Biology subjects

Cheranev, V.

Publications and source records attributed to Cheranev, V..

3 recordsLinked to original sources

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↗

bioRxiv2022

Residual DNA in enzymes may pose a challenge for DIY RNA sequencing protocols: how to deal

High-throughput RNA sequencing (RNA-seq) is widely employed for gene expression profiling. This report on do-it-yourself RNA-Seq library preparation pitfalls, highlighting their correct identification and successful overcoming, may be helpful to research groups commencing a DIY RNA-Seq workflow and facing similar problems.

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↗