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Rapid, field-deployable nucleobase detection and identification using FnCas9

Mohd. Azhar, Rhythm Phutela, Asgar Hussain Ansari, Dipanjali Sinha, Namrata Sharma, Manoj Kumar, Meghali Aich, Saumya Sharma, Riya Rauthan, Khushboo Singhal, Harsha Lad, Pradeep Kumar Patra, Govind Makharia, Giriraj Ratan Chandak, View ORCID ProfileDebojyoti Chakraborty, Souvik Maiti
doi: https://doi.org/10.1101/2020.04.07.028167
Mohd. Azhar
1CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi-110025, India
2Academy of Scientific & Innovative Research, Ghaziabad, 201002, India
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Rhythm Phutela
1CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi-110025, India
2Academy of Scientific & Innovative Research, Ghaziabad, 201002, India
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Asgar Hussain Ansari
1CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi-110025, India
2Academy of Scientific & Innovative Research, Ghaziabad, 201002, India
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Dipanjali Sinha
1CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi-110025, India
2Academy of Scientific & Innovative Research, Ghaziabad, 201002, India
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Namrata Sharma
1CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi-110025, India
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Manoj Kumar
1CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi-110025, India
2Academy of Scientific & Innovative Research, Ghaziabad, 201002, India
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Meghali Aich
1CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi-110025, India
2Academy of Scientific & Innovative Research, Ghaziabad, 201002, India
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Saumya Sharma
1CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi-110025, India
2Academy of Scientific & Innovative Research, Ghaziabad, 201002, India
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Riya Rauthan
1CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi-110025, India
2Academy of Scientific & Innovative Research, Ghaziabad, 201002, India
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Khushboo Singhal
1CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi-110025, India
2Academy of Scientific & Innovative Research, Ghaziabad, 201002, India
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Harsha Lad
3CSIR-Sickle Cell Anemia Mission Laboratory, Chhattisgarh Institute of Medical Sciences, Bilaspur 495001, Chhattisgarh, India
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Pradeep Kumar Patra
3CSIR-Sickle Cell Anemia Mission Laboratory, Chhattisgarh Institute of Medical Sciences, Bilaspur 495001, Chhattisgarh, India
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Govind Makharia
4All India Institute of Medical Sciences, Ansari Nagar East, New Delhi 110029, India
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Giriraj Ratan Chandak
5CSIR-Center for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telengana 500007
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Debojyoti Chakraborty
1CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi-110025, India
2Academy of Scientific & Innovative Research, Ghaziabad, 201002, India
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  • ORCID record for Debojyoti Chakraborty
  • For correspondence: debojyoti.chakraborty@igib.in souvik@igib.res.in
Souvik Maiti
1CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi-110025, India
2Academy of Scientific & Innovative Research, Ghaziabad, 201002, India
6CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India
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  • For correspondence: debojyoti.chakraborty@igib.in souvik@igib.res.in
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Abstract

Detection of pathogenic sequences or variants in DNA and RNA through a point-of-care diagnostic approach is valuable for rapid clinical prognosis. In recent times, CRISPR based detection of nucleic acids has provided an economical and quicker alternative to sequencing-based platforms which are often difficult to implement in the field. Here, we present FnCas9 Editor Linked Uniform Detection Assay (FELUDA) that employs a highly accurate enzymatic readout for detecting nucleotide sequences, identifying nucleobase identity and inferring zygosity with precision. We demonstrate that FELUDA output can be adapted to multiple signal detection platforms and can be quickly designed and deployed for versatile applications including rapid diagnosis during infectious disease outbreaks like COVID-19.

Competing Interest Statement

D.C., S.M., M.A., R.P., A.S.A, D.S., N.S. and S.S. are authors in provisional patent applications that have been filed in relation to this work.

Footnotes

  • Some grammatical and acronyms changes have been introduced. An updated protocol for COVID-19 detections has been added.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted April 21, 2020.
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Rapid, field-deployable nucleobase detection and identification using FnCas9
Mohd. Azhar, Rhythm Phutela, Asgar Hussain Ansari, Dipanjali Sinha, Namrata Sharma, Manoj Kumar, Meghali Aich, Saumya Sharma, Riya Rauthan, Khushboo Singhal, Harsha Lad, Pradeep Kumar Patra, Govind Makharia, Giriraj Ratan Chandak, Debojyoti Chakraborty, Souvik Maiti
bioRxiv 2020.04.07.028167; doi: https://doi.org/10.1101/2020.04.07.028167
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Rapid, field-deployable nucleobase detection and identification using FnCas9
Mohd. Azhar, Rhythm Phutela, Asgar Hussain Ansari, Dipanjali Sinha, Namrata Sharma, Manoj Kumar, Meghali Aich, Saumya Sharma, Riya Rauthan, Khushboo Singhal, Harsha Lad, Pradeep Kumar Patra, Govind Makharia, Giriraj Ratan Chandak, Debojyoti Chakraborty, Souvik Maiti
bioRxiv 2020.04.07.028167; doi: https://doi.org/10.1101/2020.04.07.028167

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