Tag: cytogenetics

A Year in Review: 2024

Posted on December 19, 2024 by - Cytogenomics, Genomics, Hi-C, Metagenomics

image of microscope and dna with Phase Genomics logo

 

Phase Genomics continues to pioneer genomic innovation, driving advancements in human health and life science research over another impactful year. Our efforts range from developing novel tools for detecting chromosomal abnormalities to managing the world’s most extensive phage-host interaction atlas, thereby accelerating genomic research and promoting a healthier future.

Our ultra-long-range sequencing technology is fostering advancements across a wide array of research applications, both at Phase Genomics and in laboratories worldwide. Utilizing our microbial platform, we are driving transformative discovery in metagenomics and ecology while making bounds in human health with cutting-edge approaches to antimicrobial research and oncology.

Thank you to our supporters, collaborators, and clients for their contributions to making this an outstanding year. Here are some key highlights from 2024.

 

Insights in oncology

This year, our cytogenetic platform uncovered novel, clinically-relevant chromosomal aberrations critical for assessing patient care in oncology. Genomic Proximity Mapping™ (GPM) is an upgraded approach to cytogenetic analysis – meeting and  surpassing current risk stratification assessments. Over the summer, researchers at Fred Hutchinson Cancer Center and University of Washington Medical Center published research that used GPM to analyze 48 patient samples, identifying known and novel chromosomal aberrations. Read the MedRxiv preprint to discover the expanding possibilities in leukemia research here » image of DNA

 

Cow burps, super bugs, and our enemy’s enemy–phages

We are actively developing solutions to address the growing threat of antimicrobial resistance and in the same stroke, advancing environmental health efforts with lysin discovery. By leveraging metagenomic data and AI, scientists can harness the evolutionary power of bacteriophages to target and eliminate harmful microbial pathogens with precision. Discover how we are turning the tables using our antimicrobial discovery platform with support from the Bill & Melinda Gates Foundation in our blog here »

 

A novel approach to vaccination

Phase Genomics’ metagenomic deconvolution technology helped crack the code on a potential new vaccine for farmed salmon to defend against sea lice by targeting the parasite’s microbiome. Published in The Economist, researcher Cristian Gallardo Escárate shares results that led to the creation of the groundbreaking invention that could ease global environmental impacts of salmon farming. More here » image of a salmon

Diving into the data 

Two new data analysis tools were made available to ProxiMeta and CytoTerra platform users this year: ProxiMeta™ Explorer and CytoTerra® Curator.  

ProxiMeta™ Explorer is an interactive, cloud-based genome-resolved metagenomic analysis platform for data visualization and exploration. The platform provides fully customizable analyses and reports for tracking genomes across time, conditions, groups, and more with a click of a button. 

CytoTerra® Curator enables users to effortlessly review, revise, and generate reports from cytogenetic data – no prior bioinformatics experience required. From curating calls to constructing circos plots, Curator provides fast, accurate insights for human genomics and oncology research.

 

Tune in to this year’s podcasts

Listen to Phase Genomics CEO, Ivan Liachko, discuss the breadth of applications supported by Phase Genomics’ ultra-long-range sequencing technology in these podcast episodes. Discover the story behind commercializing and implementing biotech innovations and get a glimpse at where this technology is taking us. 

 

Looking Forward

In 2025, we aim to elevate our technology to new heights and broaden our impact across science and medicine. We hope you will follow us on our journey on X, LinkedIn, and BlueSky as we lead genomics innovation to an insightful and healthy future. 

 

Happy New Year from our team at Phase Genomics!

 

 

Phase Genomics Highlights New Data Showcasing the Power of CytoTerra® to Extend Next-generation Cytogenetics to Solid Tumor Cancers with Genomic Proximity Mapping™

Posted on November 23, 2024 by - Uncategorized

circos plot and chromosome

 

The study presented at the 2024 Association for Molecular Pathology annual meeting underscores the ability of Genomic Proximity Mapping (GPM) for novel biomarker discovery in metastatic head and neck squamous cell carcinoma

 

SEATTLE – November 23, 2024 –Phase Genomics, Inc., a leading innovator at the forefront of genomic technology development, today announced new data demonstrating the capability of AI-powered Genomic Proximity Mapping™ (GPM) to to identify clinically actionable genomic aberrations  in head and neck squamous cell carcinoma (HNSCC). The study characterized primary tumors from metastatic and non-metastatic disease to identify potential biomarkers for the early indication of targeted therapeutic intervention in pre-metastatic HNSCC.

 

Brain metastasis (BM) is a particularly deadly and poorly understood secondary site in HNSCC. In this study, Phase Genomics’ Genomic Proximity Mapping platform, CytoTerra, extended high-resolution cytogenetic analysis to BM and non-BM HNSCC stored as formalin-fixed, paraffin-embedded samples (FFPE). CytoTerra identified BM-specific structural alterations in known and targetable oncogenes in primary tumors that were previously undetected in these samples. This analysis suggests early candidate biomarkers for future investigation to indicate novel treatment strategies in advance of aggressive secondary CNS lesions. 

 

“We are extending the horizon of discovery in oncology by unlocking new types of information for solid-tumor cancers with Genomic Proximity Mapping. It’s time to understand the full topography of the genetic map for solid tumors with next-generation cytogenetics,” said Ivan Liachko, PhD, co-founder and CEO of Phase Genomics. “Not only does GPM identify structural variants at higher resolution than current cytogenetics, our platform is a faster and simpler solution that replaces multiple tools with a single, quantitative, NGS-based assay.”

 

Traditional cytogenetics relies on a battery of mostly visual tests to identify large-scale chromosomal alterations, including karyotyping, fluorescence in situ hybridization (FISH) and chromosomal microarrays (CMA). While these tests have been integrated into care in hematology oncology for decades, current cytogenetic diagnostics are typically not amenable to solid-tumor cancers stored as FFPE, such as HNSCC. Standard next-generation sequencing panels used in HNSCC often fail to identify structural rearrangements captured  by cytogenetics.

 

In this newly published analysis, CytoTerra identified structural rearrangements that did not disrupt the coding gene sequences in metastatic HNSCC and were thus undetected by standard panel sequencing. Notable rearrangements involving the  JAK1 and EGFR loci were observed in BM HNSCC samples, as well as a novel NRG1::FAM110B fusion. These alterations were not observed in non-BM HNSCC samples, suggesting novel biomarkers of metastatic disease for future investigation. 

 

In another recent study published in Translational Medicine, investigators used GPM to characterize the tumor immune microenvironment for HNSCC BM lesions. While the majority of BM samples were enriched for HPV signature, analyses showed a lack of PD-L1 expression. GPM data identified gene alterations and large chromosomal changes with corresponding FDA-approved targeted therapies in other solid-tumor cancers. 

 

“This next-generation cytogenetic approach offers new insights into the evolution of metastatic disease, offering a path to validate early biomarkers indicative of aggressive cancer,” said Ida Deichaite, PhD, assistant adjunct professor of radiation medicine and applied science at UC San Diego and director of industry relations at UCSD’s Moores Cancer Center. “The speed, efficiency and depth of insight gained from the GPM-based platform mark a critical advancement in our tooling and position it as a potential cornerstone for future translational research in the solid tumors, like this aggressive HNSCC.” 

 

Phase Genomics shared additional insights into CytoTerra for primary and metastatic HNSCC in poster ST091, “Discovery of Biomarkers of Brain Metastasis using Genomic Proximity Mapping (GPM) on Formalin-Fixed Paraffin-Embedded Head and Neck Squamous Cell Carcinomas.” Discover more about next-generation cytogenetics powered by GPM for solid tumor cancers and connect with the Phase Genomics team at booth 1029. 

 

CytoTerra is available for research use only and is not for use as a clinical diagnostic.

 

Follow Phase Genomics on LinkedIn and X for the latest company news and information.

 

About Phase Genomics

Phase Genomics applies proprietary ultra-long-range genome sequencing technology to enable genome assembly, microbiome discovery, as well as analysis of genomic integrity and chromosomal aberrations. In addition to a comprehensive portfolio of laboratory and computational services and products, including reagent kits and genomic services, they also offer an industry-leading genome and metagenome assembly and analysis software.

Based in Seattle, WA, the company was founded in 2015 by a team of genome scientists, software engineers, and entrepreneurs. The company’s mission is to empower scientists with genomic tools that accelerate breakthrough discoveries.