Whole Genome Sequencing

Selexis offers cell bank clonality assurance by applying whole genome sequencing: the "Comprehensive Genomic Analysis"

The U.S. Food & Drug Administration (FDA) has established guidelines for characterizing mammalian cell banks to address two key issues:

  • Defining the identity of the cell bank phenotypically and genotypically
  • Ensuring the purity of the cell bank so that it is free of contaminating cell lines and adventitious agents, such as viruses and mycoplasma

With the availability of whole-genome sequencing (WGS) technologies, it is now possible to examine these issues with speed, accuracy, and sensitivity that cannot be addressed through traditional methods, such as PCR, FISH, and Southern blot. When entire genomes are sequenced, the data that are generated are unbiased compared with those from fragmented genomic DNA and even RNA, resulting in more accurate information when the appropriate bioinformatics tool is used.

WGS requires sophisticated computational capabilities and scientific expertise to comprehensively analyze and interpret data from fully sequenced genomes. Selexis, in collaboration with the University of Lausanne and the Swiss Institute of Bioinformatics, was one of the first private organizations to sequence and annotate the genome of its parental CHO-K1 cell line (completed in 2011). The combination of the sequenced and annotated CHO-K1 genome with proprietary bioinformatics tools is the pillar of the SUREscan technology. Today, SUREscan is used to generate comprehensive regulatory data packages around master cell banks.

With SUREscan, Selexis can determine the integrity of gene sequences, the integration sites, the gene copy number, and mutations in other genes that affect cell line stability and productivity with much greater confidence. Finally, SUREscan can be used to determine whether a master cell bank (MCB) or a working cell bank (WCB) is clonal by analyzing the integration sites or by examining at the fixation of single-nucleotide variants (SNVs) into single nucleotide polymorphisms (SNPs). More importantly, such a data package also supports manufacturing campaigns by providing baseline reads of WCBs that can be tracked for clonal drift, potential mutations, and potential viral contamination during manufacturing runs.

High-quality MCBs are critical for successful and cost-effective biologic manufacturing campaigns and regulatory filings, such as INDs and BLAs. A thorough genomic assessment is key to validating MCB integrity, clonality, and stability. Selexis’ SUREscan is a comprehensive technology that provides unparalleled data packages for MCB validation and reduces regulatory and manufacturing risks. It provides a unique method of “barcoding” a clonal cell line, thus tracing all of the processes that are related to it.