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
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 c...
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Frontiers Media S.A.
2023-12-01
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| Series: | Frontiers in Molecular Biosciences |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmolb.2023.1244244/full |
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| author | Pragya Gupta Pragya Gupta V. R. Arvinden V. R. Arvinden Priya Thakur Priya Thakur Rahul C. Bhoyar Vinodh Saravanakumar Narendra Varma Gottumukkala Sangam Giri Goswami Sangam Giri Goswami Mehwish Nafiz Mehwish Nafiz Aditya Ramdas Iyer Aditya Ramdas Iyer Harie Vignesh Rajat Soni Nupur Bhargava Padma Gunda Suman Jain Vivek Gupta Sridhar Sivasubbu Sridhar Sivasubbu Vinod Scaria Vinod Scaria Sivaprakash Ramalingam Sivaprakash Ramalingam |
| author_facet | Pragya Gupta Pragya Gupta V. R. Arvinden V. R. Arvinden Priya Thakur Priya Thakur Rahul C. Bhoyar Vinodh Saravanakumar Narendra Varma Gottumukkala Sangam Giri Goswami Sangam Giri Goswami Mehwish Nafiz Mehwish Nafiz Aditya Ramdas Iyer Aditya Ramdas Iyer Harie Vignesh Rajat Soni Nupur Bhargava Padma Gunda Suman Jain Vivek Gupta Sridhar Sivasubbu Sridhar Sivasubbu Vinod Scaria Vinod Scaria Sivaprakash Ramalingam Sivaprakash Ramalingam |
| author_sort | Pragya Gupta |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-08T23:56:01Z |
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| institution | Directory Open Access Journal |
| issn | 2296-889X |
| language | English |
| last_indexed | 2024-03-08T23:56:01Z |
| publishDate | 2023-12-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Molecular Biosciences |
| spelling | doaj.art-a6cb5d12882b4757acc144143da96ca82023-12-13T05:09:35ZengFrontiers Media S.A.Frontiers in Molecular Biosciences2296-889X2023-12-011010.3389/fmolb.2023.12442441244244Scalable noninvasive amplicon-based precision sequencing (SNAPseq) for genetic diagnosis and screening of β-thalassemia and sickle cell disease using a next-generation sequencing platformPragya Gupta0Pragya Gupta1V. R. Arvinden2V. R. Arvinden3Priya Thakur4Priya Thakur5Rahul C. Bhoyar6Vinodh Saravanakumar7Narendra Varma Gottumukkala8Sangam Giri Goswami9Sangam Giri Goswami10Mehwish Nafiz11Mehwish Nafiz12Aditya Ramdas Iyer13Aditya Ramdas Iyer14Harie Vignesh15Rajat Soni16Nupur Bhargava17Padma Gunda18Suman Jain19Vivek Gupta20Sridhar Sivasubbu21Sridhar Sivasubbu22Vinod Scaria23Vinod Scaria24Sivaprakash Ramalingam25Sivaprakash Ramalingam26CSIR- Institute for Genomics and Integrative Biology, New Delhi, IndiaAcademy of Scientific and Innovative Research (AcSIR), Ghaziabad, IndiaCSIR- Institute for Genomics and Integrative Biology, New Delhi, IndiaAcademy of Scientific and Innovative Research (AcSIR), Ghaziabad, IndiaCSIR- Institute for Genomics and Integrative Biology, New Delhi, IndiaAcademy of Scientific and Innovative Research (AcSIR), Ghaziabad, IndiaCSIR- Institute for Genomics and Integrative Biology, New Delhi, IndiaCSIR- Institute for Genomics and Integrative Biology, New Delhi, IndiaCSIR- Institute for Genomics and Integrative Biology, New Delhi, IndiaCSIR- Institute for Genomics and Integrative Biology, New Delhi, IndiaAcademy of Scientific and Innovative Research (AcSIR), Ghaziabad, IndiaCSIR- Institute for Genomics and Integrative Biology, New Delhi, IndiaAcademy of Scientific and Innovative Research (AcSIR), Ghaziabad, IndiaCSIR- Institute for Genomics and Integrative Biology, New Delhi, IndiaAcademy of Scientific and Innovative Research (AcSIR), Ghaziabad, IndiaCSIR- Institute for Genomics and Integrative Biology, New Delhi, IndiaCSIR- Institute for Genomics and Integrative Biology, New Delhi, IndiaCSIR- Institute for Genomics and Integrative Biology, New Delhi, IndiaThalassemia and Sickle Cell Society, Hyderabad, IndiaThalassemia and Sickle Cell Society, Hyderabad, IndiaGovernment Institute of Medical Sciences (GIMS), Greater Noida, IndiaCSIR- Institute for Genomics and Integrative Biology, New Delhi, IndiaAcademy of Scientific and Innovative Research (AcSIR), Ghaziabad, IndiaCSIR- Institute for Genomics and Integrative Biology, New Delhi, IndiaAcademy of Scientific and Innovative Research (AcSIR), Ghaziabad, IndiaCSIR- Institute for Genomics and Integrative Biology, New Delhi, IndiaAcademy of Scientific and Innovative Research (AcSIR), Ghaziabad, Indiaβ-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.https://www.frontiersin.org/articles/10.3389/fmolb.2023.1244244/fullβ-thalassemiasickle cell diseaseβ-hemoglobinopathieshigh-throughput amplicon sequencingnext-generation sequencingmolecular diagnosis |
| spellingShingle | Pragya Gupta Pragya Gupta V. R. Arvinden V. R. Arvinden Priya Thakur Priya Thakur Rahul C. Bhoyar Vinodh Saravanakumar Narendra Varma Gottumukkala Sangam Giri Goswami Sangam Giri Goswami Mehwish Nafiz Mehwish Nafiz Aditya Ramdas Iyer Aditya Ramdas Iyer Harie Vignesh Rajat Soni Nupur Bhargava Padma Gunda Suman Jain Vivek Gupta Sridhar Sivasubbu Sridhar Sivasubbu Vinod Scaria Vinod Scaria Sivaprakash Ramalingam Sivaprakash Ramalingam 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 Frontiers in Molecular Biosciences β-thalassemia sickle cell disease β-hemoglobinopathies high-throughput amplicon sequencing next-generation sequencing molecular diagnosis |
| title | 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 |
| title_full | 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 |
| title_fullStr | 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 |
| title_full_unstemmed | 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 |
| title_short | 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 |
| title_sort | 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 |
| topic | β-thalassemia sickle cell disease β-hemoglobinopathies high-throughput amplicon sequencing next-generation sequencing molecular diagnosis |
| url | https://www.frontiersin.org/articles/10.3389/fmolb.2023.1244244/full |
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