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Shmitko, A.

Publications and source records attributed to Shmitko, A..

3 recordsLinked to original sources
bioRxiv2022

DESIGNING OF CUSTOM BARCODES FOR SEQUENCING ON THE MGI PLATFORM

The recently launched MGI platform (DNBSEQ-G50, -G400 and -T7 sequencers) has been gaining popularity for next-generation sequencing. However, the barcode set for library preparation provided by the manufacturer has certain limitations on the number of samples that can be sequenced at a time and the compatibility of barcodes from different or incomplete sets as well as a ratio between the samples. In this paper, we present a protocol for designing custom barcodes expanding the pre-existing barcode set and demonstrate its performance on the MGI Tech Co. Ltd. (China) machines. We developed a universal "quad method" which allows for simultaneous sequencing of any number of samples up to 252 per lane which is multiple of 4 or 4n+2. Here, we describe this method, its analysis, verification, and integration into the sequencing as well as its validation for sequencing using the DNBSEQ G-400 machine.

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↗