DiaCarta Redefining Molecular Diagnostics Through XNA

by | Jul 2, 2018 | Blog

At a pathology lab, a researcher is working on a patient’s blood sample to extract cell-free DNA to find the potential diagnostic biomarker for cancers. Using the current DNA sequencing techniques such as next-generation sequencing (NGS) or digital droplet PCR (ddPCR), the researcher gets multiple readings of the cfDNA. However, what happens in standard real-time PCR and sequencing methods is that unless a mutated gene makes up at least 5 percent of the genome (10 percent for indels), its signal is often swamped by super-abundant wild-type DNA—the normal DNA. This drastically reduces the chances of identifying the mutant DNAs that give disease information. “It is like finding a needle in a haystack,” reveals Michael J. Powell, the Chief Scientific Officer of DiaCarta. Even after deploying these expensive techniques, if the researcher gets information on the mutant DNA, it is difficult to identify if the mutation was introduced during the analysis procedure or came from the patient. “In the current precision medicine market, the gene sequencing methods are depending on deep sequencing, which is time-consuming and not so reliable for liquid biopsy, even leading to false negative or positive reading. They are also expensive, costing patients anywhere around $5,000 to $7,000, making precision medicine inaccessible to larger masses,” says Dr. Aiguo (Adam) Zhang, CEO of DiaCarta.

Changing the scenario by manifold, DiaCarta brings to the market the science of rapid, highly sensitive mutation detection technologies and cost-effective diagnostic solutions to positively impact treatment plans, and make precision medicine accessible to all. The company’s groundbreaking technology—Xenonucleic Acid (XNA) molecular clamp technology binds the wild-type DNA as soon as it identifies it, improving detection of the mutant DNA. “Existing technologies cannot fully differentiate between wild-type DNAs and mutant templates. On the other hand, what we do is eliminate the haystack (wild-type) from the equation and magnify the needle (mutant),” says Powell. This allows the detection of mutant DNA in the presence of a large excess of wild-type template from any type of sample including FFPE, needle biopsy, whole blood, and urine. “We are addressing the critical need for liquid biopsy to detect diseases in genes such as lung and colon cancer before they become chronic with our highly sensitive methodology to increase the chances of better treatment regimes for patients.”

Finding the Needle

Under the umbrella of its XNA technology, DiaCarta’s QClamp® Gene Mutation Detection Kits are highly sensitive qPCR assays that are ideal for detecting rare and actionable somatic mutations in oncogenes producing highly sensitive and rapid tests for KRAS, NRAS, EGFR, BRAF, PIK3CA,JAK2 and c-KIT. The tests take less than 2.5 hours from start to finish with or without DNA extraction using its special QExTMDNA PCR lysis buffer or a commercially available DNA extraction kit and can detect below 0.5 percent of mutated DNA. DiaCarta’s XNA technology simplifies mutation detection as it causes a 15 to 20 degree difference in [melt] temperature when a single nucleotide polymorphism (SNPs)—genetic variations that help locate genes associated with disease—is identified, which is a 10- fold increase over other traditional PCR methods. These tests help in early detection and monitoring of lung and colon cancer or any other genetic disease. The kits provide a rapid, reproducible, and affordable solution which employs a simple workflow and existing commercial real-time PCR machines that are commonly used in research and clinical labs. “Our QClamp® tests are super sensitive and rapid. Clients don’t need to invest hundreds of thousands of dollar for a fancy digital PCR or sequencing machine. Our tests can be run on all currently available real-time PCR machines, and everything that needs to perform the tests is included in the kits,” says Zhang.

DiaCarta is also currently developing a XNA-based multiplex magnetic bead based hybridization capture detection method that can simultaneously detect a group of gene mutations from one tube of blood without the need for a next generation sequencing (NGS) system, relying on simpler detection methods, which can generate results in one day.

Extending the Trenches of XNA

DiaCarta’s XNA mediated PCR clamping technology has also proved its proficiency in qualitative detection of colorectal cancer through its ColoScape Product which is a realtime PCR in vitro diagnostic assay. Clinicians can detect the presence or absence of mutations in the targeted regions of the genes. The assay can be performed on readily available instrumentation that is already present in hospital pathology laboratories. Providing a comprehensive profile of the key CRC ‘driver’ and ‘resistance’ mutations, ColoScape directly informs oncologists of targeted therapy options without the need to reflex to another assay, unlike the existing CRC tests. DiaCarta is currently working on developing ColoScape for recurrence and monitoring and precancer detection indications. DiaCarta’s deep expertise also lies in monitoring responses of patients towards radiation, chemotherapy, and immunotherapy treatments by examining cfDNA directly from patient plasma during radiation therapy. “Currently, there exists no reliable methodology for determining radiation response during radiotherapy. Ours is a breakthrough ‘first-inclass’ test in the field of radiation therapy,” says Zhang. Leveraging the power of its groundbreaking XNA technology, the company has simplified gene editing through its “CRISPR-Quest,” a next-generation polymerase chain reaction technology. The technology provides a rapid, lowcost, ultra-sensitive quantification method for both NHEJ- and HDR-editing events. HDR and NHEJ editing events generally occur at low frequencies, necessitating ultrasensitive techniques for detection and quantification of edited alleles. Unlike other sequencing techniques that are time-consuming and require large investments in hardware and technical resources, DiaCarta’s CRISPR-Quest offers low cost, rapid and ultrasensitive quantification of both HDR and NHEJ editing events. With DiaCarta’s gene editing technology, researchers can detect the desired mutation from the beginning. Researchers are also looking at CRISPR-Quest to quantify HDR and NHEJ simultaneously to isolate conditions where there is more HDR than NHEJ. 

As a global enterprise headquartered in Richmond, CA, DiaCarta has operations across the U.S., Europe, and China. Its China operation under Dr. Effie Ho, APC GM of the company, is growing rapidly. With a clinical lab in Nanjing, DiaCarta (帝基生物) is now being recognized as one of the top leaders in precision molecular diagnostics. Among the diverse clients, Hutchinson Cancer Center in Seattle was one that was interested in monitoring minimal residual disease in leukemia patients to provide treatment to patients. There was no existing technology to help them detect the minimal residual disease. DiaCarta developed an assay based on their XNA technology to help the cancer center to monitor patient’s blood samples for minimal residual disease. In another instance, Olivia Newton-John Cancer Center in Australia was struggling to validate the genomic data using pyrosequencing for their lung cancer patients. With DiaCarta’s XNA technology, the client was able to enhance their sequencing sensitivity of pyrosequencing through XNA by a 100 fold. “We helped them find the needle in the haystack and detect the development of T790M resistance mutation in lung cancer patients that developed after the first line TKI therapy” says Dr. Powell.

Sailing Ahead with Enhanced Liquid Biopsy

As the driving force of DiaCarta, Zhang is an active entrepreneur and executive in the biotech and pharmaceutical industries bagging numerous innovations subject to patent pending applications under his name. On the other hand, Powell is a highly celebrated scientific leader with over two decades of experience in molecular diagnostic assay research and development, qPCR and other nucleic acid amplification technologies, and automated instrumentation platforms. With an underlying passion for discovering new opportunities in the field of molecular diagnostics, Powell and Zhang are always busy in showcasing their creativity through various innovative products. For instance, Powell is working on creating portable devices to carry out tests outside labs. DiaCarta’s move to always be ahead of the industry trends is backed by its team of experienced industry veterans who can translate creative ideas into solid products that are validated in the industry. Evidently, the company has piqued the interest of a leading financial services group, BVCF, FFC and GHC to invest in DiaCarta’s core XNA technology and diagnostic products to augment its functionalities. “In the precision medicine realm, investors are becoming more rigid, funding only those companies whose products are clinically acceptable and widely adopted by customers. We are able to successfully meet these requirements with our core technology that is clinically validated,” says Zhang. Augmenting its existing value proposition in the market, DiaCarta is set to expand its technology for liquid biopsy cancer detection. The company’s XNA technology is making significant inroads into gene editing to improve the ability to edit single nuclear type and screen the end results. The prowess of DiaCarta’s XNA technology will also be applied to remove challenges associated with immunotherapy especially in reducing costs in capturing responses. “Our technology can rapidly adapt to the emerging trends in the medical field including immunotherapy,” says Powell. With XNA technology, physicians can easily monitor the genetic landscape of a patient prior to e.g. CAR-T therapy to ensure that the immunotherapy treatment works without side effects and detect responses immediately. DiaCarta also sets its vision beyond cancer treatments, diving into pre-natal, rare disease and cardiovascular issues that can be treated with the detection of genetic mutations.

Lead Source

HPV-driven Cancers and Somatic Mutations in These Cancers

Next-generation sequencing (NGS) is a powerful tool that has seen a fast increase in clinical labs although only a few NGS tests have been approved by the FDA. However, there have been a lot of debate on if variants from NGS sequencing should be confirmed either by Sanger sequencing, the gold standard, or other techniques such as quantitative PCR, or the combination, or other methods.

cfDNA Quantitation for Research and Clinical Applications

Next-generation sequencing (NGS) is a powerful tool that has seen a fast increase in clinical labs although only a few NGS tests have been approved by the FDA. However, there have been a lot of debate on if variants from NGS sequencing should be confirmed either by Sanger sequencing, the gold standard, or other techniques such as quantitative PCR, or the combination, or other methods.

Confirmation of NGS for False-negative Variants Using XNA Technology

Next-generation sequencing (NGS) is a powerful tool that has seen a fast increase in clinical labs although only a few NGS tests have been approved by the FDA. However, there have been a lot of debate on if variants from NGS sequencing should be confirmed either by Sanger sequencing, the gold standard, or other techniques such as quantitative PCR, or the combination, or other methods.

XNA Molecular Clamps Help Identify False-positive T790M Mutation

Eighty five percent of the lung cancer patients are non-small cell lung cancer (NSCLC) patients. Among this population, patients with exon 19 deletion and L858R mutations respond well to the first (such as erlotinib and gefitinib) and second generation (such as afatinib and dacomitinib) of tyrosine kinase inhibitors (TKIs). However, all the respondents develop resistance after 9 to 14-month period and more than 50% of the resistance cases are due to the single point mutation at exon 20, T790M.

Colorectal Cancer: Early Screening Could Save Your Life

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