CriSNPr: a single interface for the curated and de novo design of gRNAs for CRISPR diagnostics using diverse Cas systems
- CSIR Institute of Genomics and Integrative Biology, India
- CSIR-Institute of Genomics and Integrative Biology, India
Abstract
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/.
Data availability
The current manuscript is a computational study, so no new data has been generated for this manuscript. Experimental validation results have been presented in figures in the manuscript. The source code and related datasets have been indicated in the manuscript and also uploaded here: http://crisnpr.igib.res.in/download. All other validation data have been presented in the main manuscript itself.
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DbSNP: The NCBI database of genetic variationDbSNP: The NCBI database of genetic variation.
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Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021.Nucleic Acids Research, doi.org/10.1093/nar/gkaa1022.
Article and author information
Author details
Debojyoti Chakraborty
Funding
CSIR (HCP23)
- Souvik Maiti
- Debojyoti Chakraborty
EMBO (GAP252)
- Debojyoti Chakraborty
Lady Tata Memorial Trust (GAP198)
- Debojyoti Chakraborty
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Tony Yuen, Icahn School of Medicine at Mount Sinai, United States
Version history
- Preprint posted: February 17, 2022 (view preprint)
- Received: February 17, 2022
- Accepted: February 7, 2023
- Accepted Manuscript published: February 8, 2023 (version 1)
- Version of Record published: February 20, 2023 (version 2)
Copyright
© 2023, Ansari et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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CriSNPr: a single interface for the curated and de novo design of gRNAs for CRISPR diagnostics using diverse Cas systems
eLife 12:e77976.
https://doi.org/10.7554/eLife.77976
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