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CRISPR-SNP-Chip  advance genetic testing for medical diagnostics

Single-nucleotide polymorphisms (SNPs)account for over 50% of disease-causing mutations in humans. In addition toresiding at the core of human health genetics, SNPs play a considerable role ininfectious disease prevention, ageing, pharmacology and agriculture and are adriving force in evolutionary change. Specific SNPs have been associated with reducingthe rubella vaccine’s effectiveness by impinging on key cytokine pathways. SNPswere also implicated in an outbreak of coronavirus, causing severe acuterespiratory syndrome (SARS). In the agriculture industry, it is crucial forcrop yield to plant seeds with the highest possible resistance to commonpathogens. SNPs play an essential role in determining breeding procedures asthey serve as markers for resistance screening. Furthermore, SNPs can be usedas genome stability markers for quality control of genetically modified seedsbefore their release. Although the applications for SNP detection are abundantacross many research disciplines and industries, current methods for SNPgenotyping have limited their widespread employment outside of a traditionallaboratory.

Keck Graduate Institute (KGI) AssistantProfessor and University of California, Berkeley Visiting Scientist Dr. KianaAran first introduced the CRISPR-Chip technology in 2019. Now just two yearslater, she has expanded on its application to develop CRISPR-SNP-Chip, whichenables detection of single point mutations without amplification in SickleCell Disease and Amyotrophic lateral sclerosis (ALS).

"The field of CRISPR-based diagnosticsis rapidly evolving due to CRISPR programmability and ease of use," Aransays. "However, the majority of CRISPR-based diagnostics platforms arestill relying on target amplifications or optical detections. Thereprogrammability of CRISPR combined with optics-free highly scalable graphenetransistors will allow us to bring the diagnostics power of the CRISPR to itsfull potential.

"The ability to detect singlenucleotide polymorphisms (SNPs) is at the core of human health genetics butdetection of SNPs is also very important in pharmacology, and agriculture, andis a driving force in evolutionary change such as mutations conferringresistance to antibiotics. Eliminating the need for amplification and opticswill make SNP genotyping readily accessible."

The SNP-Chip technology is an extension ofpreviously reported CRISPR-ChipTM, a technology that is capable of detectinglarge insertion and deletions. It earned a spot on the cover of NatureBiomedical Engineering in June 2019.

With graphene transistors, the authors nowutilized a few versions of CAS enzymes and gRNA designs and monitored variousdifferent electrical signals obtained from graphene transistors to construct anew version of CRISPR-ChipTM, which ultimately enabled SNP detection withoutamplification. The newly developed CRISPR-Chip set, called SNP-Chip, is anothermajor milestone in reshaping nucleic-acid-based detection methods.

Merging a diversity of CRISPR-Cas biologywith electronics via Cardean Transistors opens up a whole new range ofpossibilities for diagnostic applications. Using the Cas9 orthologue for SNPdetection is just the tip of the iceberg.

In this article, the utility of SNP-Chipwas validated for testing SNP mutation in samples obtained from patients withSickle Cell Disease and ALS. In both of these clinical models, the platform wasable to discriminate healthy from mutated gene within the whole human genomewithout amplification and by simple swapping of gRNA to target desired DNAsequences indicating the ease of platform reconfiguration for different DNAtargets.

SNP-Chip has the potential to greatlyimpact medical diagnostics and basic research as it can dramatically reduce thetime and cost of SNP geotyping, monitor the efficiency of gRNA designs, andfacilitate the quality control process involved in CRISPR-based gene editing.

SNP-Chip's digital, direct, rapid, andaccurate SNP analysis will revolutionize the screening for genetic mutations.This new technology will inform the discovery of processes underlying diseaseand aging and will enable faster, more effective clinical translation.

Amplification-free detection of a targetgene with single nucleotide mismatch specificity has the potential tostreamline genetic research and diagnostics. Furthermore, it would provide moreflexibility for biosensing applications previously confined to a laboratory setting.

The researchers showed that the device,called CRISPR-SNP-Chip, could accurately detect single nucleotide polymorphisms(SNPs), or point mutations, in sickle cell and ALS diseases without the need toamplify the DNA.

Cardea Bio is a San Diego-based biotechnologycompany that provided the primary funding for this work.

Building on earlier research of theCRISPR-Chip, the researchers used electronic transistors made from graphene todetect genetic mutations in minutes. DNA samples are placed on the chip, andthousands of CRISPR molecules scan for specific mutations. If CRISPR binds withthe target, it creates an electrical charge that is detected by the device.


Fig. The CRISPR-SNP-Chip device uses CRISPR molecules and graphene transistors to detect target single-point-mutations in DNA samples. (Photo courtesy of Cardea Bio).

Cardea CRISPR-Chip™: the DNA Search Engine

By combining thousands of CRISPR-dcas9 molecules with Cardea’s Biology-gated Transistors, our proprietary and patented CRISPR-Chip technology has the power to search genomes for specific sequences of interest. While the opportunities are endless, CRISPR-Chip has successfully proven Genome Sensor’s capabilities to detect genetic mutations such as sickle cell disease and Duchenne muscular dystrophy (DMD). Learn more about our applications powered by CRISPR-Chip and other Cardean chipsets.



• First-ever Amplification-free DNA testing

• Nature BME June 2019 cover story and most read article + many international news articles

• Without the need for amplification, DNA testing will no longer be trapped inside of complicated DNA

labs. CRISPR-Chip™ enables easy-to-use rapid DNA testing for Point-of-Care & Point-of-Need environments


Discrimination of single-point mutations in unamplified genomic DNA via Cas9 immobilized on a graphene field-effect transistor