AsCRISPR: A Web Server for Allele-Specific Single Guide RNA Design in Precision Medicine

Zhao, Guizhe; Li, Jinchen; Tang, Yu

doi:10.1089/crispr.2020.0071

Cited by 10 publications

(11 citation statements)

References 59 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…While this manuscript was being written, a few web servers that design gRNAs specifically for targeting SNVs across the genome, particularly in an allele-specific manner, were reported in the literature ( Rabinowitz et al, 2020 ; Chen et al, 2020a ; Zhao et al, 2020 ; Keough et al, 2019 ). These present an important advancement toward gRNA design for precision medicine in general.…”

Section: Discussionmentioning

confidence: 99%

CriSNPr, a single interface for the curated and de novo design of gRNAs for CRISPR diagnostics using diverse Cas systems

Ansari

Kumar

Sarkar

et al. 2023

eLife

View full text Add to dashboard Cite

CRISPR-based diagnostics (CRISPRDx) have improved clinical decision-making, especially during the COVID-19 pandemic, by detecting nucleic acids and identifying variants. This has been accelerated by the discovery of new and engineered CRISPR effectors, which have expanded the portfolio of diagnostic applications to include a broad range of pathogenic and non-pathogenic conditions. However, each diagnostic CRISPR pipeline necessitates customized detection schemes based on the fundamental principles of the Cas protein used, its guide RNA (gRNA) design parameters, and the assay readout. This is especially relevant for variant detection, a low-cost alternative to sequencing-based approaches for which no in silico pipeline for the ready-to-use design of CRISPR-based diagnostics currently exists. In this manuscript, we fill this lacuna using a unified webserver, CriSNPr (CRISPR-based SNP recognition), which provides the user with the opportunity to de-novo design gRNAs based on six CRISPRDx proteins of choice (Fn/enFnCas9, LwCas13a, LbCas12a, AaCas12b, and Cas14a) and query for ready-to-use oligonucleotide sequences for validation on relevant samples. Furthermore, we provide a database of curated pre-designed gRNAs as well as target/off-target for all human and SARS-CoV-2 variants reported thus far. CriSNPr has been validated on multiple Cas proteins, demonstrating its broad and immediate applicability across multiple detection platforms. CriSNPr can be found at http://crisnpr.igib.res.in/.

show abstract

Section: Discussionmentioning

confidence: 99%

CriSNPr, a single interface for the curated and de novo design of gRNAs for CRISPR diagnostics using diverse Cas systems

Ansari

Kumar

Sarkar

et al. 2023

eLife

View full text Add to dashboard Cite

show abstract

“…While this manuscript was being prepared, a few web-servers that design gRNAs specifically for targeting SNVs across the genome, especially in an allele-specific manner have been reported in the literature (62)(63)(64)(65). These present an important advancement towards gRNA design for precision medicine in general.…”

Section: Discussionmentioning

confidence: 99%

CriSNPr: a single interface for the curated and de-novo design of gRNAs for CRISPR diagnostics using diverse Cas systems

Chakraborty

Ansari

Kumar

et al. 2022

Preprint

View full text Add to dashboard Cite

Nucleic acid detection and variant calling through CRISPR-based diagnostics (CRISPRDx) has facilitated clinical decision-making, particularly during the COVID-19 pandemic. This has been further accelerated through the discovery of newer and engineered CRISPR effectors, expanding the portfolio of such diagnostic applications to a wide variety of pathogenic and non-pathogenic conditions. However, each diagnostic CRISPR pipeline requires customized detection schemes originating from fundamental principles of the Cas protein used, its guide RNA (gRNA) design parameters, and the assay readout. This is particularly relevant for variant detection, an attractive low-cost alternative to sequencing-based approaches for which no in silico pipeline for the ready-to-use design of CRISPR-based diagnostics currently exists. In this manuscript, we fill this lacuna using a unified webserver CriSNPr (CRISPR based SNP recognition), which provides the user the opportunity to de-novo design gRNAs based on six CRISPRDx proteins of choice (Fn/enFnCas9, LwCas13a, LbCas12a, AaCas12b, and Cas14a) and query for ready-to-use oligonucleotide sequences for validation on relevant samples. In addition, we provide a database of curated pre-designed gRNAs and target/off-target for all human and SARS-CoV-2 variants reported so far. CriSNPr has been validated on multiple Cas proteins and highlights its broad and immediate scope of utilization across multiple detection platforms. CriSNPr is available at URL http://crisnpr.igib.res.in/.

show abstract

“…Patients with HNSCCs caused by HR‐HPV would undergo thorough profiling to identify specific genetic alterations and the status of their p53 gene. Based on the patient's genetic profile, a specific guide RNA (gRNA) would be designed to target the regulatory region of the p53 gene 165 . The CRISPRa/dCas9 system would be engineered to carry the gRNA and the necessary activation domains.…”

Section: Treatments In Personalized Medicinementioning

confidence: 99%

“…The CRISPRa/dCas9 system would be engineered to carry the gRNA and the necessary activation domains. Before treatment, cancer cells from the patient would be collected and tested in vitro to verify the efficacy and safety of the CRISPRa/dCas9 system in activating the p53 gene 165 . This step would also help ensure the specificity of the treatment.…”

Section: Treatments In Personalized Medicinementioning

confidence: 99%

Developments and future prospects of personalized medicine in head and neck squamous cell carcinoma diagnoses and treatments

Jayawickrama,

Ranaweera,

Pradeep

et al. 2024

Cancer Reports

View full text Add to dashboard Cite

BackgroundPrecision healthcare has entered a new era because of the developments in personalized medicine, especially in the diagnosis and treatment of head and neck squamous cell carcinoma (HNSCC). This paper explores the dynamic landscape of personalized medicine as applied to HNSCC, encompassing both current developments and future prospects.Recent FindingsThe integration of personalized medicine strategies into HNSCC diagnosis is driven by the utilization of genetic data and biomarkers. Epigenetic biomarkers, which reflect modifications to DNA that can influence gene expression, have emerged as valuable indicators for early detection and risk assessment. Treatment approaches within the personalized medicine framework are equally promising. Immunotherapy, gene silencing, and editing techniques, including RNA interference and CRISPR/Cas9, offer innovative means to modulate gene expression and correct genetic aberrations driving HNSCC. The integration of stem cell research with personalized medicine presents opportunities for tailored regenerative approaches. The synergy between personalized medicine and technological advancements is exemplified by artificial intelligence (AI) and machine learning (ML) applications. These tools empower clinicians to analyze vast datasets, predict patient responses, and optimize treatment strategies with unprecedented accuracy.ConclusionThe developments and prospects of personalized medicine in HNSCC diagnosis and treatment offer a transformative approach to managing this complex malignancy. By harnessing genetic insights, biomarkers, immunotherapy, gene editing, stem cell therapies, and advanced technologies like AI and ML, personalized medicine holds the key to enhancing patient outcomes and ushering in a new era of precision oncology.

show abstract

AsCRISPR: A Web Server for Allele-Specific Single Guide RNA Design in Precision Medicine

Cited by 10 publications

References 59 publications

CriSNPr, a single interface for the curated and de novo design of gRNAs for CRISPR diagnostics using diverse Cas systems

CriSNPr, a single interface for the curated and de novo design of gRNAs for CRISPR diagnostics using diverse Cas systems

CriSNPr: a single interface for the curated and de-novo design of gRNAs for CRISPR diagnostics using diverse Cas systems

Developments and future prospects of personalized medicine in head and neck squamous cell carcinoma diagnoses and treatments

Contact Info

Product

Resources

About