Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Sicko, Robert J., Stevens, Colleen F., Hughes, Erin E., Leisner, Melissa, Ling, Helen, Saavedra-Matiz, Carlos A., Caggana, Michele, Kay, Denise M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8628990/
https://www.ncbi.nlm.nih.gov/pubmed/34842611
http://dx.doi.org/10.3390/ijns7040073
_version_ 1784607113995091968
author Sicko, Robert J.
Stevens, Colleen F.
Hughes, Erin E.
Leisner, Melissa
Ling, Helen
Saavedra-Matiz, Carlos A.
Caggana, Michele
Kay, Denise M.
author_facet Sicko, Robert J.
Stevens, Colleen F.
Hughes, Erin E.
Leisner, Melissa
Ling, Helen
Saavedra-Matiz, Carlos A.
Caggana, Michele
Kay, Denise M.
author_sort Sicko, Robert J.
collection PubMed
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 (CFTR) gene analysis. After full gene sequencing, a tiered strategy is used to first analyze only a specific panel of 338 clinically relevant CFTR 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.
format Online
Article
Text
id pubmed-8628990
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-86289902021-11-30 Validation of a Custom Next-Generation Sequencing Assay for Cystic Fibrosis Newborn Screening Sicko, Robert J. Stevens, Colleen F. Hughes, Erin E. Leisner, Melissa Ling, Helen Saavedra-Matiz, Carlos A. Caggana, Michele Kay, Denise M. Int J Neonatal Screen Article 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 (CFTR) gene analysis. After full gene sequencing, a tiered strategy is used to first analyze only a specific panel of 338 clinically relevant CFTR 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. MDPI 2021-11-02 /pmc/articles/PMC8628990/ /pubmed/34842611 http://dx.doi.org/10.3390/ijns7040073 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Sicko, Robert J.
Stevens, Colleen F.
Hughes, Erin E.
Leisner, Melissa
Ling, Helen
Saavedra-Matiz, Carlos A.
Caggana, Michele
Kay, Denise M.
Validation of a Custom Next-Generation Sequencing Assay for Cystic Fibrosis Newborn Screening
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 Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8628990/
https://www.ncbi.nlm.nih.gov/pubmed/34842611
http://dx.doi.org/10.3390/ijns7040073
work_keys_str_mv AT sickorobertj validationofacustomnextgenerationsequencingassayforcysticfibrosisnewbornscreening
AT stevenscolleenf validationofacustomnextgenerationsequencingassayforcysticfibrosisnewbornscreening
AT hugheserine validationofacustomnextgenerationsequencingassayforcysticfibrosisnewbornscreening
AT leisnermelissa validationofacustomnextgenerationsequencingassayforcysticfibrosisnewbornscreening
AT linghelen validationofacustomnextgenerationsequencingassayforcysticfibrosisnewbornscreening
AT saavedramatizcarlosa validationofacustomnextgenerationsequencingassayforcysticfibrosisnewbornscreening
AT cagganamichele validationofacustomnextgenerationsequencingassayforcysticfibrosisnewbornscreening
AT kaydenisem validationofacustomnextgenerationsequencingassayforcysticfibrosisnewbornscreening