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.

Autor:	Gupta P; CSIR- Institute for Genomics and Integrative Biology, New Delhi, India.; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India., Arvinden VR; CSIR- Institute for Genomics and Integrative Biology, New Delhi, India.; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India., Thakur P; CSIR- Institute for Genomics and Integrative Biology, New Delhi, India.; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India., Bhoyar RC; CSIR- Institute for Genomics and Integrative Biology, New Delhi, India., Saravanakumar V; CSIR- Institute for Genomics and Integrative Biology, New Delhi, India., Gottumukkala NV; CSIR- Institute for Genomics and Integrative Biology, New Delhi, India., Goswami SG; CSIR- Institute for Genomics and Integrative Biology, New Delhi, India.; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India., Nafiz M; CSIR- Institute for Genomics and Integrative Biology, New Delhi, India.; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India., Iyer AR; CSIR- Institute for Genomics and Integrative Biology, New Delhi, India.; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India., Vignesh H; CSIR- Institute for Genomics and Integrative Biology, New Delhi, India., Soni R; CSIR- Institute for Genomics and Integrative Biology, New Delhi, India., Bhargava N; CSIR- Institute for Genomics and Integrative Biology, New Delhi, India., Gunda P; Thalassemia and Sickle Cell Society, Hyderabad, India., Jain S; Thalassemia and Sickle Cell Society, Hyderabad, India., Gupta V; Government Institute of Medical Sciences (GIMS), Greater Noida, India., Sivasubbu S; CSIR- Institute for Genomics and Integrative Biology, New Delhi, India.; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India., Scaria V; CSIR- Institute for Genomics and Integrative Biology, New Delhi, India.; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India., Ramalingam S; CSIR- Institute for Genomics and Integrative Biology, New Delhi, India.; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
Jazyk:	angličtina
Zdroj:	Frontiers in molecular biosciences [Front Mol Biosci] 2023 Dec 13; Vol. 10, pp. 1244244. Date of Electronic Publication: 2023 Dec 13 (Print Publication: 2023).
DOI:	10.3389/fmolb.2023.1244244
Abstrakt:	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. Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. (Copyright © 2023 Gupta, Arvinden, Thakur, Bhoyar, Saravanakumar, Gottumukkala, Goswami, Nafiz, Iyer, Vignesh, Soni, Bhargava, Gunda, Jain, Gupta, Sivasubbu, Scaria and Ramalingam.)
Databáze:	MEDLINE
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