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Utilization of archived neonatal dried blood spots for genome-wide genotyping
INTRODUCTION: Heel pricks are performed on newborns for diagnostic screenings of various pre-symptomatic metabolic and genetic diseases. Excess blood is spotted on Guthrie cards and archived by many states in biobanks for follow-up diagnoses and public health research. However, storage environment m...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7034898/ https://www.ncbi.nlm.nih.gov/pubmed/32084225 http://dx.doi.org/10.1371/journal.pone.0229352 |
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author | Sok, Pagna Lupo, Philip J. Richard, Melissa A. Rabin, Karen R. Ehli, Erik A. Kallsen, Noah A. Davies, Gareth E. Scheurer, Michael E. Brown, Austin L. |
author_facet | Sok, Pagna Lupo, Philip J. Richard, Melissa A. Rabin, Karen R. Ehli, Erik A. Kallsen, Noah A. Davies, Gareth E. Scheurer, Michael E. Brown, Austin L. |
author_sort | Sok, Pagna |
collection | PubMed |
description | INTRODUCTION: Heel pricks are performed on newborns for diagnostic screenings of various pre-symptomatic metabolic and genetic diseases. Excess blood is spotted on Guthrie cards and archived by many states in biobanks for follow-up diagnoses and public health research. However, storage environment may vary across biobanks and across time within biobanks. With increased applications of DNA extracted from spots for genetic studies, identifying factors associated with genotyping success is critical to maximize DNA quality for future studies. METHOD: We evaluated 399 blood spots, which were part of a genome-wide association study of childhood leukemia risk in children with Down syndrome, archived at the Michigan Neonatal Biobank between 1992 and 2008. High quality DNA was defined as having post-quality control call rate ≥ 99.0% based on the Illumina GenomeStudio 2.0 GenCall algorithm after processing the samples on the Illumina Infinium Global Screening Array. Bivariate analyses and multivariable logistic regression models were applied to evaluate effects of storage environment and storage duration on DNA genotyping quality. RESULTS: Both storage environment and duration were associated with sample genotyping call rates (p-values < 0.001). Sample call rates were associated with storage duration independent of storage environment (p-trend = 0.006 for DBS archived in an uncontrolled environment and p-trend = 0.002 in a controlled environment). However, 95% of the total sample had high genotyping quality with a call rate ≥ 95.0%, a standard threshold for acceptable sample quality in many genetic studies. CONCLUSION: Blood spot DNA quality was lower in samples archived in uncontrolled storage environments and for samples archived for longer durations. Still, regardless of storage environment or duration, neonatal biobanks including the Michigan Neonatal Biobanks can provide access to large collections of spots with DNA quality acceptable for most genotyping studies. |
format | Online Article Text |
id | pubmed-7034898 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-70348982020-02-27 Utilization of archived neonatal dried blood spots for genome-wide genotyping Sok, Pagna Lupo, Philip J. Richard, Melissa A. Rabin, Karen R. Ehli, Erik A. Kallsen, Noah A. Davies, Gareth E. Scheurer, Michael E. Brown, Austin L. PLoS One Research Article INTRODUCTION: Heel pricks are performed on newborns for diagnostic screenings of various pre-symptomatic metabolic and genetic diseases. Excess blood is spotted on Guthrie cards and archived by many states in biobanks for follow-up diagnoses and public health research. However, storage environment may vary across biobanks and across time within biobanks. With increased applications of DNA extracted from spots for genetic studies, identifying factors associated with genotyping success is critical to maximize DNA quality for future studies. METHOD: We evaluated 399 blood spots, which were part of a genome-wide association study of childhood leukemia risk in children with Down syndrome, archived at the Michigan Neonatal Biobank between 1992 and 2008. High quality DNA was defined as having post-quality control call rate ≥ 99.0% based on the Illumina GenomeStudio 2.0 GenCall algorithm after processing the samples on the Illumina Infinium Global Screening Array. Bivariate analyses and multivariable logistic regression models were applied to evaluate effects of storage environment and storage duration on DNA genotyping quality. RESULTS: Both storage environment and duration were associated with sample genotyping call rates (p-values < 0.001). Sample call rates were associated with storage duration independent of storage environment (p-trend = 0.006 for DBS archived in an uncontrolled environment and p-trend = 0.002 in a controlled environment). However, 95% of the total sample had high genotyping quality with a call rate ≥ 95.0%, a standard threshold for acceptable sample quality in many genetic studies. CONCLUSION: Blood spot DNA quality was lower in samples archived in uncontrolled storage environments and for samples archived for longer durations. Still, regardless of storage environment or duration, neonatal biobanks including the Michigan Neonatal Biobanks can provide access to large collections of spots with DNA quality acceptable for most genotyping studies. Public Library of Science 2020-02-21 /pmc/articles/PMC7034898/ /pubmed/32084225 http://dx.doi.org/10.1371/journal.pone.0229352 Text en © 2020 Sok et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Sok, Pagna Lupo, Philip J. Richard, Melissa A. Rabin, Karen R. Ehli, Erik A. Kallsen, Noah A. Davies, Gareth E. Scheurer, Michael E. Brown, Austin L. Utilization of archived neonatal dried blood spots for genome-wide genotyping |
title | Utilization of archived neonatal dried blood spots for genome-wide genotyping |
title_full | Utilization of archived neonatal dried blood spots for genome-wide genotyping |
title_fullStr | Utilization of archived neonatal dried blood spots for genome-wide genotyping |
title_full_unstemmed | Utilization of archived neonatal dried blood spots for genome-wide genotyping |
title_short | Utilization of archived neonatal dried blood spots for genome-wide genotyping |
title_sort | utilization of archived neonatal dried blood spots for genome-wide genotyping |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7034898/ https://www.ncbi.nlm.nih.gov/pubmed/32084225 http://dx.doi.org/10.1371/journal.pone.0229352 |
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