Allele Frequencies Research Articles

Genotyping methods to distinguish Plasmodium falciparum recrudescence from new infection for the assessment of antimalarial drug efficacy: an observational, single-centre, comparison study

Distinguishing Plasmodium falciparum recrudescence from new infections is crucial for the assessment of antimalarial drug efficacy against Pfalciparum. We aimed to compare the efficacy of different genotyping methods to assess their effect on drug efficacy estimates, particularly in patients from high-transmission settings with polyclonal infections. In this head-to-head comparison study, we compared five different genotyping methods currently used: fast capillary electrophoresis (F-CE) using msp1, msp2, and glurp; high-resolution capillary electrophoresis (H-CE) using msp1, msp2, and glurp; H-CE using microsatellites; targeted amplicon deep sequencing (TADS) using single nucleotide polymorphism (SNP)-rich markers; and high-resolution melting (HRM) analysis using msp1 and msp2. We assessed their sensitivity in detecting minority clones in polyclonal infections, their reproducibility, and the genetic diversity of the markers used. Our study used four well characterised Pfalciparum laboratory strains mixed in varying ratios, and 20paired samples collected from an in-vivo clinical trial. The experiments were performed at the Swiss Tropical and Public Health Institute in Basel, Switzerland between May 5, 2020, and Aug 23,2021. H-CE using msp1 and msp2 and TADS revealed the highest sensitivity in detecting minority clones (up to ratios of 1:100 for H-CE and 50:1:1:1 for TADS in the FCB1:HB3 and 3D7:K1:HB3:FCB1 laboratory strain mixtures, respectively), highest reproducibility (intra-assay: 99% and 91% for H-CE and TADS, respectively; inter-assay: 98% and 92% for H-CE and TADS, respectively), and highest genetic diversity in the used markers (up to 36and32unique genotypes in 20paired samples for H-CE using msp2 and TADS using cpmp, respectively). Microsatellites assessed by H-CE had a lower genetic diversity compared with msp1, msp2, and glurp assessed by H-CE and the SNP-rich markers assessed by TADS, with a maximum of 13unique genotypes, and some genotypes having allelic frequencies larger than 30%.Markers used by TADS gave the most consistent results in distinguishing recrudescence from new infection across all methods (in 18of 20pairs of samples vs 15of 20pairs for H-CE). WHO currently recommends replacing glurp with microsatellites. However, in this study, the replacement of glurp with microsatellites did not change the genotyping outcome, probably due to the lower genetic diversity of microsatellites. More studies with large sample sizes are required to identify the most suitablemicrosatellites that could replace glurp. Our study indicates that TADS should be considered the gold standardfor genotyping to distinguish recrudescence from new infection, and that it should be used to validate other methods. Swiss Tropical and Public Health Institute.

Assessing the Impacts of Adaptation to Native-Range Habitats and Contemporary Founder Effects on Genetic Diversity in an Invasive Fish.

Species invading non-native habitats can cause irreversible environmental damage and economic harm. Yet, how introduced species become widespread invaders remains poorly understood. Adaptation within native-range habitats and rapid adaptation to new environments may both influence invasion success. Here, we examine these hypotheses using 7058 SNPs from 36 native, 40 introduced and 19 farmed populations of tench, a fish native to Eurasia. We examined genetic structure among these populations and accounted for long-term evolutionary history within the native range to assess whether introduced populations exhibited lower genetic diversity than native populations. Subsequent to infer genotype-environment correlations within native-range habitats, we assessed whether adaptation to native environments may have shaped the success of some introduced populations. At the broad scale, two glacial refugia contributed to the ancestry and genomic diversity of tench. However, native, introduced and farmed populations of admixed origin exhibited up to 10-fold more genetic diversity (i.e., observed heterozygosity, expected heterozygosity and allelic richness) compared to populations with predominantly single-source ancestry. The effects of introduction to a new location were also apparent as introduced populations exhibited fewer private alleles (mean = 9.9 and 18.9 private alleles in introduced and native populations, respectively) and higher population-specific Fst compared to native populations, highlighting their distinctiveness relative to the pool of allelic frequencies across tench populations. Finally, introduced populations with varying levels of genetic variation and similar genetic compositions have become established and persisted under strikingly different climatic and ecological conditions. Our results suggest that lack of prior adaptation and low genetic variation may not consistently hinder the success of introduced populations for species with a demonstrated ability to expand their native range.

Dopamine neuron dysfunction and loss in the PrknR275W mouse model of juvenile parkinsonism.

Mutations in the PRKN gene encoding the protein parkin cause autosomal recessive juvenile parkinsonism (ARJP). Harnessing this mutation to create an early-onset Parkinson's disease mouse model would provide a unique opportunity to clarify the mechanisms involved in the neurodegenerative process and lay the groundwork for the development of neuroprotective strategies. To this end, we created a knock-in mouse carrying the homozygous PrknR275W mutation, which is the missense mutation with the highest allelic frequency in PRKN patients. We evaluated the anatomical and functional integrity of the nigrostriatal dopamine (DA) pathway, as well as motor behaviour in PrknR275W mice of both sexes. We report here that PrknR275W mice show early DA neuron dysfunction, age-dependent loss of DA neurons in the substantia nigra, decreased DA content and stimulus-evoked DA release in the striatum, and progressive motor impairment. Together, these data show that the PrknR275W mouse recapitulates key features of ARJP. Thus, these studies fill a critical need in the field by introducing a promising new Parkinson's disease model in which to study causative mechanisms of the disease and test therapeutic strategies.

Frequency of CD40-1C>T polymorphism (rs1883832) and association with response to treatment in children with primary immune thrombocytopenia.

To investigate whether (cluster of differentiation) CD40-1C>T (rs1883832) contributes to predisposition and treatment response of primary immune thrombocytopenia (pITP) in children. A case-control study that included 100 children with newly diagnosed pITP and 50 age- and sex-matched healthy controls. CD40 rs1883832 was genotyped using TaqMan allele discrimination real-time polymerase chain reaction (PCR). Patients were categorized into responders and non-responders according to their response to corticosteroids and thrombopoietin-receptor agonists (TPO-RA) at 3-month intervals. The genotypic distribution of the CD40 rs1883832 was significantly different among cases and controls (CC 48% vs. 30%; CT 44% vs. 42%; TT 8% vs. 28%; p=.003). Compared with controls, children with newly diagnosed pITP had significantly higher C allele frequency (70% vs. 51%; odds ratio [OR] 2.2, 95% confidence interval [CI]: 1.3-3.8; p=.001). The association between C allele frequency and pITP risk was evident in females (OR 4.3, 95% CI: 2.1-8.8; p<.001), but not in males (OR 0.9, 95% CI: 0.4-2.1; p=.822). Compared with responders, the C allele frequency was significantly higher among non-responders to corticosteroids (87% vs. 66%; OR 3.4, 95% CI: 1.2-11.7; p=.012), but not to TPO-RA (92% vs. 85%; OR 2, 95% CI: 0.2-107; p=.550). CD40 rs1883832 polymorphism may contribute to predisposition and response to upfront corticosteroids therapy of pediatric pITP. These findings improve our understanding of the compound pathophysiology of ITP, suggest important clinical potentials, and open the door for further research on the mechanistic role of CD40 rs1883832 in ITP development and progression.

Developmental Validation of the Microreader 23HS Plex ID System: A Novel Supplementary Non-CODIS STR Multiplex Assay for Forensic Application.

A novel supplementary non-CODIS STR multiplex assay designated as the "Microreader 23HS Plex ID System" was developed. The Microreader 23HS Plex ID System enables simultaneous profiling of 23 STR loci and the amelogenin locus. The majority of these loci are non-CODIS STRs (D4S2408, D9S2157, D20S161, D3S2459, D18S1364, D13S305, D1S2142, D19S400, D6S1017, D7S1517, D2S1776, D2S1360, D3S1744, D16S3391, D3S1545, D11S4463, D20S85, D1S549, D10S2325, D21S2055), with the exception of three CODIS STRs (D2S441, D12S391, and D22S1045). Followed the recommendations of Scientific Working Group on DNA Analysis Methods (SWGDAM) and the Chinese validation standards, a comprehensive set of validation studies were conducted, encompassing PCR conditions, stutter ratio and peak height balance, sensitivity, precision and accuracy, reproducibility, species specificity, inhibition, as well as mixture testing. The results demonstrated that the Microreader 23HS Plex ID System is a reliable and robust assay, with well-balanced peak heights, high precision and accuracy, species specificity, and resistance to common inhibitors. The sensitivity of the assay was determined to be 0.125ng of template DNA. In mixture study, all minor alleles were detected in two-sample mixtures across various ratios (1:19, 1:9, 1:4, 3:7, 2:3, 1:1, 3:2, 4:1, 9:1, and 19:1). In population study, a total of 500 unrelated individuals of Han ethnicity from East China were genotyped. The allele frequencies and forensic population genetic parameters were calculated, with a cumulative random match probability of 7.757×10-27, and a total power of discrimination exceeding 0.999,999,999,999,999,999,999,999,99. In conclusion, the Microreader 23HS Plex ID System shows promise as a valuable supplementary tool for forensic applications, particularly in addressing complex kinship testing and challenges posed by STR mutation.

Frequency of rs35803318 single nucleotide polymorphism of ACE2 gene among the Kazakhs

In the article the results of genotyping of DNA samples obtained from the study participants on the single nucleotidepolymorphism (SNP) rs35803318 (C/T) of the ACE2 gene were presented. Genotyping was carriedout by real-time polymerase chain reaction (PCR) using the technique Amplification of the Refractory MutationSystem (ARMS). The frequencies of rs35803318 (C/T) genotypes and alleles in 96 representatives of theKazakh ethnic group living in the Karaganda region were analyzed. The ACE2 gene (angiotensin-convertingenzyme 2) was extensively investigated due to its role in susceptibility to infection by the SARS-CoV-2 viruscausing COVID-19. The ACE2 gene encodes a protein that serves as a receptor for the virus, and its variationscan affect a person's susceptibility to infection. The ACE2 protein plays a role in the regulation of angiotensinand the effect on blood pressure. Therefore, there is a link between ACE2 gene polymorphisms, includingrs35803318, and the development of cardiovascular diseases. According to the results of our study,the CT genotype (63.5 %) is the most common among Kazakhs, the CC genotype was 20.8 % and theTT genotype was 15.6 %. The distribution of polymorphism alleles is as follows: allele C — 52.6 %, allele A— 47.4 %.

Frequency and relationship of HLA allele in Turkish patients with Fanconi anemia

Purpose: Fanconi anemia (FA) is a childhood disorder inherited in an autosomal recessive manner. It is characterized by bone marrow failure, a range of congenital physical abnormalities, increased susceptibility to cancer, chromosomal instability, and heightened sensitivity to cross-linking agents. The aim of this study was to determine the role of the HLA Class I and Class II alleles in genetic susceptibility to Fanconi anemia in Turkish patients. Materials and Methods: In this study, we retrospectively evaluated the HLA-A, -B, and -DRB1 allele frequencies of patients with Fanconi anemia who underwent hematopoietic stem cell transplantation between 2010 and 2021. HLA-A, -B, -DR of all patients and healthy Turkish individuals were genotyped. Results: The study included 86 patients with Fanconi anemia and 300 healthy controls. The most common antigens in patients with Fanconi were HLA-A*02, HLA-B*35 and DRB1*11. Moreover, in the patient group, the HLA-A*23 allele was significantly lower than the control group. When we evaluated the patient group according to gender the HLA-A*01 allele was significantly higher in the female patient group. Conclusion: Our study provides valuable insights into the genetic susceptibility of Turkish patients with Fanconi anemia, focusing on the role of HLA Class I and Class II alleles. HLA-B*14 may be a risk factor and HLA-A*23 may be protective for Fanconi anemia. These results contribute to our understanding of the complex genetic factors underlying Fanconi anemia and may have implications for improved diagnosis, prognosis, and potential therapeutic interventions for affected individuals.

Impacts of Matrix Metalloproteinase-8 Genotypes, Smoking, Alcohol Drinking, and Helicobacter Pylori Infection on Gastric Cancer.

In gastric cancer (GCa) tissues, mRNA expression of matrix metalloproteinase-8 (MMP-8) is notably reduced compared to healthy tissues. Furthermore, abnormally low or elevated serum levels of MMP-8 have been linked to a significantly poor prognosis. The involvement of MMP-8 genotypes in susceptibility to GCa remains underexplored. We aimed to assess the influence of MMP-8 genotypes on GCa susceptibility and their potential interactions with smoking, alcohol consumption, and Helicobacter pylori (H. pylori) infection. The study utilized polymerase chain reaction-based restriction fragment length polymorphism (PCR-RFLP) to analyze MMP-8 rs11225395, rs34009635, and rs35866072 genotypes in 161 GCa patients and 483 controls. No statistically significant difference was detected in the distribution of genotypic (p for trend=0.3635) or allelic (p=0.1954) frequencies of MMP-8 rs11225395. Under a dominant model, combined CT+TT genotypes showed no association with GCa risk [odds ratio (OR)=0.77, 95% confidence interval (95%CI)=0.54-1.10, p=0.1852]. Similarly, no association was observed for MMP-8 rs34009635 or rs35866072. Importantly, individuals with the MMP-8 rs11225395 CC genotype demonstrated a significant increase in GCa risk when exposed to smoking (OR=4.04, 95%CI=2.28-7.16, p=0.0001), alcohol consumption (OR=2.83, 95%CI=1.64-4.89, p=0.0002), and H. pylori infection (OR=3.53, 95%CI=2.12-5.90, p=0.0001). The findings indicate that individuals carrying the MMP-8 rs11225395 CC genotype have increased susceptibility to GCa, especially when combined with risk factors, such as smoking, alcohol consumption, and H. pylori infection. These results suggest that MMP-8 genotype-based preventive strategies, including lifestyle alterations and targeted infection treatments, may be valuable in mitigating GCa development.

A Comprehensive Analysis of HLA-A and HLA-DR Allele Frequencies and Haplotype Associations in a Korean Population of 790 Individuals

A Comprehensive Analysis of HLA-A and HLA-DR Allele Frequencies and Haplotype Associations in a Korean Population of 790 Individuals

Similarities and differences between brain and skin GNAQ p.R183Q driven capillary malformations.

Capillary malformations (CM) are congenital vascular irregularities of capillary and venous blood vessels that appear in the skin, leptomeninges of the brain, and the choroid of the eye in the disorder known as Sturge Weber Syndrome (SWS). More common are non-syndromic CM found only in the skin, without brain or ocular involvement. A somatic activating mutation in GNAQ (p.R183Q) is found in ~ 90% of syndromic and non-syndromic CM specimens and is present in CD31pos endothelial cells isolated from brain and skin CM specimens. Endothelial expression of the GNAQ p.R183Q variant is sufficient to form CM-like vessels in mice. Given the distinct features and functions of blood vessels in the brain versus the skin, we examined the features of CM vessels in both tissues to gain insights into the pathogenesis of CM. Herein, we present morphologic characteristics of CM observed in specimens from brain and skin. The GNAQ p.R183Q variant allelic frequency in each specimen was determined by droplet digital PCR. Sections were stained for endothelial cells, tight junctions, mural cells, and macrophages to assess the endothelium as well as perivascular constituents. CM blood vessels in brain and skin were enlarged, exhibited fibrin leakage and reduced zona occludin-1 and claudin-5, and were surrounded by MRC1pos/LYVE1pos macrophages. In contrast, the CMs from brain and skin differ in endothelial sprouting activity and localization of mural cells. These characteristics might be helpful in the development of targeted and/or tissue specific therapies to prevent or reverse non-syndromic and syndromic CM.

Forensic characteristics of 38 Y-STR loci in the Hui population from Shaanxi Province, Northwest China

In this study, we genotyped 939 unrelated healthy individuals to investigate the genetic polymorphisms of 38 Y chromosome short tandem repeats(Y-STRs) loci included in the Yfiler™ Platinum kit in the Hui population of Shaanxi Province. Comprehensive population comparisons were performed using analysis of molecular variance(AMOVA), multidimensional scaling(MDS), and molecular evolutionary genetics analysis(MEGA) to explore population relationships. The allele frequencies of the single-copy loci ranged from 0.001 to 0.940 (DYS645), while those of the multi-copy loci ranged from 0.001 to 0.138 (DYS527). The highest genetic diversity (GD) value was observed for DYS385 (0.9723), and the lowest for DYS645 (0.1138). A total of 849 distinct haplotypes were identified among the 939 Hui individuals, with 808 (95.2 %) being unique. Haplotype diversity (HD), haplotype match probability, and discriminatory power (DC) in the Shaanxi Hui population were 0.9996, 0.0015, and 0.9041, respectively. Interpopulation comparisons based on Rst genetic distance values, phylogenetic trees, and MDS indicated that the Shaanxi Hui population has a close genetic relationship with the Ningxia Hui, Qinghai Hui, Xinjiang Hui, and Yunnan Hui populations. The population genetic stratification largely coincides with geographic distribution and language families. Our study revealed that the 38 Y-STR loci exhibit high genetic polymorphisms in the Hui population from Shaanxi Province.

HLA Diversity in Transylvanian Ethnic Groups: Consequences for Hematopoietic Cell Transplantation

The HLA profile is essential in cell and tissue transplantation, particularly in patients with autoimmune conditions and infections. Due to the extreme polymorphism in certain HLA loci, it also serves as a key tool for population genetic analysis. This study aimed to identify the allele and haplotype distributions of HLA class I (A, B, and C) and class II (DRB1) genotypes in unrelated hematopoietic stem cell donors. A retrospective analysis was conducted between 2016 and 2020 on 9832 Transylvanian volunteers, divided into Romanian and Hungarian groups based on self-reported ethnicity. Using PCR-SSO for HLA typing, significant differences were found in allele frequencies between ethnic groups. A total of 19 HLA-A, 31 HLA-B, 14 HLA-C, and 13 HLA-DRB1 distinct allele groups were identified between ethnic groups. Notably, B*18, B*51, and C*12 were more frequent in Romanians, while B*44, B*40, and C*07 were more common in Hungarians. Differences in haplotype distributions were also observed, with HLA-A*02~B*18~C*07~DRB1*11 being significantly more frequent in Romanians. Understanding these population-specific HLA profiles can improve donor matching for hematologic diseases, enhancing patient outcomes and access to life-saving hematopoietic stem cell transplantation.

Genetic Predisposition to Prediabetes in the Kazakh Population.

The aim of this study was to conduct a comparative analysis of the population frequencies of the minor allele of polymorphic variants in the genes TCF7L2 (rs7903146) and PPARG (rs1801282), based on the genome-wide association studies analysis data associated with the risk of developing prediabetes, in an ethnically homogeneous Kazakh population compared to previously studied populations worldwide. This study utilized a genomic database consisting of 1800 ethnically Kazakh individuals who were considered in healthy condition. Whole-genome genotyping was performed using Illumina OmniChip 2.5-8 arrays, which interrogated approximately 2.5 million single nucleotide polymorphisms. The distribution of genotypes for the TCF7L2 (rs7903146) and PPARG (rs1801282) polymorphisms in the Kazakh sample was found to be in Hardy-Weinberg equilibrium (p > 0.05). The minor G allele of the "Asian" protective polymorphism rs1801282 in the PPARG gene was observed at a frequency of 13.8% in the Kazakh population. This suggests a potentially more significant protective effect of this polymorphism in reducing the risk of prediabetes among Kazakhs. The frequency of the unfavorable T allele of the insulin secretion-disrupting gene TCF7L2 (rs7903146) in Kazakhs was 15.2%. Studying the associations of genetic markers for prediabetes enables the timely identification of "high-risk groups" and facilitates the implementation of effective preventive measures. Further results from replicative genomic research will help identify significant polymorphic variants of genes underlying the alteration of prediabetes status.

Tissue factor (F3) gene variants and thrombotic risk among middle-aged and older adults: A population-based cohort study

BackgroundTissue factor (TF), encoded by the F3 gene, is the main initiator of blood coagulation. The molecular epidemiology of the F3 gene and the relation to venous thromboembolism (VTE) remains to be determined. ObjectivesThe aim was to determine the molecular epidemiology and the importance of F3 variants for incident VTE by analysis of the population-based MDC study (Malmö Diet and Cancer), consisting of unselected middle-aged and older individuals. MethodsThe exons of F3 were analyzed in a total of 28,794 individuals from the MDC cohort, and of these, 2584 (9 %) were affected by VTE during follow‐up (1991–2018). Qualifying variants used in gene-collapsing analysis were defined as loss-of-function or non-benign (PolyPhen-2) missense variants with minor allele frequency less than 0.1 %. ResultsExon sequencing of the F3 gene identified 61 different variants, 3′ UTR variants (n = 5), 5′ UTR variants (n = 9) synonymous (n = 10), in frame insertion (n = 1), splice region variants (n = 2), missense (n = 33) or loss-of-function variants (n = 1). No associations between common F3 gene variants and incident VTE were found. Seventeen rare variants were classified as qualifying and included in collapsing analysis (16 non-benign missense and 1 loss-of-function variants). The prevalence of F3 qualifying variants was 0.14 %. Seven individuals with F3 qualifying variants had VTE, while 34 individuals had no VTE. The adjusted VTE model was significant (hazard ratio = 2.1 [95 % confidence interval, 1.02–4.48], P-value = 0.045). ConclusionsQualifying F3 gene variants are very rare, indicating a constrained gene. Rare but not common variation in the F3 gene may be involved in VTE.

Low remission rates and high incidence of adverse events in a prospective VEXAS syndrome registry.

We aimed to gather real-world clinical evidence of detailed disease activity, treatments, remission rates, and adverse events (AEs) associated with vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic (VEXAS) syndrome in a prospective study. Patients in Japan suspected of having VEXAS syndrome were enrolled in a registry study. A novel disease activity measure (VEXASCAF) assessing 11 symptoms associated with VEXAS syndrome was evaluated at enrolment and after 3 months. AEs, survival, CRP levels, and treatments were also recorded at enrolment and 3 months after enrolment. All exons of UBA1 were sequenced using a next-generation sequencer to determine the variant allele frequencies of pathogenic variants in the peripheral blood of all patients. Of the 55 registered patients, 30 patients were confirmed to have pathogenic variants of UBA1. All patients were male, with a median age of 73.5 years. VEXASCAF and CRP levels decreased significantly at 3 months post-enrolment, but the oral prednisolone dose did not change. Only two patients achieved complete remission according to FRENVEX at 3 months after enrolment. During the observation period of 6 months, 28 AEs were observed, including 3 deaths, 4 malignancies from two cases, 2 thromboses, and 13 infections (including 4 mycobacterial infections). Inflammation of the lung and cervical region (i.e. parotid and submandibular gland swelling, tonsillitis, cervical swelling, and pain) were the most common AEs. Patients with VEXAS syndrome required high-dose glucocorticoids to achieve remission, and complications-such as malignancy, thrombosis, and infection-occurred frequently within a short observation period.

Genetic Variations and Serum Levels of Leptin and Ghrelin in Autism Spectrum Disorder.

This study aims to examine leptin and ghrelin gene polymorphisms and serum levels in children with autism spectrum disorder (ASD). The study comprised a case group of 40 children aged 2-7 diagnosed with ASD and a control group of 40 healthy children. The severity of ASD symptoms was assessed using the Childhood Autism Rating Scale and the Autism Behavior Checklist. Leptin and ghrelin gene variants were genotyped using polymerase chain reaction (PCR) restriction fragment length polymorphism (RFLP) methods. Serum ghrelin and leptin levels were measured using enzyme-linked immunosorbent assay kits. In this study, gene polymorphisms and allele frequencies were examined, and no significant difference was found (P > .05 for all). Our findings indicated no significant difference in leptin serum levels between the groups (P = .584). However, ghrelin serum levels were significantly lower in the ASD group (P = .027). Receiver operating curve analysis to determine the cutoff value of serum ghrelin level as a diagnostic indicator for ASD resulted in a cutoff value of 885.7 pg/mL with 42.50% sensitivity and 85% specificity (P = .021). No significant relationship was found between leptin and ghrelin serum levels and the severity of ASD (P > .05 for all). Our study is the first to evaluate leptin and ghrelin gene polymorphisms in ASD. Our findings indicate no association between leptin and ghrelin gene polymorphisms and ASD. However, our study suggests that ghrelin serum levels may potentially contribute to the etiology of ASD. More research is needed to understand the role of leptin and ghrelin in ASD.

Estimation of Chloride Channel Residual Function and Assessment of Targeted Drugs Efficiency in the Presence of a Complex Allele [L467F;F508del] in the CFTR Gene.

Complex alleles of the CFTR gene complicate the diagnosis of cystic fibrosis (CF), the classification of its pathogenic variants, affect the clinical picture of the disease and can affect the efficiency of targeted drugs. The total frequency of complex allele [L467F;F508del] in the Russian population of patients with CF is 0.74%, and in patients with the F508del/F508del genotype, its frequency reaches 8%. This article presents multi-faceted study of the complex allele [L467F;F508del] in a cohort of patients with genotypes [L467F;F508del]/class I (c.3532_3535dup, c.1766+2T>C, W1310X, 712-1G>T), and data for a unique patient with the genotype [L467F;F508del]/[L467F;F508del]. Using the intestinal current measurement method, it was demonstrated the absence of CFTR function for [L467F;F508del]/class I and [L467F;F508del]/[L467F;F508del] genotypes. In intestinal organoids, it was shown that [L467F;F508del] in combination with class I variants and in the homozygotes abolishes the efficacy of both two-component (ivacaftor+lumacaftor; ivacaftor+tezacaftor) and three-component (ivacaftor+tezacaftor+elexacaftor) targeted drugs. When prescribing ivacaftor+tezacaftor+elexacaftor to three patients, they did not have a clinical effect after 6-12 months.

Clinical utility of ctDNA by amplicon based next generation sequencing in first line non small cell lung cancer patients.

The assessment of ctDNA has emerged as a minimally invasive avenue for molecular diagnosis and real-time tracking of tumor progression in NSCLC. However, the evaluation of ctDNA by amplicon-based NGS has been not endorsed by all the healthcare systems and remains to be fully integrated into clinical routine practice. To compare tissue single-gene with plasma multiplexed testing, we retrospectively evaluated 120 plasma samples from 12 consecutive patients with advanced non-squamous NSCLC who were part of a prospective study enrolling treatment-naïve patients and in which tissue samples were evaluated using a single-gene testing approach. While the plasma ctDNA detection of EGFR and BRAF mutations had an acceptable level of concordance with the archival tissue (85%), discordance was seen in all the patients in whom ALK alterations were only detected in tissue samples. Among six responders and six non-responders, early ctDNA mutant allelic frequency (MAF) reduction seemed to predict radiologic responses and longer survival, whereas increasing MAF values with the emergence of co-mutations like BRAFV600E, KRASG12V or TP53M237I seemed to be an early indicator of molecular and radiologic progression. This report using an amplicon-based NGS assay on ctDNA underscores the real-life need for plasma and tissue genotyping as complementary tools in the diagnostic and therapeutic decision-making process.

Novel variants and genotype-phenotype correlation in a multicentre cohort of GNE myopathy in China

BackgroundGlcNAc2-epimerase (GNE) myopathy is a rare autosomal recessive disorder caused by pathogenic variants in the GNE gene, which is essential for the sialic acid biosynthesis pathway.ObjectiveThis multi-centre study aimed to...

Frequency of pharmacogenomic variants affecting safety and efficacy of immunomodulators and biologics in a South Asian population from Sri Lanka

BackgroundImmunomodulators are important for management of autoimmune diseases and hematological malignancies. Significant inter-individual variation in drug response/reactions exists due to genetic polymorphisms. We describe frequency of identified genetic polymorphisms among Sri Lankans.MethodsSri Lankan data were obtained from an anonymized database of 670 participants. Data on variants and global distribution of Minor Allele frequency (MAF) of other populations (South Asian, Ashkenazi-Jewish, East-Asian, European-Finnish, European-non-Finnish, Latino-American, African/African-American) were obtained from pharmGKB online database.ResultsSLC19A1 (rs1051266) variant had a MAF (95% CI) of 63.3% (60.7–65.9). Other common variants included FCGR3A (rs396991), MTHFR (rs1801133), ITPA (rs1127354), CYP2C9*3 (rs1057910) and NUD15*3 (rs116855232), with MAFs of 35.3% (32.7–37.9), 12.2% (10.4–13.9), 10.9% (9.2–12.6), 9.8% (8.2–11.4), 8.3% (6.8–9.8) respectively. Less commonly present variants included CYP2C9*2 (rs1799853) (2.5%[1.7–3.4]), TPMT*3C (rs1142345) (1.9%[1.1–2.6]), TPMT*3B (rs1800460) (0.2%[0–0.5]), CYP3A5*6 (rs10264272) (0.2%[0–0.4]) and CYP3A4*18 (rs28371759) (0.1%[0–0.2]). The SLC19A1 (rs1051266), NUD15*3 (rs116855232), CYP2C9*3 (rs1057910), FCGR3A (rs396991), and ITPA (rs1127354) showed significantly higher frequencies in Sri Lankans compared to many other populations, exceptions include FCGR3A in Ashkenazi-Jewish and ITPA in East-Asians. Conversely, MTHFR (rs1801133), TPMT*3B (rs1800460), and CYP2C9*2 (rs1799853) were significantly less prevalent among Sri Lankans than in many other populations. Sri Lankans exhibited lower prevalence of TPMT*3C (rs1142345) compared to European-non-Finnish, Latino-Americans, and African/African-Americans; CYP3A4*18 (rs28371759) compared to East-Asians; and CYP3A5*6 (rs10264272) compared to African/African-Americans and Latino-Americans.ConclusionSri Lankans exhibit higher frequencies in variants reducing methotrexate efficacy (SLC19A1), increasing azathioprine myelotoxicity (NUDT15), and lower frequencies in variants linked to increased azathioprine toxicity (TPMT*3B, TPMT*3C), reduced tacrolimus efficacy (CYP3A4*18), and methotrexate toxicity risk (MTHFR). Beneficial variants enhancing rituximab efficacy (FCGR3A) are more prevalent, while those reducing tacrolimus dosage (CYP3A5*6) are less common. This highlights need for targeted medication strategies to improve treatment outcomes.