The Tapestri Genome Integrity CNV Solution enables the assessment of genome-wide copy number variants (CNVs) across 1000s of cells at a resolution of 5-15Mb, comparable to g-banding. 

The solution consists of Tapestri core kit reagents, the Tapestri Single-Cell DNA Genome-Wide CNV Panel comprising 500 validated amplicons that tile nearly the entire genome (Fig 1), and analytical software.

Figure 1. The Tapestri® Single-Cell DNA Genome-Wide CNV Panel contains 500 amplicons (91.15 kb) that tile the entire human genome (except the y chromosome) and provides CNV information at 5-15 Mb resolution. 

This powerful solution can be used for several purposes, as outlined below:

1. Genome integrity analysis of genome-edited cells

Although genome editing has opened the door to innovative ways of constructing advanced therapeutics, we know that double-strand breaks (DSBs) caused by CRISPR and other genome editors can have unwanted side effects. If not repaired properly, these breaks can result in large CNV events around the cut sites in the genome. 

It is now possible to co-analyze genome-editing targets (on- and off-targets), predicted translocations, and genome integrity in the same cells. For instance, if you have a sample of triple-edited cells, you can assess the CNV signature in the edited vs non-edited cells, or cells with different editing patterns.

The genome integrity algorithm is integrated into the Tapestri® Genome Editing Software. If you want to co-measure gene editing targets and genome integrity you will need to combine the Single-Cell DNA Genome-Wide CNV Panel with a custom panel containing your GE targets.

For information on combining two panels, see this support article.

It is also possible to co-analyze cell-surface proteins in GE+GI projects for those who want to assess immunophenotypic signatures or confirm gene knockouts at the protein level.  

2. Genome integrity analysis of human pluripotent stem cells 

Human pluripotent stem cells (e.g., iPSCs, ESCs) are widely used for regenerative medicine and are the starting material for promising allogeneic cell therapies. However, stem cells are susceptible to genomic alterations, particularly during reprogramming, expansion, and differentiation. Testing for genome integrity is recommended for starting materials, in-process controls, and cell banks. 

The Tapestri® Genome Integrity CNV Solution is a convenient assay that can evaluate gross genome-wide CNVs at a much higher throughput than conventional g-banding (1000s of cells instead of 20-100) and reports distinct clones containing CNVs instead of an averaged CNV measurement in the entire sample. For more information about the assay performance, please see the Genome Integrity FAQ support article.

For a more thorough assessment of hPSCs we also offer the Human Pluripotent Stem Cell CNV Panel, which can be co-analyzed with the Genome-Wide CNV Panel. This panel contains 47 amplicons that, when combined with the Genome-Wide CNV Panel, cover 76.2% of structural variants recurrent in hPSCs.1 Together, these two panels comprehensively evaluate hPSCs for better safety assessments of stem cell-based therapeutics.

It is possible to design a custom panel with SNVs and smaller CNVs (up to 1 kb) to combine with the Genome-Wide CNV Panel. For information on combining two panels, see this support article.

The Tapestri Single-Cell Genome Integrity CNV Software enables easy analysis of unmodified stem cells (i.e., not gene-edited) for cases when the genome-wide CNV panel is used alone or combined with other SNV or CNV targets.

3. Genome integrity analysis of tumors

The presence of genomic alterations, whether small (SNVs, indels) or large (SVs) is a hallmark of cancer. More light is being shed on the importance of whole and sub-chromosome aneuploidy to understanding cancer onset, evolution, and resistance to therapies..2,3  Whole genome sequencing and other bulk technologies report averaged readouts of CNV signatures, but do not resolve the CNV-based clonal heterogeneity of tumors.

By assessing single cells, the Tapestri® Genome Integrity CNV Solution identifies individual CNV-based clones — enabling a deeper understanding of tumor evolution and treatment response. A better understanding of such heterogeneity is critical given recent evidence that aneuploidy has clinical relevance as a prognostic marker, may guide patient stratification, and may even serve as a therapeutic target.

For those who do not require an assessment of CNVs across the entire genome, it is possible to construct a custom panel using a subset of amplicons in the Genome-Wide CNV panel to target specific chromosomes or regions. The advantage of this approach is that the amplicons in the Genome-Wide CNV panel have been validated, so there is more assurance that they will amplify evenly than if one were to design new amplicons and not test them. Custom panels containing a subset of the Genome-Wide CNV panel amplicons can be analyzed using the Genome Integrity analysis software. 

References:

1. Assou, S. et al. 2020. Recurrent Genetic Abnormalities in Human Pluripotent Stem Cells: Definition and Routine Detection in Culture Supernatant by Targeted Droplet Digital PCR. Stem Cell Reports. doi: 10.1016/j.stemcr.2019.12.004

2. Sansregret, L. and Swanton, C. 2017. The Role of Aneuploidy in Cancer Evolution. Cold Spring Harb Perspect Med. doi: 10.1101/cshperspect.a028373
   
   
3. Ben-David, U. and Amon, A. 2019. Context is everything: aneuploidy in cancer. Nature Reviews Genetics. doi: 10.1038/s41576-019-0171-x