The first Russian human genome standard E701 was developed through a collaborative research involving four laboratories: Pirogov Russian National Research Medical University, National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V.I.Kulakov, National Research Center Kurchatov Institute, and National Medical Research Radiological Centre. Whole-genome sequencing of short reads on various platforms (MGI Tech, Illumina) and alignment to the reference human genome GRCh38.p14 were performed for the E701 sample. Subsequently, 3842 877 genomic variants were identified, which can be used as a standard for calculating statistical quality metrics while analyzing sequencing data. This variant set was additionally filtered by the GIAB high-confidence regions version 4.2.1, yielding 3262 154 variants. Moreover, E701 sample has undergone multiple whole-exome sequencing using five different enrichment panels for exome–genome concordance analysis. Furthermore, 9096 bi-allelic variants were identified on the autosomes and the X chromosome, with a minor allele frequency exceeding 0.4. Additionally, mitochondrial DNA sequencing was performed with the breadth of coverage over 99.9% at 1000×.

Auditory neuropathy spectrum disorder (ANSD) is often missed by standard hearing tests, accounting for up to 10% of hearing impairments (HI) and commonly linked to variants in 23 genes. We assessed 122 children with HI, including 102 with sensorineural hearing loss (SNHL) and 20 with ANSD. SNHL patients were genotyped for common GJB2 variants using qPCR, while ANSD patients underwent whole exome sequencing, with variants analyzed across 249 genes. Homozygous GJB2 variants were found in 54.9% of SNHL patients. In 60% of ANSD patients, variants were detected in OTOF (25%), CDH23, TMC1, COL11A1, PRPS1, TWNK, and HOMER2 genes, including eight novel variants. Transient evoked otoacoustic emissions testing revealed differences at 4000 Hz (p = 0.0084) between the ANSD and SNHL groups. The auditory steady-state response (ASSR) test showed significant differences at 500 Hz (p = 2.69 × 10⁻⁴) and 1000 Hz (p = 0.0255) compared to pure-tone audiometry (PTA) in ANSD patients. Our questionnaire shows that the parents of children with SNHL often report an improved quality of life with hearing aids or cochlear implants, while parents of children with ANSD frequently experience uncertainty about outcomes (p = 0.0026), leading to lower satisfaction.

Whole exome sequencing (WES) is essential for identifying genetic variants linked to diseases. This study compares available to date four exome enrichment kits: Agilent SureSelect Human All Exon v8, Roche KAPA HyperExome Probes, Vazyme VAHTS Target Capture Core Exome Panel, and Nanodigmbio NEXome Plus Panel v1. We evaluated target design, coverage statistics, and variant calling accuracy across these four different exome capture products. All kits showed high coverage completeness, with mean x10 coverage exceeding 97.5% and x20 coverage above 95%. Roche exhibited the most uniform coverage, indicated by the lowest fold-80 scores, while Nanodigmbio had more on-target reads due to fewer off-target reads. Variant calling performance, evaluated using in-lab standard E701 DNA sample, showed high recall rates for all kits, especially Agilent v8. All kits achieved an F-measure above 95.87%. Nanodigmbio had the highest precision with the fewest false positives but a slightly lower F-measure than other kits. This study also highlights the performance of new Chinese solutions from Vazyme and Nanodigmbio, which were comparable to Agilent v8 and Roche KAPA kits. These findings assist researchers and clinicians in selecting appropriate exome capture solutions.

Background: Auditory Neuropathy Spectrum Disorder (ANSD) is often missed by common hearing screening tests, still accounting for up to 10% of hearing impairments. ANSD has an underlying genetic factor being mostly caused by pathogenic variants in 13 genes. Methods: We examined 122 children with impaired hearing, including 102 pediatric patients (mean age was 3.7±4.1 years) with sensorineural hearing loss (SNHL) of varying severity and 20 children with a clinically confirmed ANSD (mean age was 5.65±4.63 years). For children with SNHL, we genotyped the most frequent variants (c.35delG, c.167delT, c.235delC, c.313-326del14 and c.358-360delGAG) in the GJB2 gene using quantitative PCR. For children with a clinically confirmed ANSD, we performed the whole exome sequencing and studied the obtained variants in a custom panel of 248 genes. Results: Our findings show that fifty-six (54.9%) SNHL patients carried homozygous variants in GJB2 gene. In 12 (60%) ANSD patients, we detected variants in nucleotide sequences of the OTOF (25%), CDH23, TMC1, COL11A1, PRPS1 and HOMER2 genes (8 of which had not been previously described). Transient Evoked Otoacoustic Emissions testing revealed differences at 500 Hz (AS, p = 0.04181) and 4000 Hz (AD, p = 0.00126) between the ANSD and SNHL patient groups. The Auditory Steady-State Response (ASSR) test demonstrated significant differences at all frequencies (p < 0.01). When comparing the results obtained from the pure-tone audiometry and ASSR tests in ANSD patients revealed statistically significant differences at 500 (AD, AS) and 1000 (AD) Hz. Conclusions: These findings indicate that audiologists and otorhinolaryngologists should use the ASSR test in clinical practice for differential diagnosis of auditory neuropathies. According to the survey data from the parents of hearing-impaired children, rehabilitation was more successful in SNHL patients compared to ANSD patients.

Using Escherichia coli BW25113 as a host, we isolated a novel lytic phage from the commercial poly-specific therapeutic phage cocktail Sextaphage^® (Microgen, Russia). We provide genetic and phenotypic characterization of the phage and describe its host range on the ECOR collection of reference E. coli strains. The phage, hereafter named Sxt1, is a close relative of classical coliphage T3 and belongs to the Teetrevirus genus, yet its internal virion proteins, forming an ejectosome, differ from those of T3. In addition, the Sxt1 lateral tail fiber (LTF) protein clusters with those of the phages from the Berlinvirus genus. A comparison of T7, T3, and Sxt1 LTFs reveals the presence of insertions leading to the elongation of Sxt1 tail fibers, which, together with the difference in the HRDRs (host range-determining regions), might explain the expanded host specificity for the Sxt1.

Disorders of sex development (DSD) represent a group of congenital conditions in which there is a discrepancy between the chromosomal and (or) gonadal sex and the structure of the genitals. Within the DSD there is a subgroup of 46,XX testicular DSD (46,XX TDSD), which may be caused by the translocation of the SRY gene, and more rarely — due to other causes (SRY-negative forms). In this report, we present an observation of a patient with SRY-negative 46,XX TDSD, in whom the condition was initially regarded as a virile form of congenital adrenal hyperplasia, then as idiopathic intrauterine virilization in a girl. Due to the development of virilization at the age of 11, the presence of testicular tissue was suspected. Molecular genetic analysis (whole exome sequencing with Sanger validation) revealed a de novo variant in exon 9 of the WT1 gene (chr11:32413528T>C), which, according to predictions, did not lead to a change in the amino acid sequence (p.Thr479=, NM_024426.6), but disrupted splicing, resulting in a previously described in 46,XX TDSD a change in the C-terminal domain of WT1. After verification of the diagnosis, a gonadectomy was performed and estrogen replacement therapy was prescribed. Thus, we have described a patient with a rare form of 46,XX TDSD caused by a variant in the WT1 gene. The presented observation illustrates the difficulties of differential diagnosis of intrauterine virilization syndrome in female karyotype.