Zhanna A. Repinskaia

Background/Objectives: The application of pharmacogenomics (PGx) in pediatrics is limited by the lack of age-oriented interpretation, as adult algorithms do not account for ontogenetic changes in drug-metabolizing enzymes and transport proteins. We aimed to evaluate the clinical applicability of PGx data in Russian children, to assess directional interaction between genotype-based recommendations and enzyme ontogeny, and develop recommendations for age-oriented PGx reporting. Methods: We analyzed whole-exome sequencing data from 524 pediatric patients and 635 newborns. Pharmacogenomic annotations were filtered according to PharmGKB/ClinPGx evidence levels (1A–2B) and the “Pediatrics” tag. In 100 pediatric patients, medical records were retrospectively reviewed for pharmacotherapy and adverse drug reactions (ADRs). An allele-frequency-weighted ADR cost index (AFW-ADR) was calculated for 25 gene–variant–drug–ADR associations (in pediatric cohort), with cost anchors graded by proxy quality. A utilization-weighted variant (AFW-ADR × f_drug) was additionally calculated. Results: Clinically relevant annotations accounted for 5% of initial annotations in both cohorts; 67.6% and 67.2% of these in pediatric and neonatal cohorts, respectively, involved risk alleles with altered function. ADRs occurred in 21% of pediatric patients; only 2/21 cases were explained by high-evidence annotations. Genotype-based recommendations and neonatal enzyme ontogeny were directionally aligned in 5 of 11 assessable gene–drug pairs (45.5%). In the AFW-ADR ranking, the highest values were MTHFR rs1801133–methotrexate toxicity ($22,368), CYP2C9*2/*3–phenytoin SJS/DRESS/TEN ($10,020 and $9540), UGT1A1*28–irinotecan neutropenia ($4658), and HLA-A*31:01–carbamazepine SJS/DRESS/TEN ($3720); however, MTHFR is not clinically actionable. After weighting by pediatric drug utilization, methotrexate remained first, carbamazepine rose to the top ranks, followed by phenytoin, while UGT1A1*28–irinotecan fell to the lowest ranks. This index does not incorporate penetrance and should be interpreted as an exploratory prioritization framework. Conclusions: Age is critical for pediatric PGx interpretation because current reporting approaches do not adequately incorporate ontogeny. We propose an age-oriented PGx model incorporating patient age, ontogenetic adjustment, evidence-level stratification, and multidisciplinary clinical assessment, requiring prospective validation.

Background: Personalized pharmacotherapy requires systematic consideration of genetic factors influencing drug efficacy and safety. The accumulation of large-scale whole-exome sequencing (WES) resources provides an opportunity to assess population frequencies of clinically significant pharmacogenetic variants; however, the applicability of exome-based pharmacogenomics across populations, particularly those underrepresented in existing reference datasets, requires further evaluation. Materials and methods: A retrospective analysis of 6102 anonymized sequencing datasets obtained between 2020 and 2025 was performed using the DNBSEQ-G400 (MGI) platform and Agilent SureSelect Human All Exon v6/v7/v8 enrichment kits. SNV and indel detection, CNV analysis, high-resolution HLA typing, and diplotype assignment for key pharmacogenes were conducted. Pharmacogenomic annotations were derived from ClinPGx (formerly PharmGKB) (levels of evidence 1 A–2B), CPIC, and PharmVar. Haplotype phasing (SHAPEIT5), genotype imputation (IMPUTE5), and phased linkage disequilibrium analysis were performed using a reference panel of 814 Russian whole-genome sequences generated with the same bioinformatic workflow to assess the feasibility of reconstructing clinically relevant non-coding pharmacogenetic variants not captured by WES. Results: WES reliably detected 33 of 34 Very Important Pharmacogenes (VIPs), allowing determination of allele frequencies, metabolizer statuses for 13 VIPs, and HLA diversity. The highest allelic and phenotypic variability was observed in CYP2D6 , CYP2C19 , and CYP2B6 . A total of 663 ClinPGx annotations were identified, predominantly related to drug metabolism (50.38%) and toxicity (29.56%), involving psychotropic drugs, anticoagulants, statins, opioid analgesics, antineoplastic agents, and immunosuppressants. However, at least 32 drugs require assessment of non-coding pharmacogenetic variants or accurate CYP2D6 copy number determination – both beyond standard WES capability. Phased haplotype analysis demonstrated that haplotype-based imputation was feasible for only a limited subset of clinically relevant non-coding pharmacogenetic variants, whereas the majority lacked informative exonic proxies required for accurate inference from WES data. Conclusion: These findings represent one of the largest reference resource to date of pharmacogenetically significant variant and HLA allele frequencies in the Russian population. The results confirm WES as a robust and scalable platform for population-level pharmacogenomic screening and broader clinical genomic applications, while demonstrating that haplotype-based imputation cannot fully overcome the intrinsic limitations of exome sequencing for comprehensive pharmacogenomic profiling. Selection of genomic testing strategies should balance diagnostic completeness, analytical complexity, cost, scalability, and long-term potential for reanalysis.

Introduction: The application of pharmacogenomics (PGx) in pediatrics is limited by the lack of age-oriented interpretation approaches, as algorithms developed for adults do not account for ontogenetic changes in the activity of drug-metabolizing enzymes and transport proteins. The aim of this study was to evaluate the clinical applicability of pharmacogenomic data in Russian children, assess the concordance between genotype-based recommendations and the ontogenetic status of drug-metabolizing enzymes, and develop recommendations for the generation of age-oriented PGx reports. Methods: We analyzed whole-exome sequencing (WES) data from 524 pediatric patients and 635 newborns, filtering pharmacogenomic annotations according to PharmGKB/ClinPGx evidence levels (1A–2B) and the presence of the “Pediatrics” tag. The concordance between genotype-based recommendations and the ontogenetic status of drug-metabolizing enzymes was assessed in newborns. In a pediatric subgroup of 100 patients, a retrospective analysis of medical records was performed to evaluate the structure of pharmacotherapy and the frequency of adverse drug reactions (ADRs). A “PGx–ADR–cost” database was created, and the relative population burden index was calculated for 27 gene–variant–drug–ADR associations. Results: Clinically relevant annotations (requiring drug avoidance or dose modification) accounted for only 5% of all initial pharmacogenomic annotations in both cohorts; 67.6% (pediatric cohort) and 67.2% (neonatal cohort) of these were related to alleles with altered function. Concordance between genotype-based recommendations and the ontogenetic status of drug-metabolizing enzymes in newborns was observed in only 5 of 14 (35.71%) gene–drug pairs. ADRs were identified in 21% of the 100 pediatric patients; however, only two cases could be explained by high-evidence PharmGKB/ClinPGx annotations. Ranking by relative population burden identified UGT1A1*28 –irinotecan-induced neutropenia and HLA-A*31:01 –carbamazepine-induced severe cutaneous reactions as priority associations. Conclusions: Age represents a critical factor in the interpretation of pharmacogenomic data in children, as current approaches to PGx reporting do not adequately incorporate the ontogenetic context. We propose a pediatric PGx interpretation model that includes mandatory reporting of patient age, ontogenetic adjustment, evidence-level stratification, and multidisciplinary clinical assessment. Prospective validation is required to confirm the clinical utility of the proposed approach.

Adverse drug reactions (ADRs) remain a major public health issue, and genetic factors contribute importantly to interindividual variability in drug response. Pharmacogenetic testing helps reduce ADR risk by optimizing drug selection and dosage, particularly in monogenic disorders. Whole-exome sequencing of 6739 samples from the Russian population was performed on the DNBSEQ-G400 platform (MGI). Variants in 48 genes were examined, focusing on inherited arrhythmias, enzyme deficiencies (Glucose-6-Phosphate Dehydrogenase Deficiency [G6PDD], Porphyrias), Dravet Syndrome (DS) and Malignant Hyperthermia (MH). Variants reported as pathogenic (P), likely pathogenic (LP), or variants of uncertain significance (VUS) in ClinVar were manually re-evaluated using ACMG criteria. A total of 75 unique variants in 18 genes were observed in 119 individuals (1.77%), including 21 carriers and 13 women with a G6PD mutation. Of these, 44 variants were classified as P, 24 as LP, and 7 as VUS. Missense variants accounted for the largest proportion (73.33%). The most affected genes were KCNQ1 (24/119), which exhibited the highest number of unique variants (18), G6PD (20/119), SCN1A (15/119), and RYR1 (14/119). Regarding associated conditions, mutations linked to arrhythmias were found in 51 individuals, MH in 27, G6PDD in 20, DS in 15, and Porphyrias in 6. Integrating common and rare clinically actionable genetic variants with attention to penetrance and clinical validity may improve medication safety, reduce preventable ADRs, and enhance personalized pharmacotherapy.

Background/Objectives: AA amyloidosis is a serious complication of chronic inflammation, which may arise in the setting of inborn errors of immunity (IEIs) due to recurrent or persistent infections. Common variable immunodeficiency (CVID) is the most frequent symptomatic IEI in adults, yet its association with secondary AA amyloidosis remains rarely reported. Case presentation: We describe a 37-year-old male with a history of recurrent pneumonia, chronic sinusitis, and osteomyelitis with sepsis since childhood. At age 33, he developed bilateral pneumonia after COVID-19, followed by repeated lower respiratory tract infections. At age 36, nephrotic syndrome (proteinuria 10.69 g/day, hypoalbuminemia) led to kidney and gastric mucosa biopsies, which confirmed AA amyloidosis. Immunological workup revealed panhypogammaglobulinemia (IgG 0.1 g/L, IgA 0.01 g/L, IgM 0.28 g/L), markedly reduced switched memory B cells, and an inverted CD4⁺/CD8⁺ ratio. Chest CT showed bronchiectasis, bronchiolitis, and mediastinal lymphadenopathy. Whole-exome sequencing excluded known monogenic IEIs, autoinflammatory, or hereditary amyloidosis genes; a heterozygous likely pathogenic variant in ODAD2 (associated with primary ciliary dyskinesia) was considered incidental. A diagnosis of CVID with secondary AA amyloidosis was established. Conclusions: This case illustrates that CVID may remain undiagnosed for decades and present with secondary AA amyloidosis as the first major complication. In any patient with nephrotic syndrome and a history of recurrent or unusual infections, an IEI should be actively excluded. Early recognition of CVID and appropriate immunoglobulin replacement therapy can prevent infectious exacerbations and potentially halt amyloid progression.

This study evaluates primary template-directed amplification (PTA) for whole exome sequencing (WES) of small fibroblast cell groups, which mimics the limit

Background: The ACE Y215C mutation is a common, functionally damaging missense variant (~1.5% allele frequency) associated with reduced plasma ACE levels and increased Alzheimer’s disease (AD) risk. In CHO and HEK cell models, this mutation caused a ~3–6-fold decrease in ACE surface expression, soluble ACE levels, and ACE enzymatic activity compared to those of wild-type ACE. Methods: Circulating ACE levels and activity were measured in EDTA plasma obtained from 84 carriers of the ACE Y215C mutation using a set of mAbs to the ACE. The mAbs 5B3/1G12 binding ratio was revealed as a sensitive marker for the circulating Y215C ACE mutant. Whole-exome and whole-genome sequencing (WES/WGS) were performed to identify genetic variants potentially modifying circulating ACE levels. In parallel, published sequencing and proteomic data from 35,559 Icelanders participants were analyzed to identify genes influencing ACE shedding. Sequence comparison was performed between carriers with elevated and reduced ACE concentrations to identify the potential protective variants that may compensate for decreased ACE levels due to the Y215C mutation itself. Results: Most carriers of the Y215C ACE mutation demonstrated significantly decreased ACE levels (median is 62% of control ACE levels). However, substantial inter-individual variability was observed in plasma ACE activity among carriers. Comparative sequencing analysis revealed 9648 variants unique to individuals with elevated ACE, mapping to 5779 protein-coding genes and enriched for pathways related to intracellular and transmembrane transport. Conclusions: The presence of the damaging ACE mutation Y215C does not invariably result in low plasma ACE or, likely, elevated AD risk. Therefore, combined blood ACE phenotyping and whole-exome sequencing are recommended to more accurately assess ACE-related AD susceptibility in mutation carriers.

Damaging mutations of the Angiotensin I-converting enzyme (ACE) that result in low ACE levels may increase the risk of developing late-onset Alzheimer’s disease (AD). We quantified blood ACE levels in EDTA-plasma from 147 subjects with 23 different heterozygous ACE mutations (and 70 controls) and estimated the effect of these mutations on ACE phenotype, using a set of monoclonal antibodies (mAbs) to ACE and two ACE substrates. We identified several mutations in both ACE domains (including the most frequent ACE mutation, Y215C), which led to decreased ACE levels in the blood, and thus could be considered as putative risk factors for late-onset AD. The precipitation of several ACE mutants (Q259R, A725P, C734Y) by specific mAbs changed significantly, and therefore, these mAbs could be markers of these mutations. Analysis of 50 of the most frequent ACE mutations demonstrates that more than 1.5% of the adult population may have mutations which lead to decreased ACE levels, and thus, the role of low ACE levels in the development of AD may be underappreciated. Intriguingly, statistical and cluster analyses of longevity patients revealed trends towards higher frequency of cognitive impairment among affected individuals with damaging ACE mutations. Systematic analysis of blood ACE levels in patients with various ACE mutations identifies individuals with low blood ACE levels who may be at increased risk for late-onset AD. Patients with transport-deficient ACE mutations theoretically could benefit from therapeutic treatment with a combination of chemical and pharmacological chaperones and proteasome inhibitors, as was demonstrated previously on a cell model of the transport-deficient ACE mutation Q1069R. Moreover, clinical association analysis suggests a trend linking damaging ACE mutations with increased risk of cognitive impairment.

Introduction: Langerhans cell histiocytosis (LCH) is a rare clonal myeloid disorder characterized by tissue infiltration with pathological antigen-presenting cells morphologically and phenotypically similar to Langerhans cells. Activating mutations in the MAPK/ERK signaling pathway play a key role in the pathogenesis of LCH. The aim of this study was to characterize the morphological and molecular features of the neoplastic process. Materials and Methods: This study presents a clinical case of a 34-year-old patient with a rare mixed form of LCH combined with Erdheim-Chester disease (ECD), involving multiple organs including kidneys, skin, bones, ENT organs, eyes, and the central nervous system. The patient also had diabetes insipidus, chronic external otitis, and presumptive hereditary forms of anemia and hemochromatosis. A comprehensive histopathological evaluation was performed, including histochemical, immunohistochemical, and immunofluorescent analyses, alongside molecular genetic testing using whole exome sequencing (WES) of blood and skin samples. The patient demonstrated a partial clinical and laboratory response to targeted therapy with trametinib and desmopressin. Results: Comparison of WES data from blood and skin revealed 71,953 shared variants consistent with likely germline changes, as well as 3,081 unique somatic variants in skin and 2,633 unique variants in blood. Low-level mosaic BRAF V600E mutation (VAF = 1%) was detected in the skin, alongside pathogenic germline variants in the STEAP3 (c.523-2A>T, NM_182915.3) and SLC40A1 (c.332T>A, p.Met111Lys, NM_014585.6) genes. Immunofluorescence analysis of the trephine biopsy revealed diverse cellular populations, including sparse tryptase-positive mast cells, which showed minimal contact with each other or other labeled cells. The populations of Vimentin⁺CD11b^–CD34⁺ and Vimentin⁺CD11b⁺CD34^– cells (excluding endothelial cells) accounted for median values of 0.68% and 7.78%, respectively, of the total Vimentin⁺ cells. Regarding CD68 and S100 expression, CD68⁺ cells predominated (median = 55.61%), S100⁺ cells constituted a median of 43.02%, whereas CD68⁺S100⁺ cells were the rarest (median = 2.174%), reflecting the transition of Langerhans cells to LCH cells, encompassing up to 4.81% of the cellular population. This hybrid microenvironment paralleled the patient’s systemic inflammatory activity (elevated acute-phase reactants), multi-organ involvement, and renal interstitial fibrosis/tubular atrophy with reduced kidney function, without serological or histological evidence of vasculitis. Conclusion: This case illustrates the histological heterogeneity and hybrid pathology of mixed histiocytosis, where canonical dendritic LCH cells coexist with macrophage-rich ECD-like stroma. An integrated approach involving a multidisciplinary clinical team, thorough molecular genetic testing, and the application of targeted therapy is essential for improving prognosis and quality of life in young patients.

This study evaluates primary template-directed amplification (PTA) for whole exome sequencing (WES) on small fibroblast cell groups, mimicking the limited cell quantities typical of trophectoderm embryo biopsies. PTA’s consistent amplification reduces allelic dropout (ADO) and impoves uniform coverage, overcoming challenges associated with conventional methods such as multiple displacement amplification (MDA). Using fibroblast samples alongside well-characterised genomic references (E701, NA12878), we benchmarked PTA-WES, achieving 97.5% target region coverage at 10x, meeting American College of Medical Genetics and Genomics (ACMG) standards. Preliminary results from embryo biopsies sequenced with PTA-WES showed a median coverage of 102x, significantly improving upon the variability and coverage gaps observed in MDA-WES. The findings support PTA’s potential to enhance the clinical applicability of WES for preimplantation genetic testing for monogenic disorders (PGT-M), expanding capabilities to detect inherited and de novo mutations in embryos. Further optimisation and variant detection analyses are planned to evaluate PTA’s robustness for routine clinical use.