ARIMA Genomics, Inc., a biotechnology company focused on accelerating the adoption of genome structure information toward medical research, diagnosis and therapy, has announced the full commercial launch of the HiChIP application built on its existing Arima-HiC platform.
With this launch, researchers can now obtain long-range chromatin interactions specifically enriched at genomic locations occupied by proteins of interest from a single experiment, enabling speed to discovery and publication with reduced costs.
This public launch brings to a close successful market development and beta testing programmes that yielded further proof of market need, improved product performance with enhanced quality control, and delivered valuable feedback from customer validations. “We are very pleased with the data obtained with the Arima HiChIP protocol,” said Tamas Ordog, Professor of Physiology
at Mayo Clinic.
“The results show great reproducibility and excellent overall quality, and the kit saves time and sequencing cost. We particularly value the straightforward quality control steps and the ease of use – overall, Arima HiChIP is of great value.” Key opinion leader Peter Scacheri, Professor at Case Western University and Member of the Case Comprehensive Cancer Center, stated, “We are pleased with the informative nature and quality of the Arima-HiChIP data.”
HiChIP data can inform mechanistic underpinnings of gene regulation and how it eventually leads to a disease state. Enriching for active chromatin features through H3K27ac or H3K4me4 HiChIP enables our discovery of high-resolution chromatin looping events that facilitate gene control in muscle stem cells during the transition from a state of quiescence to their commitment toward differentiation into regenerating myofibers, during muscle regeneration in healthy conditions, aging or diseases such as muscular dystrophies,” said Lorenzo Puri, Professor, Development, Aging and Regeneration Programme at Sanford Burnham Prebys Medical Discovery Institute.
Recognizing the value of HiChIP and in the absence of commercially validated kits, the scientific community had been home brewing this biochemistry. “We have been home brewing HiChIP because it provides critical insights that were previously obtained by performing separate HiC and ChIP-Seq experiments,” said Yin Shen, Assistant Professor at University of California, San Francisco, who studies the genetics of Neuropsychiatry.
“Arima-HiChIP generated superior data quality and reproducibility even with our most challenging terminally differentiated neuronal samples, where our homebrew version previously failed, thus saving us from substantial repeat costs.”
Feedback and data generated by early customers also helped to understand the positioning of HiChIP in the context of related assays such as HiC and ChIP-Seq. In particular, while HiC reflects the global framework of genome organization, HiChIP enriches for targeted chromatin interactions originating from specific genomic locations of research interest. Depending on the requirements of the study, a researcher can leverage comprehensive HiC, finer resolution HiChIP, or, both.
“The combined analysis of this HiChIP data with our genome-wide HiC data is pivotal to our understanding of both the broader compartmentalization and topological frameworks that influence gene regulation, but also the finer resolution connections between specific cis-regulatory elements, added Puri.
Importantly, because the chromatin interaction data from HiChIP reflect the inherent folding (and misfolding) of the genome in three-dimensions, this can also inform aspects of misregulated genes on a rearranged cancer chromosome – critical insights missed from traditional ChIP-Seq experiments.
“Not only do we observe intra-chromosomal cis-regulatory interactions across cancer genomes, but also inter-chromosomal ectopic cis-regulatory interactions on rearranged chromosomes. We think this data will help better delineate the relationship between genetic and epigenetic driver events in cancer,” added Scacheri.
In response to customer needs for data analysis, the company collaborated with academic partners to optimize community-validated open-source bioinformatics tools such as MAPS. The Arima MAPS pipeline automatically outputs easily understandable quality control statistics and upon user’s push-button to proceed, it generates chromatin interaction heatmaps and arc plots to be readily visualized in genome browsers. In addition to the streamlined data analyses, the company’s focus to enhance customer service and support experience is part of its sustained efforts to expedite sample-to-discovery and publication.
“The Arima Technical Support Team has been outstanding,” added Ordog.
The company has developed HiChIP on its existing Arima-HiC platform to enable both HiC and HiChIP from one universal Arima kit. Additionally, the company has scaled its operations and strengthened its commercial team to make these kits globally accessible.
“The launch of our customer-validated Arima-HiChIP kits and services marks a significant milestone, because it enables commercialization of both a targeted HiC approach and also an enhancement to traditional ChIP-Seq,” said Joseph Spidle, Commercial Director at Arima Genomics.
“Our goal is to add meaningful and scientifically relevant applications to the Arima-HiC platform as we democratize the availability of genomic structural insights to accelerate basic and disease related research.”
– Mar. 18, 2020 @ 14:12 GMT |