Traditionally, Southern blot analysis is the method of choice to satisfy FDA’s requirements of charactering cell line genetic stability. Avance Biosciences is now offering two NGS approaches to analyze the transgene insertion sites.
The first approach performs whole genome sequencing on gDNA extracted from the cell line of interest. Illumina’s PCR-free method is used for library preparation with the sequencing performed on a HiSeq. The paired-end sequencing reads generated are analyzed using a proprietary NGS analysis pipeline involving multiple rounds of mapping and assembly to elucidate the insertion junctions. The main advantages of this approach are that a reference genome sequence is not required and this method can be easily validated.
The second approach involves ligation of an adaptor followed by a nested PCR to pull down sequence fragments with insertion junctions. Sequencing can be performed on an Illumina’s MiSeq, and the paired-end sequencing reads analyzed to identify insertion junctions. The main advantage is that many samples can be analyzed easily once the assay is established. This method does require knowledge of the host genome sequence.