Description
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Genomic Proximity MappingTM (GPM): Characterize chromosomal abnormalities with unmatched specificity and sensitivity by Proximity Ligation Sequencing
- Genome-wide detection of chromosomal abnormalities in a single NGS-based assay
- A single NGS-based assay replacing karyotyping, FISH, and chromosomal microarrays, and offering better resolution
- Comprehensive cytogenetic information from a wide variety of sample types, including blood, cells, and tissue including low tumor fraction specimens, enabling new insights in oncology and genetic disease research
- Works with FFPE tissue sections for retrospective studies
- Identifies known and novel structural variants undetectable by other tools, including complex karyotypes and chromothripsis
- Detects additional CNV´s, inversions, translocations, disruptions
- Detects actionable gene fusions (ex. BCL-ABL, NTRK), Homologous Recombination Deficiency (HRD), and gene amplifications/deletions
- Identifies multiple breakpoints and translocation partners
- Scalable, fast, and cost-effective—no cell culture or dedicated instrumentation required
- Detects significantly more variants than Whole Genome Sequencing, whilst requiring >50x lower sequencing depth
- Integrated sample-to-report product including free cloud-based data analysis and visualization; no advanced NGS experience needed
Next Generation Cytogenetics with Genomic Proximity Mapping (GPM)
Powered by GPM, Phase Genomics´ CytoTerra® Cytogenetics Platform enables next-generation cytogenetics to characterize the breadth of chromosome abnormalities—with a single NGS-based assay.
The assay resolution is higher than karyotyping, FISH, and CMA combined, and the technology detects complex rearrangements, which are impossible to be called by Whole Genome Sequencing:
- Balanced translocations involving repetitive sequences
- Recurrent inversions with high sequence identity
- Low level mosaicisms
- Segmental duplications
- Stretches of loss of heterozygosity
Less Time. Less Resources. One Assay.
Phase Genomics´ proprietary library preparation method, combined with standard short-read sequencing at >50x lower sequencing depth compared to Whole Genome Sequencing, is used to map and measure the spatial relationship between any two loci across the full complement of chromosomes in a cell. Advanced computational tools extract this sequential information to detect genetic variation and characterize all major types of chromosomal abnormalities.
How it works:
Proximity ligation is used to trap short-, long-, and ultra-long-range intracellular DNA contacts (black arcs) from tissue, blood, or other sample types. Chimeric junctions originating from the same cell are recovered, converted into a short-read sequencing library, and subjected to paired-end sequencing. The proximity ligation signal increases as the genomic distance between any two loci across the genome decreases. AI-driven CytoTerra software extrapolates this unique information with a high degree of confidence, enabling the genome-wide detection of all major types of chromosomal abnormalities.
CytoTerra® Data: Assess all major structural variant classes in a single assay
Representative examples (visualizations) of different types of chromosomal abnormalities, including unbalanced, balanced, and complex rearrangements. The balanced translocation, unbalanced translocation, and inversion in the top row of the figure are indicated by specific patterns on a proximity interaction matrix and can be detected using computational tools in the CytoTerra Platform. Duplications, deletions, and aneuploidies (examples in the bottom row) are also detected by the CytoTerra Platform, and may be visualized using a coverage plotting script.
CytoTerra® Data: Publications
Yeung et al.: Evaluation of Acute Myeloid Leukemia Genomes using Genomic Proximity Mapping
CytoTerra® Curator: Integrated Bioinformatics for Easy Analysis
- Identify breakpoint calls (inversions, translocations, insertions, etc.) and regional calls (deletions, duplications, copy neutral loss of heterozygosity, ploidy number, etc.)
- Simultaneously view your sample’s data with control data to easily identify variants
- User-friendly platform – no previous bioinformatics experience needed
- Included with the CytoTerra Platform
When purchasing the Cytoterra Cytogenetics Platform Kit and Data Analysis Package, you get free access to CytoTerra Curator, which makes managing cytogenetic data simple – no prior bioinformatic knowledge is needed. Curator is a data curation platform that enables users to review, revise, and visualize data generated on the CytoTerra Platform. Once sequence data generated with the Hi-C kit is uploaded to the CytoTerra Platform cloud, it is processed by a suite of variant callers to generate callsets highlighting potential regions of chromosomal aberration. These callsets can be visualized and interacted with on Curator for review and report generation with a click of a button.
- Review: View variant calls generated on the CytoTerra platform and compare them to a control genome, allowing for easy interpretation of breakpoint and region variants.
- Revise: Generate your own callsets by utilizing Curator’s built-in tools to select regions of interest, annotate heat maps, and identify chromosomal aberrations.
- Report: Create publication-ready visualizations and reports from your selected callsets.
CytoTerra® Workflow
The CytoTerra Platform provides an NGS-based sample-to-report cytogenetics assay that starts with a crude pre- or post-natal sample, and ends with a comprehensive and actionable report in standard ISCN and sequence-based nomenclature. The entire process (depicted below) can be completed in less than five days and is scalable to large numbers of samples.
The CytoTerra workflow, from sample to report: A proximity ligation library is prepared from a biological sample. Paired-end sequencing is performed on the Illumina® platform. Fully automated, cloud-based analysis is performed with Phase Genomics’ proprietary computational tools.