SCAN: a nanopore-based, cost effective decision-supporting tool for mass screening of aneuploidies
Abstract In developed countries, Newborn Screening (NBS) programs aim to detect treatable yet clinically silent disorders. The selection of disorders to be included in NBS considers severity, treatment availability, prevalence, and analysis cost. However, numerous genetic disorders remain excluded f...
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| Format: | Article |
| Language: | English |
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BMC
2024-11-01
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| Series: | Human Genomics |
| Online Access: | https://doi.org/10.1186/s40246-024-00690-w |
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| author | Anne Kristine Schack M. Carmen Garrido-Navas David Galevski Gjorgji Madjarov Lukasz Krych |
| author_facet | Anne Kristine Schack M. Carmen Garrido-Navas David Galevski Gjorgji Madjarov Lukasz Krych |
| author_sort | Anne Kristine Schack |
| collection | DOAJ |
| description | Abstract In developed countries, Newborn Screening (NBS) programs aim to detect treatable yet clinically silent disorders. The selection of disorders to be included in NBS considers severity, treatment availability, prevalence, and analysis cost. However, numerous genetic disorders remain excluded from routine testing due to high expenses and specialized equipment requirements. Here we present SCAN, a novel, non-invasive, and cost-effective decision-support tool utilizing nanopore sequencing for estimating proportions of chromosomes responsible for the most common aneuploidies. SCAN combines DNA enrichment (amplification), barcoding, nanopore sequencing, and machine learning predictive modeling. In a proof-of-concept study for Klinefelter Syndrome, SCAN achieved 100% sensitivity, specificity, and accuracy, becoming the world’s first IVD-certified genetic test utilising nanopore sequencing. Further model training shows promise in expanding this assay to detect other chromosomal aneuploidies included in the protocol. |
| format | Article |
| id | doaj-art-59be9e53d0784492ad95bc3cd4757e6c |
| institution | Kabale University |
| issn | 1479-7364 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | BMC |
| record_format | Article |
| series | Human Genomics |
| spelling | doaj-art-59be9e53d0784492ad95bc3cd4757e6c2024-11-24T12:35:29ZengBMCHuman Genomics1479-73642024-11-011811710.1186/s40246-024-00690-wSCAN: a nanopore-based, cost effective decision-supporting tool for mass screening of aneuploidiesAnne Kristine Schack0M. Carmen Garrido-Navas1David Galevski2Gjorgji Madjarov3Lukasz Krych4gMendel ApSCONGEN, Genetic Counselling ServicesFaculty of Computer Science and Engineering, University Ss Cyril and MethodiusFaculty of Computer Science and Engineering, University Ss Cyril and MethodiusFood Microbiology and Fermentation, University of CopenhagenAbstract In developed countries, Newborn Screening (NBS) programs aim to detect treatable yet clinically silent disorders. The selection of disorders to be included in NBS considers severity, treatment availability, prevalence, and analysis cost. However, numerous genetic disorders remain excluded from routine testing due to high expenses and specialized equipment requirements. Here we present SCAN, a novel, non-invasive, and cost-effective decision-support tool utilizing nanopore sequencing for estimating proportions of chromosomes responsible for the most common aneuploidies. SCAN combines DNA enrichment (amplification), barcoding, nanopore sequencing, and machine learning predictive modeling. In a proof-of-concept study for Klinefelter Syndrome, SCAN achieved 100% sensitivity, specificity, and accuracy, becoming the world’s first IVD-certified genetic test utilising nanopore sequencing. Further model training shows promise in expanding this assay to detect other chromosomal aneuploidies included in the protocol.https://doi.org/10.1186/s40246-024-00690-w |
| spellingShingle | Anne Kristine Schack M. Carmen Garrido-Navas David Galevski Gjorgji Madjarov Lukasz Krych SCAN: a nanopore-based, cost effective decision-supporting tool for mass screening of aneuploidies Human Genomics |
| title | SCAN: a nanopore-based, cost effective decision-supporting tool for mass screening of aneuploidies |
| title_full | SCAN: a nanopore-based, cost effective decision-supporting tool for mass screening of aneuploidies |
| title_fullStr | SCAN: a nanopore-based, cost effective decision-supporting tool for mass screening of aneuploidies |
| title_full_unstemmed | SCAN: a nanopore-based, cost effective decision-supporting tool for mass screening of aneuploidies |
| title_short | SCAN: a nanopore-based, cost effective decision-supporting tool for mass screening of aneuploidies |
| title_sort | scan a nanopore based cost effective decision supporting tool for mass screening of aneuploidies |
| url | https://doi.org/10.1186/s40246-024-00690-w |
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