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Rebrikov, D.

Publications and source records attributed to Rebrikov, D..

7 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↗
bioRxiv2022

Performance Comparison Of Agilent New SureSelect All Exon v8 Probes With v7 Probes For Exome Sequencing

Exome sequencing may become routine in health care it increases the chance of pinpointing the genetic cause of an individual patients condition and thus making an accurate diagnosis. It is important for facilities providing genetic services to keep track of changes in the technology of exome capture in order to maximize throughput while reducing cost per sample. In this study, we focused on comparing the newly released exome probe set Agilent SureSelect Human All Exon v8 and the previous probe set v7. In preparation for higher throughput of exome sequencing using the DNBSEQ-G400, we evaluated target design, coverage statistics, and variants across these two different exome capture products. Although the target size of the v8 design has not changed much compared to the v7 design (35.24 Mb vs 35.8 Mb), the v8 probe design allows you to call more of SNVs (+3.06%) and indels (+8.49%) with the same number of raw reads per sample on the common target regions (34.84 Mb). Our results suggest that the new Agilent v8 probe set for exome sequencing yields better data quality than the current Agilent v7 set.

genomics↗
bioRxiv2021

SYSTEM ANALYSIS OF THE SEQUENCING QUALITY OF HUMAN WHOLE EXOME SAMPLES ON BGI NGS PLATFORM

Human whole exome sequencing (WES) is now the standard for most medical genetics applications worldwide. The leaders are manufacturers of enrichment kits that base their protocols on a hybridization approach using cRNA or cDNA biotinylated samples specific to regions of interest in the genome. Recently, platforms from the Chinese company MGI Tech have been successfully promoted in the markets of many countries in Europe and Asia. There is no longer any question about their reliability and the quality of the data obtained. However, very few task-specific kits for WES, in particular, are presented for these sequencers. We have developed our solution for library pre-capture pooling and exome enrichment using Agilent probes. In this work, we demonstrate on a set of standard benchmark samples from the Platinum Genome Collection that our protocol, called "RSMU_exome", is superior to the kit from MGI Tech in qualitative and quantitative terms. It allows detecting more SNVs and CNVs with superior sensitivity and specificity values, generates fewer PCR duplicates, allows more samples to be pooled in a single enrichment, and requires less raw data to produce results comparable to the MGI Tech solution. Also, our protocol is significantly cheaper than the kit from the Chinese manufacturer.

genomics↗
bioRxiv2020

Runcer-Necromancer: A Method To Rescue Data From An Interrupted Run On MGISEQ-2000

During the sequencing process, problems can occur with any device including the MGISEQ-2000 (DNBSEQ-G400) platform. We encountered a power outage that resulted in a temporary shutdown of a sequencer in the middle of the run. Since barcode reading in MGISEQ-2000 takes place at the end of the run, it was impossible to use non-demultiplexed raw data. We decided to completely use up the same cartridge with reagents and flow cell loaded with DNB and started a new run in a shortened custom mode. We figured out how the MGISEQ-2000 converts preliminary data in .cal format into .fastq files and wrote a script named "Runcer-Necromacer" for merging .fastq files based on the analysis of their headers (available online: https://github.com/genomecenter/runcer-necromancer). Read merging proved to be possible because the MGISEQ-2000 flow cell has a patterned structure and each DNB has invariable coordinates on it, regardless of its position on the flow cell stage. We demonstrated the correctness of data merging by comparing sample analysis results with previously obtained .fastq files for them. Thus, we confirmed that it is possible to restart the device and save both parts of the interrupted run.

bioinformatics↗