Leveraging Next-Generation Sequencing Application from Identity to Purity Profiling of Nucleic Acid-Based Products
<b>Background/Objectives</b>: The nucleic acid-based product (NAP) portfolio is expanding continuously and provides safer curative options for many disease indications. Nucleic acid-based products offer several advantages compared to proteins and virus-based products. They represent an e...
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MDPI AG
2024-12-01
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| Series: | Pharmaceutics |
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| Online Access: | https://www.mdpi.com/1999-4923/17/1/30 |
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| author | Rucha Wadapurkar Swarda Deo Renuka Khanzode Ajay Singh |
| author_facet | Rucha Wadapurkar Swarda Deo Renuka Khanzode Ajay Singh |
| author_sort | Rucha Wadapurkar |
| collection | DOAJ |
| description | <b>Background/Objectives</b>: The nucleic acid-based product (NAP) portfolio is expanding continuously and provides safer curative options for many disease indications. Nucleic acid-based products offer several advantages compared to proteins and virus-based products. They represent an emerging field; thus, their quality control and regulatory landscape is evolving to ensure adequate quality and safety. Next-Generation Sequencing (NGS) is mostly recommended for NAP identity testing, and we are leveraging its application for impurity profiling. <b>Methods</b>: We proposed a workflow for the purity assessment of NAPs through short-read Illumina NGS followed by data analysis of mRNA vaccine and pDNA samples. We determined the sequence identity, DNA and RNA contamination, off-target RNA contamination, and poly-A count with the proposed workflow. <b>Results</b>: Our workflow predicted most of the critical quality controls of mRNA vaccine and plasmid DNA samples, especially focusing on the identity and the nucleotide-based impurities. Additionally, NGS data interpretation also assisted in strategic decisions for NAP manufacturing process optimizations. <b>Conclusions</b>: We recommend the adaptation of incremental NGS data by regulatory agencies to identify nucleotide-based impurities in NAPs. Perhaps NGS adaptation under cGMP compliance needs to be deliberated with the regulatory bodies, especially focusing on the methods qualification and validation part, starting from the sample collection, NGS library preparation, NGS run, and its data analysis pipeline. |
| format | Article |
| id | doaj-art-a81cbc0cd7d940809d5e4a7c664a883c |
| institution | Kabale University |
| issn | 1999-4923 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Pharmaceutics |
| spelling | doaj-art-a81cbc0cd7d940809d5e4a7c664a883c2025-01-24T13:45:38ZengMDPI AGPharmaceutics1999-49232024-12-011713010.3390/pharmaceutics17010030Leveraging Next-Generation Sequencing Application from Identity to Purity Profiling of Nucleic Acid-Based ProductsRucha Wadapurkar0Swarda Deo1Renuka Khanzode2Ajay Singh3Gennova Biopharmaceuticals Ltd., ITBT Park, Hinjawadi Phase 2 Rd, Hinjewadi Rajiv Gandhi Infotech Park, Hinjawadi, Pune 411057, IndiaGennova Biopharmaceuticals Ltd., ITBT Park, Hinjawadi Phase 2 Rd, Hinjewadi Rajiv Gandhi Infotech Park, Hinjawadi, Pune 411057, IndiaGennova Biopharmaceuticals Ltd., ITBT Park, Hinjawadi Phase 2 Rd, Hinjewadi Rajiv Gandhi Infotech Park, Hinjawadi, Pune 411057, IndiaGennova Biopharmaceuticals Ltd., ITBT Park, Hinjawadi Phase 2 Rd, Hinjewadi Rajiv Gandhi Infotech Park, Hinjawadi, Pune 411057, India<b>Background/Objectives</b>: The nucleic acid-based product (NAP) portfolio is expanding continuously and provides safer curative options for many disease indications. Nucleic acid-based products offer several advantages compared to proteins and virus-based products. They represent an emerging field; thus, their quality control and regulatory landscape is evolving to ensure adequate quality and safety. Next-Generation Sequencing (NGS) is mostly recommended for NAP identity testing, and we are leveraging its application for impurity profiling. <b>Methods</b>: We proposed a workflow for the purity assessment of NAPs through short-read Illumina NGS followed by data analysis of mRNA vaccine and pDNA samples. We determined the sequence identity, DNA and RNA contamination, off-target RNA contamination, and poly-A count with the proposed workflow. <b>Results</b>: Our workflow predicted most of the critical quality controls of mRNA vaccine and plasmid DNA samples, especially focusing on the identity and the nucleotide-based impurities. Additionally, NGS data interpretation also assisted in strategic decisions for NAP manufacturing process optimizations. <b>Conclusions</b>: We recommend the adaptation of incremental NGS data by regulatory agencies to identify nucleotide-based impurities in NAPs. Perhaps NGS adaptation under cGMP compliance needs to be deliberated with the regulatory bodies, especially focusing on the methods qualification and validation part, starting from the sample collection, NGS library preparation, NGS run, and its data analysis pipeline.https://www.mdpi.com/1999-4923/17/1/30NGSnucleic acidmRNA vaccineCOVID-19sequencing |
| spellingShingle | Rucha Wadapurkar Swarda Deo Renuka Khanzode Ajay Singh Leveraging Next-Generation Sequencing Application from Identity to Purity Profiling of Nucleic Acid-Based Products Pharmaceutics NGS nucleic acid mRNA vaccine COVID-19 sequencing |
| title | Leveraging Next-Generation Sequencing Application from Identity to Purity Profiling of Nucleic Acid-Based Products |
| title_full | Leveraging Next-Generation Sequencing Application from Identity to Purity Profiling of Nucleic Acid-Based Products |
| title_fullStr | Leveraging Next-Generation Sequencing Application from Identity to Purity Profiling of Nucleic Acid-Based Products |
| title_full_unstemmed | Leveraging Next-Generation Sequencing Application from Identity to Purity Profiling of Nucleic Acid-Based Products |
| title_short | Leveraging Next-Generation Sequencing Application from Identity to Purity Profiling of Nucleic Acid-Based Products |
| title_sort | leveraging next generation sequencing application from identity to purity profiling of nucleic acid based products |
| topic | NGS nucleic acid mRNA vaccine COVID-19 sequencing |
| url | https://www.mdpi.com/1999-4923/17/1/30 |
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