats in Asendabo, Arjo Dedessa, and Gambella in 2019 and 2020. Collected larvae were reared to adults and identified morphologically. Female An. gambiae s.l. were allowed to feed on infected blood containing the same number of gametocytes obtained from P. falciparum and P. vivax gametocyte-positive individuals using indirect membrane feeding methods. Polymerase Chain Reaction (PCR) was used to identify An. gambiae s.l. sibling species. Three hundred thirty An. gambiae s.l. were genotyped using Restricted Fragment Length Polymorphism (RFLP) PCR and sub samples were sequenced to validate the TEP1 genotyping. Among the 330 samples genotyped, two TEP1 alleles, TEP1*S1 (82% frequency) and TEP1*R1 (18% frequency), were identified. Three equivalent genotypes, TEP1*S1/S1, TEP1*R1/R1, and TEP1*S1/R1, had mean frequencies of 65.15%, 2.12%, and 32.73%, respectively. The nucleotide diversity was ranging from 0.36554 to 0. 46751 while haplotype diversity ranged from 0.48871 to 0.63161, across all loci. All sample sites had positive Tajima's D and Fu's Fs values. There was a significant difference in the TEP1 allele frequency and genotype frequency among mosquito populations (p < 0.05), except populations of Anopheles arabiensis from Asendabo and Gambella (p > 0.05). In addition, mosquitoes with the TEP1 *RR genotype were susceptible and produced fewer Plasmodium oocysts than mosquitoes with the TEP1 *SR and TEP1 *SS genotypes. The alleles identified in populations of An. arabiensis were TEP1*R1 and TEP1*S1. There was no significant variation in TEP1*R1 allele frequency between the high and low transmission areas. Furthermore, An. arabiensis carrying the TEP1*R1 allele was susceptible to Plasmodium infection. Further studies on vector-parasite interactions, particularly on the TEP1 gene, are required for vector control techniques.

The Human 8-oxoG DNA Glycosylase 1 (OGG1) Ser326Cys Polymorphism in Infertile Men.

8-hydroxy-2'-deoxyguanosine (8-OHdG) is a form of oxidative DNA damage caused by oxidative stress (OS), which is considered a major factor in male infertility. The cellular defense system against 8-OHdG involves base excision repair (BER) with the enzyme 8-Oxoguanine DNA glycosylase 1 (OGG1). However, studies on the single-nucleotide polymorphism (SNP) OGG1 Ser326Cys have demonstrated that the Cys326Cys genotype could be the cause of an increment in oxidative DNA damage. In this study, the OGG1 Ser326Cys polymorphism and its effect on DNA oxidation were evaluated in 118 infertile men. Polymorphic screening was performed using TaqMan allelic discrimination assays, and oxidative DNA damage was evaluated through the quantification of 8-OHdG and total antioxidant capacity (TAC); in addition, electrical bioimpedance spectroscopy (EBiS) measurements were used as a reference for different electrical properties associated with 8-OHdG concentrations. The detected Cys (G) allele frequency (0.4) was higher compared to the allele frequency reported in the "Allele Frequency Aggregator" (ALFA) and "Haplotype Map" (HapMap) projects for American populations (0.21-0.29), suggesting that the Cys (G) allele carrier could be a factor associated with American infertile populations. The values of 8-OHdG were twofold higher in carriers of the Cys326Cys (GG) genotype than the other genotypes and, in concordance, the TAC levels were threefold lower in Cys326Cys (GG) genotype carriers compared to the other genotypes. Moreover, the EBiS magnitude exhibited potential for the detection of different oxidative damage in DNA samples between genotypes. The Cys326Cys (GG) genotype is associated with oxidative DNA damage that could contribute to male infertility.

Host-dependent C-to-U RNA editing in SARS-CoV-2 creates novel viral genes with optimized expressibility.

Rampant C-to-U RNA editing drives the mutation and evolution of SARS-CoV-2. While much attention has been paid to missense mutations, the C-to-U events leading to AUG and thus creating novel ORFs were uninvestigated. By utilizing the public time-course mutation data from the worldwide SARS-CoV-2 population, we systematically identified the "AUG-gain mutations" caused by C-to-U RNA editing. Synonymous mutations were of special focus. A total of 58 synonymous C-to-U sites are able to create out-of-frame AUG in coding sequence (CDS). These 58 synonymous sites showed significantly higher allele frequency (AF) and increasing rate (dAF/dt) than other C-to-U synonymous sites in the SARS-CoV-2 population, suggesting that these 58 AUG-gain events conferred additional benefits to the virus and are subjected to positive selection. The 58 predicted new ORFs created by AUG-gain events showed the following advantages compared to random expectation: they have longer lengths, higher codon adaptation index (CAI), higher Kozak scores, and higher tRNA adaptation index (tAI). The 58 putatively novel ORFs have high expressibility and are very likely to be functional, providing an explanation for the positive selection on the 58 AUG-gain mutations. Our study proposed a possible mechanism of the emergence of de novo genes in SARS-CoV-2. This idea should be helpful in studying the mutation and evolution of SARS-CoV-2.

Evaluation relationship between VDR gene and clinical and inflammatory factors in patients with RRMS.

Adipocyte levels including leptin and FABS-4 levels, adiponectin, obesity, and vitamin D can be related to the occurrence and exacerbation of MS disease. This research aimed at determining the relationship between VDR gene changes and clinical and inflammatory factors in patients with relapsing-remitting multiple sclerosis (RRMS). This case/control study was conducted based on the ethical principles of Helsinki. RRMS disease was confirmed based on history, clinical signs, radiological signs, and neurologist's diagnosis. The research population consisted of healthy people and patients with RRMS referring to Hazrat Rasool Akram Hospital between 2021 and 2023 who met the criteria for entering the research. FokI polymorphism is associated with a substantial increase in risk, with an odds ratio of 7.28, for those with the FF genotype who have RRMS compared to healthy individuals (OR=7.28: 95% CI; 1.86, 28.41). The presence of FokI polymorphism significantly raises the likelihood of developing RRMS in persons with the FF genotype compared to healthy individuals, with an odds ratio of 28.7. RRMS patients with genotypes did not exhibit a significant increase in risk compared to controls for FokI, ApaI, TaqI, and BsmI polymorphisms. None of the studied polymorphisms revealed a significant risk in obese patients with different genotypes compared to the obese people. Further research, including more cases, is needed to avoid results that could be inflated by small samples or low frequencies of minor alleles.

Polymorphic variants of the dopamine receptor gene DRD2 (rs6277, rs1800497) in adolescents with problematic video game use

Problematic video games use, as a specific form of problematic Internet use, is widespread among adolescents and can have negative effects on their mental and somatic well-being. An increasing incidence of addictive video gaming, as well as the overuse of the Internet, among the young population makes the current study of susceptibility factors, including the genetic component, relevant. There has been a number of investigations related to the involvement of gene variants of the neurotransmitter system in the development of Internet addiction, with the results being different for various ethnic groups. The dopamine type 2 receptor gene (DRD2) is one of the candidate genes for susceptibility to video game addiction. The aim of the work was to study polymorphic variants of the dopamine receptor gene DRD2 (rs6277, rs1800497) in Russian adolescents with problematic use of computer video games. A sampling of 407 adolescents aged 14.1±1.8 years was tested, of which 56 (13.8 %) were identified as having problems with the pathological use of video games use based on the GASA scale results. Boys in the sample proved to be addicted to video games more than girls (p = 0.041). As a result of comparing the allele frequency of DRD2 (rs6277), a tendency to a higher frequency of the minor allele T was revealed in the group of adolescents with problematic video game use compared with adolescents without problematic video game use (i. e. 0.563 and 0.466, respectively, p = 0.06). When using the dominant inheritance model, it was revealed that adolescents with problematic use of video games were statistically significantly more likely to carry the T (CT+TT) allele (p = 0.04, OR = 2.14, CI = 1.01–4.53). The T allele DRD2 (rs6277) is associated with low expression of the dopamine receptor D2 and leads to decreasing the density and affinity of extrastriatal dopamine type 2 receptors, which is associated with impaired social communication as well. We suggest that the presence of CT and TT genotypes of rs6277 DRD2 may be a potential risk factor for developing problematic video game use in adolescents.

The impact of lethal and sub-lethal exposure of emamectin benzoate on populations of Spodoptera litura (Lepidoptera: Noctuidae) under laboratory conditions

Emamectin benzoate is an avermectin bio-insecticide commonly used for managing several insect pests including Spodoptera litura (Fabricius) (Lepidoptera: Noctuidae), a major polyphagous pest of many cultivated crops. The current study was conducted to evaluate the effects of emamectin benzoate on the fitness of S. litura populations exhibiting differential susceptibility to insecticide. The selection process and all the bioassays were carried out using 6-day-old 2nd instar larvae of S. litura. A field-collected population of S. litura was divided into two groups: one selected with emamectin benzoate for eight generations (EB-Sel) and the other kept unexposed (Unsel-Lab) to insecticide in the laboratory. An increase in resistance ratio from 1.71-fold in the F1 generation to 22.54-fold in the F8 generation of the EB-Sel population was observed compared to the Unsel-Lab (F8) population. The EB-Sel and Unsel-Lab populations were treated with their respective lethal and sub-lethal concentrations which resulted in an extended development period, decreased larval survival, and adult emergence along with increased morphological abnormalities in adults. Significant reductions were observed in both male and female longevity, fecundity, egg hatching, net reproductive rate (R0), intrinsic rate of increase (rm), and finite rate of increase (λ) in EB-Sel and Unsel-Lab populations. Higher concentrations of the insecticide also reduced the relative fitness (Rf) of S. litura larvae, with maximum effect at LC50 of the EB-Sel population where the Rf value was 0.32 compared to the Unsel-Lab population. Both populations have been affected by emamectin benzoate exposure, however, the impact was more pronounced in the EB-Sel population indicating fitness costs. Our results suggested the fitness cost linked to emamectin benzoate resistance in S. litura which might favor managing insecticide resistance by reducing the frequency of resistant alleles by removing selection pressure. Consequently, our research provides significant insights to devise better pest management strategies for S. litura.

Genetic variants in patients with multiple arterial aneurysms

PurposeThe aim of this study was to identify causal genetic variants in patients with multiple arterial aneurysms.MethodsFrom a total cohort of 3107 patients diagnosed with an arterial aneurysm from 2006 to 2016, patients with known hereditary connective tissue diseases, vasculitis, or other arterial pathologies (n = 918) were excluded. Of the remaining cohort (n = 2189), patients with at least 4 aneurysms at different arterial locations (n = 143) were included. Nine blood samples of respective patients were available and derived from the institutional vascular biomaterial bank, and analyzed by whole exome sequencing (WES). Possible candidate variants were selected based on in silico predictions: (I) Truncating variants or (II) Variants that were classified as likely pathogenic (SIFT score < 0.05 or PolyPhen score > 0.9) and with low (< 0.001) or unknown gnomAD allele frequency. The human genome databases GeneCards and MalaCards were used to correlate the variants with regard to possible associations with vascular diseases.ResultsA total of 24 variants in 23 different genes associated with vascular diseases were detected in the cohort. One patient with eight aneurysms was heterozygous for a variant in SMAD3, for which pathogenic variants are phenotypically associated with Loeys-Dietz syndrome 3. A heterozygous variant in TNXB was found in a patient with five aneurysms. Homozygous or compound heterozygous pathogenic variants in this gene are associated with Ehlers-Danlos syndrome (classical-like). Another patient with six aneurysms carried two heterozygous TET2 variants together with a heterozygous PPM1D variant. Pathogenic variants in these genes are associated with clonal hematopoiesis of indeterminate potential (CHIP), a known risk factor for cardiovascular disease.ConclusionAll nine patients in this study carried variants in genes associated with vascular diseases. Current knowledge of the specific variants is insufficient to classify them as pathogenic at the present time, underlining the need for a better understanding of the consequences of genetic variants. WES should be considered for patients with multiple arterial aneurysms to detect germline variants and to improve clinical management for the individual and family members.

Rare variant contribution to the heritability of coronary artery disease

Whole genome sequences (WGS) enable discovery of rare variants which may contribute to missing heritability of coronary artery disease (CAD). To measure their contribution, we apply the GREML-LDMS-I approach to WGS of 4949 cases and 17,494 controls of European ancestry from the NHLBI TOPMed program. We estimate CAD heritability at 34.3% assuming a prevalence of 8.2%. Ultra-rare (minor allele frequency ≤ 0.1%) variants with low linkage disequilibrium (LD) score contribute ~50% of the heritability. We also investigate CAD heritability enrichment using a diverse set of functional annotations: i) constraint; ii) predicted protein-altering impact; iii) cis-regulatory elements from a cell-specific chromatin atlas of the human coronary; and iv) annotation principal components representing a wide range of functional processes. We observe marked enrichment of CAD heritability for most functional annotations. These results reveal the predominant role of ultra-rare variants in low LD on the heritability of CAD. Moreover, they highlight several functional processes including cell type-specific regulatory mechanisms as key drivers of CAD genetic risk.

Validation of gene polymorphisms (rs2682818 and rs2043556) in has-miR-618 and has-miR-605 with the breast cancer susceptibility

BackgroundBreast cancer (BC) is one of the most frequent types of cancer and the second leading cause of cancer-affiliate death among ladies. BC is a heterogeneous sickness that is impacted by environment and genetic elements. Diagnosis in the early stages impacts treatment and patient survival rate. miRNA can play a vital role in BC's early stages of tumorigenesis. Single nucleotide polymorphism (SNP) can cause changes in miRNA expression and function, which are related to the risk of several cancers. AimThe goal of this examination is to assess the affiliation among two has-miR-605 (rs2043556A > G) and has-miR-618 (rs2682818 C > A) gene polymorphisms with the risk of BC in the Iranian ladies. MethodsOur case-control examination assessed two hundred whole blood samples of one hundred ladies with BC and one hundred healthy ladies. Hence, to assess the connection between the presence of SNP miRNA genes and the risk of BC, genotyping was done by the usage of the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method, then the usage of the Chi-square test of SPSS software statistically analyzed the acquired result. ResultsOur findings confirmed a statistically substantial distinction within the genotype frequency of the has-miR-618 gene polymorphism among the groups (P = 0.043), whereas no statistically substantial distinction inside the genotype frequency of the has-miR-605 gene polymorphism among the control and case (P = 0.183). In addition, the allelic frequency of two polymorphisms, (rs2043556 A > G) G allele (OR = 2.163, CI 95 % = 1.56–2.988, P = 0.022) and (rs2682818 C > A) A allele (OR = 3.997, CI 95 % = 1.584–10.081, P = 0.002) substantially enhance the risk of BC. ConclusionThe results show that the G allele of rs2043556 and the A allele of rs2682818 increase the risk of BC in the women population of East Azerbaijan province.

A Study on the Morphology and Molecular Biology of Tropical Strawberries

The studies on the morpho-molecular characteristics of different strawberry genotypes were conducted at Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh. BARI Strawberry 1, BARI Strawberry 2, BARI Strawberry 3, FA 005, and Festival were used for this experiment. This study was undertaken to assess five tropical strawberry genotypes at morphological and molecular level. BARI Strawberry 2 was recognised as the preeminent genotype among five strawberry cultivars based on fruit production per plant (594.73 grammes), yield per hectare (19.39 tonnes), and fruit count per plant (32.42). The SSR technique was utilised to assess genetic variation and connections among five strawberry cultivars. Initially, ten primers were evaluated, and finally, three primers—EMFv104, ARSFL-10, and ARSFL-15—were selected for analysis. ARSFL-10 produced the fewest polymorphic alleles (3), while the markers EMFv104 and ARSFL-15 generated the most polymorphism alleles (4). The allele frequency for each location ranged from 0.4 (EMFv104) to 0.6 (ARSFL-10). The PIC values ranged from 0.672 on EMFv104 to 0.4992 on ARSFL-10. EMFv104 and ARSFL-15 demonstrated gene diversity scores of 0.72, whereas ARSFL-10 achieved a value of 0.56. The genotypes demonstrating the minimal genetic dissimilarity were BARI Strawberry 1 and Festival, with a value of 0.16667. Primer EMFv104 and ARSFL-15 are regarded as the most efficacious SSR markers for strawberry genotypes.

Evaluation of blood MSI burden dynamics to trace immune checkpoint inhibitor therapy efficacy through the course of treatment.

Analysis of serial liquid biopsy (LB) samples has been found to be a promising approach for the monitoring of tumor dynamics in the course of therapy for patients with colorectal cancer (CRC). Currently, somatic mutations are used for tracing the dynamics of the tumor via LB. However, the analysis of the dynamic changes in the molecular signatures such as microsatellite instability (MSI) is not currently used. We hypothesized that changes in blood MSI burden (bMSI) could be registered using serial LB sampling in the course of immune checkpoint inhibitors (ICI), and that its changes could potentially correlate with treatment outcomes. We report the preliminary findings of the observational trial launched to study (NCT06414304) the dynamics of bMSI in 9 MSI-positive CRC patients receiving ICI. NGS-based MSI testing was performed on both pre-treatment FFPE and serial LB samples. For patients who had detectable bMSI burden in any of the LB samples (n = 8, 89%), median bMSI was 1.4% (range, 0.01-40%). Among patients with detectable MSI in available FFPE samples, median MSI burden was 29.3% (range, 10-40%). bMSI detected in baseline LB and FFPE samples were positively correlated (Pearson's R 0.47). Maximal variant allele frequencies of driver mutations observed in LB were also positively correlated with bMSI burden (Pearson's R 0.7). Patients who had clinical benefit had undetectable bMSI burden at follow-up. Our results provide the rationale for further validation of bMSI as a predictive biomarker of ICI in MSI-positive patients.

Rare variant analyses in 51,256 type 2 diabetes cases and 370,487 controls reveal the pathogenicity spectrum of monogenic diabetes genes.

Type 2 diabetes (T2D) genome-wide association studies (GWASs) often overlook rare variants as a result of previous imputation panels' limitations and scarce whole-genome sequencing (WGS) data. We used TOPMed imputation and WGS to conduct the largest T2D GWAS meta-analysis involving 51,256 cases of T2D and 370,487 controls, targeting variants with a minor allele frequency as low as 5 × 10-5. We identified 12 new variants, including a rare African/African American-enriched enhancer variant near the LEP gene (rs147287548), associated with fourfold increased T2D risk. We also identified a rare missense variant in HNF4A (p.Arg114Trp), associated with eightfold increased T2D risk, previously reported in maturity-onset diabetes of the young with reduced penetrance, but observed here in a T2D GWAS. We further leveraged these data to analyze 1,634 ClinVar variants in 22 genes related to monogenic diabetes, identifying two additional rare variants in HNF1A and GCK associated with fivefold and eightfold increased T2D risk, respectively, the effects of which were modified by the individual's polygenic risk score. For 21% of the variants with conflicting interpretations or uncertain significance in ClinVar, we provided support of being benign based on their lack of association with T2D. Our work provides a framework for using rare variant GWASs to identify large-effect variants and assess variant pathogenicity in monogenic diabetes genes.

Allele frequencies of PRLR truncating variants in heat-tolerant taurine cattle native to Latin America.

Allele frequencies of PRLR truncating variants in heat-tolerant taurine cattle native to Latin America.

Polymorphism of ADAMTS-13 gene rs28503257 in Iraqipatients with Hypertension

The aim of this study was to investigate the association of polymorphism of ADAMTS-13 gene to the susceptibility of hypertension in patients with hypertension in an Iraqi population. Forty-five hypertensive patients (23 males and 22 females), their age 40-70 years and 35 healthy controls (18 males and 17 females), their age range between 40-70 years. were selected from Wasit Province using a convenient sampling method. Genetic polymorphism of ADAMTS13) rs28503257 A/G was carried out using TaqMan -PCR. In patients and controls, the genotypic and allelic distributions of adisentgrine and metallopeptedase with a thrombospondin type1 motife13(ADAMTS13) rs28503257 A/G of the study populations were consistent with Hardy-Weinberg equilibrium. The genotypes frequecies of ADAMTS-13 rs 28503257 A/G of patients with hypertension manifested non-significant differences when compared with healthy control group AA =40(89%), AG =5(11) in patients vs. 30(86), 5(14) P=0.67 in controls for each genotype respectively. There were no hypertensive patients or controls carrying the genotype GG in the study sample. The A and G allele frequencies in SNP rs28503257 A/G were not significantly different between the two groups (P&gt;0.05). The A allele was the major one in studied groups with a percent of (0.9286) and (0.9444) in control and patients groups respectively. Whereas the A allele was the minor one with a percent of (0.0714) and (0.0556) in these groups respectively. The association analysis revealed that individuals carrying the homozygous AA genotype were assocaited with hypertension OR=1.3333 (CI95% 0.3537 to 5.0259) and P= 0.6709 indicating that a positive association with the disease.However,the individuals with a hetrozygous AG genotype showed negative association with the disease OR= 0.7500 (CI95% 0.1990 to 2.8271) ,P=0.6709. Although no individuals carrying the genotype GG were observed in patients and controls, the odds ratio can be calculated in the presence of other genotypes OR= 0.7802 (CI95% 0.0151 to 40.2986), P= 0. 9019.These results suggest that the A allele may be considered as a risk allele in hypertension whereas the G allele is a protective allele agianst hypertension. The genetic model for ADAMTS-13 in comparison between hypertensive patients and controls .The dominant model indicated that patients of(AG+GG/AA) genotypes decreased the association with hypertension comparing with control with OR=1.333 CI95%0.3537 to 5.025: patients (40/5 and 0.00) in patients vs.(30/5 and 0.00) with OR== 0.7500(CI95%0.1990 to 2.8271) , P =0.6709,P=0.6709.The recessive model revealed that patients carrier the genotype(AA+AG/GG) increased the association with the disease (0.0/40 and 5) in patients compared with controls(0.00/30 and 5) with OR=1.2817(CI95% 0.0248 to 66.199), P=0. 9019.The Over dominant model revealed that patients carrier the genotype (AA+GG/AG) increased the association with the disease (0.040 and 5) in patients compared with controls (0.00/30 and 5) with OR=1.3333(CI95%0.3537 to5.0259),P=0.6709. In coclusion, the polymorphisms ADAMTS-13 rs28503257 variant A/G with are associated with the susceptibility of hypertension.