Validation of a Custom Next-Generation Sequencing Assay for Cystic Fibrosis Newborn Screening
Newborn screening (NBS) for Cystic Fibrosis (CF) is associated with improved outcomes. All US states screen for CF; however, CF NBS algorithms have high false positive (FP) rates. In New York State (NYS), the positive predictive value of CF NBS improved from 3.7% to 25.2% following the implementatio...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-11-01
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| Series: | International Journal of Neonatal Screening |
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| Online Access: | https://www.mdpi.com/2409-515X/7/4/73 |
| _version_ | 1827672068643094528 |
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| author | Robert J. Sicko Colleen F. Stevens Erin E. Hughes Melissa Leisner Helen Ling Carlos A. Saavedra-Matiz Michele Caggana Denise M. Kay |
| author_facet | Robert J. Sicko Colleen F. Stevens Erin E. Hughes Melissa Leisner Helen Ling Carlos A. Saavedra-Matiz Michele Caggana Denise M. Kay |
| author_sort | Robert J. Sicko |
| collection | DOAJ |
| description | Newborn screening (NBS) for Cystic Fibrosis (CF) is associated with improved outcomes. All US states screen for CF; however, CF NBS algorithms have high false positive (FP) rates. In New York State (NYS), the positive predictive value of CF NBS improved from 3.7% to 25.2% following the implementation of a three-tier IRT-DNA-SEQ approach using commercially available tests. Here we describe a modification of the NYS CF NBS algorithm via transition to a new custom next-generation sequencing (NGS) platform for more comprehensive cystic fibrosis transmembrane conductance regulator (<i>CFTR</i>) gene analysis. After full gene sequencing, a tiered strategy is used to first analyze only a specific panel of 338 clinically relevant <i>CFTR</i> variants (second-tier), followed by unblinding of all sequence variants and bioinformatic assessment of deletions/duplications in a subset of samples requiring third-tier analysis. We demonstrate the analytical and clinical validity of the assay and the feasibility of use in the NBS setting. The custom assay has streamlined our molecular workflow, increased throughput, and allows for bioinformatic customization of second-tier variant panel content. NBS aims to identify those infants with the highest disease risk. Technological molecular improvements can be applied to NBS algorithms to reduce the burden of FP referrals without loss of sensitivity. |
| first_indexed | 2024-03-10T03:53:37Z |
| format | Article |
| id | doaj.art-6481f5b849294e69b1df70935f9b46cb |
| institution | Directory Open Access Journal |
| issn | 2409-515X |
| language | English |
| last_indexed | 2024-03-10T03:53:37Z |
| publishDate | 2021-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Neonatal Screening |
| spelling | doaj.art-6481f5b849294e69b1df70935f9b46cb2023-11-23T08:50:08ZengMDPI AGInternational Journal of Neonatal Screening2409-515X2021-11-01747310.3390/ijns7040073Validation of a Custom Next-Generation Sequencing Assay for Cystic Fibrosis Newborn ScreeningRobert J. Sicko0Colleen F. Stevens1Erin E. Hughes2Melissa Leisner3Helen Ling4Carlos A. Saavedra-Matiz5Michele Caggana6Denise M. Kay7New York State Newborn Screening Program, Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USANew York State Newborn Screening Program, Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USANew York State Newborn Screening Program, Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USAApplied Genomics Technologies Cluster, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USAApplied Genomics Technologies Cluster, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USANew York State Newborn Screening Program, Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USANew York State Newborn Screening Program, Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USANew York State Newborn Screening Program, Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USANewborn screening (NBS) for Cystic Fibrosis (CF) is associated with improved outcomes. All US states screen for CF; however, CF NBS algorithms have high false positive (FP) rates. In New York State (NYS), the positive predictive value of CF NBS improved from 3.7% to 25.2% following the implementation of a three-tier IRT-DNA-SEQ approach using commercially available tests. Here we describe a modification of the NYS CF NBS algorithm via transition to a new custom next-generation sequencing (NGS) platform for more comprehensive cystic fibrosis transmembrane conductance regulator (<i>CFTR</i>) gene analysis. After full gene sequencing, a tiered strategy is used to first analyze only a specific panel of 338 clinically relevant <i>CFTR</i> variants (second-tier), followed by unblinding of all sequence variants and bioinformatic assessment of deletions/duplications in a subset of samples requiring third-tier analysis. We demonstrate the analytical and clinical validity of the assay and the feasibility of use in the NBS setting. The custom assay has streamlined our molecular workflow, increased throughput, and allows for bioinformatic customization of second-tier variant panel content. NBS aims to identify those infants with the highest disease risk. Technological molecular improvements can be applied to NBS algorithms to reduce the burden of FP referrals without loss of sensitivity.https://www.mdpi.com/2409-515X/7/4/73cystic fibrosis (CF)next-generation sequencing (NGS)newborn screening (NBS)IRT-DNA-SEQ algorithm |
| spellingShingle | Robert J. Sicko Colleen F. Stevens Erin E. Hughes Melissa Leisner Helen Ling Carlos A. Saavedra-Matiz Michele Caggana Denise M. Kay Validation of a Custom Next-Generation Sequencing Assay for Cystic Fibrosis Newborn Screening International Journal of Neonatal Screening cystic fibrosis (CF) next-generation sequencing (NGS) newborn screening (NBS) IRT-DNA-SEQ algorithm |
| title | Validation of a Custom Next-Generation Sequencing Assay for Cystic Fibrosis Newborn Screening |
| title_full | Validation of a Custom Next-Generation Sequencing Assay for Cystic Fibrosis Newborn Screening |
| title_fullStr | Validation of a Custom Next-Generation Sequencing Assay for Cystic Fibrosis Newborn Screening |
| title_full_unstemmed | Validation of a Custom Next-Generation Sequencing Assay for Cystic Fibrosis Newborn Screening |
| title_short | Validation of a Custom Next-Generation Sequencing Assay for Cystic Fibrosis Newborn Screening |
| title_sort | validation of a custom next generation sequencing assay for cystic fibrosis newborn screening |
| topic | cystic fibrosis (CF) next-generation sequencing (NGS) newborn screening (NBS) IRT-DNA-SEQ algorithm |
| url | https://www.mdpi.com/2409-515X/7/4/73 |
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