Whole genome sequencing

Tumor clones exhibit distinct genetic compositions of single nucleotide variants (SNVs) and insertions/deletions (indels). Intra-tumor heterogeneity plays a key role in cancer development. Tumor clones may have varying proliferative and metastatic potentials, for instance. This heterogeneity plays a key role in therapy resistance and the frequent lethal outcome of cancer.

Nuclei in 384-well plates are digested with NlaIII, after which the genomic fragments (following end processing) are ligated to barcoded adapters containing a unique molecular identifier (UMI), cell-specific barcode, and T7 promoter allowing linear amplification by in vitro transcription (IVT).

By enzymatically cutting the genomic DNA a well-defined sequencing start is obtained, which increases the overlap in coverage between individual cells. Other whole-genome single-cell sequencing methods that rely on random priming or random integration by transposases do not share this advantage. However, it is still very costly to sequence single-cell genomes for many cells. Single-Cell Core will therefore also provide a targeted-genome single-cell sequencing method by using bait oligos that can be used to enrich sequencing libraries for specific genomic regions. This helps us to enrich ~1000 genomic regions spanning about 1 Mb in total. This enrichment allows a 100-fold gain in sequencing depth and a corresponding 100-fold decrease in sequencing costs.