Biology subjects

Samitova, A.

Publications and source records attributed to Samitova, A..

3 recordsLinked to original sources

bioRxiv2024

PRECISE EXOME ANALYSIS OF BLASTOCYST BIOPSY SCALE SAMPLES USING PRIMARY TEMPLATE-DIRECTED AMPLIFICATION

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. PTAs 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 PTAs 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 PTAs robustness for routine clinical use.

genetics↗

bioRxiv2024

Experience in developing the human genome standard E701

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, 3842877 high confidence genomic variants were identified, which can be used as a standard for calculating statistical quality metrics while analyzing sequencing data. Furthermore, 9096 biallelic 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 1000X.

genomics↗

bioRxiv2024

Comparative evaluation of four exome enrichment solutions in 2024: Agilent, Roche, Vazyme and Nanodigmbio

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.

genomics↗