Evaluate transgene integrations and complex genomic landscapes with Xdrop™

Targeted enrichment of single molecules resolves complex genomic structures

Getting insights about precise integration pattern of non-host DNA, such as CRISPR gene editing, transgenes and different viruses, is of outmost importance to understand how the integrated material will impact the host cell. Integrations at unintended positions can interfere with host gene function either by integration inside a host gene and thus disrupt gene function; or into or around transcriptional start sites and thus affecting expression of host gene. Off-target integrations can also affect host cells by creating hotspots for cancer pre-disposition mutations and/or chromosomal rearrangements.

The ability to uncover complex genomics such as within plant hybrids as well as human somatic variations in e.g. HLA gene complex is a prerequisite to fully understand genotype phenotype correlations in plant and immunology research, respectively.

The current methods available are laborious, expensive and have low throughput. The Xdrop™ technology offers a quicker, more accurate and more affordable option to depict and understand complex genomic landscapes.

In a recent paper, we show that working with single molecules provided by the Xdrop™ platform enables resolving complex genomic structures with use of either downstream long read (Pacific Biosciences and Oxford Nanopore technologies) or short read (Illumina) sequencing.

In addition, the Xdrop™ enrichment technology only requires that the sequence of a few hundred bases is known within an otherwise unknown sequence context. This makes it possible to map viral integration sites in the host genome eliminating the requirement to carry out very deep whole genome sequencing and simplifying analysis.

The Samplix team has worked with researchers at Uppsala University to detect integration patterns of human papilloma virus HPV18 in the cervical cancer cell line HeLa. The integration pattern of HPV18 in human chromosome 8q24.21 is known to be extremely complex and a potential driver for cervical carcinoma. Considerable interest exists to understand the mechanisms and roles of viral integrations in mediating diseases such as cancer.

With Xdrop™ enrichment, targeting a small 99 bp of HPV18 viral sequence, we show that in HeLa cells, HPV18 is integrated into the human genome at three different sites of chromosome 8.

HPV18 figur web

Figure A. Resolving integration patterns of HPV18 virus in human HeLa cancer cell line. The HPV18 DNA (shown in green) was demonstrated to have three different integration patterns within human chromosome 8 (shown in blue) as indicated by the circled numbers on the panels. Top: viral integration sites; bottom: wildtype human reference chromosome 8.

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Single molecule enrichment