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Gupta P, Arvinden VR, Thakur P, Bhoyar RC, Saravanakumar V, Gottumukkala NV, Goswami SG, Nafiz M, Iyer AR, Vignesh H, Soni R, Bhargava N, Gunda P, Jain S, Gupta V, Sivasubbu S, Scaria V, Ramalingam S. Scalable noninvasive amplicon-based precision sequencing (SNAPseq) for genetic diagnosis and screening of β-thalassemia and sickle cell disease using a next-generation sequencing platform. Front Mol Biosci 2023; 10:1244244. [PMID: 38152111 PMCID: PMC10751313 DOI: 10.3389/fmolb.2023.1244244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 11/16/2023] [Indexed: 12/29/2023] Open
Abstract
β-hemoglobinopathies such as β-thalassemia (BT) and Sickle cell disease (SCD) are inherited monogenic blood disorders with significant global burden. Hence, early and affordable diagnosis can alleviate morbidity and reduce mortality given the lack of effective cure. Currently, Sanger sequencing is considered to be the gold standard genetic test for BT and SCD, but it has a very low throughput requiring multiple amplicons and more sequencing reactions to cover the entire HBB gene. To address this, we have demonstrated an extraction-free single amplicon-based approach for screening the entire β-globin gene with clinical samples using Scalable noninvasive amplicon-based precision sequencing (SNAPseq) assay catalyzing with next-generation sequencing (NGS). We optimized the assay using noninvasive buccal swab samples and simple finger prick blood for direct amplification with crude lysates. SNAPseq demonstrates high sensitivity and specificity, having a 100% agreement with Sanger sequencing. Furthermore, to facilitate seamless reporting, we have created a much simpler automated pipeline with comprehensive resources for pathogenic mutations in BT and SCD through data integration after systematic classification of variants according to ACMG and AMP guidelines. To the best of our knowledge, this is the first report of the NGS-based high throughput SNAPseq approach for the detection of both BT and SCD in a single assay with high sensitivity in an automated pipeline.
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Affiliation(s)
- Pragya Gupta
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - V. R. Arvinden
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Priya Thakur
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rahul C. Bhoyar
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
| | | | | | - Sangam Giri Goswami
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mehwish Nafiz
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Aditya Ramdas Iyer
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Harie Vignesh
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
| | - Rajat Soni
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
| | - Nupur Bhargava
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
| | - Padma Gunda
- Thalassemia and Sickle Cell Society, Hyderabad, India
| | - Suman Jain
- Thalassemia and Sickle Cell Society, Hyderabad, India
| | - Vivek Gupta
- Government Institute of Medical Sciences (GIMS), Greater Noida, India
| | - Sridhar Sivasubbu
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Vinod Scaria
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sivaprakash Ramalingam
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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