Handpicking extrachromosomal DNA

CRISPR catches extrachromosomal DNA

CRISPR-CATCH is a method that facilitates isolation of extrachromosomal DNA containing oncogenes from human cancer cells.

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  • It has been 25 years since the release of GATTACA, a film that tells the story of a credible near future in which society’s inequalities, formerly associated with race and class, have been replaced with new prejudices based on genetic determinism. Here we compare GATTACA’s fictional technologies with reality’s state of the art, assessing the legal protections afforded in today’s society against GATTACA’s dystopian future in which personal freedom and privacy rights are substantially curtailed by genomic innovations. We further discuss how GATTACA’s prescient forewarnings are still relevant today in light of the current trajectory of genomic science and technology.

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  • High-throughput experimental platforms have revolutionized the ability to profile biochemical and functional properties of biological sequences such as DNA, RNA and proteins. By collating several data modalities with customizable tracks rendered using intuitive visualizations, genome browsers enable an interactive and interpretable exploration of diverse types of genome profiling experiments and derived annotations. However, existing genome browser tracks are not well suited for intuitive visualization of high-resolution DNA sequence features such as transcription factor motifs. Typically, motif instances in regulatory DNA sequences are visualized as BED-based annotation tracks, which highlight the genomic coordinates of the motif instances but do not expose their specific sequences. Instead, a genome sequence track needs to be cross-referenced with the BED track to identify sequences of motif hits. Even so, quantitative information about the motif instances such as affinity or conservation as well as differences in base resolution from the consensus motif are not immediately apparent. This makes interpretation slow and challenging. This problem is compounded when analyzing several cellular states and/or molecular readouts (such as ATAC-seq and ChIP–seq) simultaneously, as coordinates of enriched regions (peaks) and the set of active transcription factor motifs vary across cell states.

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