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Next generation sequencing for clinical diagnostics: Five year experience of an academic laboratory

Clinical laboratories have adopted next generation sequencing (NGS) as a gold standard for the diagnosis of hereditary disorders because of its analytic accuracy, high throughput, and potential for cost-effectiveness. We describe the implementation of a single broad-based NGS sequencing assay to mee...

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Autores principales: Hartman, Paige, Beckman, Kenneth, Silverstein, Kevin, Yohe, Sophia, Schomaker, Matthew, Henzler, Christine, Onsongo, Getiria, Lam, Ham Ching, Munro, Sarah, Daniel, Jerry, Billstein, Bradley, Deshpande, Archana, Hauge, Adam, Mroz, Pawel, Lee, Whiwon, Holle, Jennifer, Wiens, Katie, Karnuth, Kylene, Kemmer, Teresa, Leary, Michaela, Michel, Stephen, Pohlman, Laurie, Thayanithy, Venugopal, Nelson, Andrew, Bower, Matthew, Thyagarajan, Bharat
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6403447/
https://www.ncbi.nlm.nih.gov/pubmed/30891420
http://dx.doi.org/10.1016/j.ymgmr.2019.100464
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author Hartman, Paige
Beckman, Kenneth
Silverstein, Kevin
Yohe, Sophia
Schomaker, Matthew
Henzler, Christine
Onsongo, Getiria
Lam, Ham Ching
Munro, Sarah
Daniel, Jerry
Billstein, Bradley
Deshpande, Archana
Hauge, Adam
Mroz, Pawel
Lee, Whiwon
Holle, Jennifer
Wiens, Katie
Karnuth, Kylene
Kemmer, Teresa
Leary, Michaela
Michel, Stephen
Pohlman, Laurie
Thayanithy, Venugopal
Nelson, Andrew
Bower, Matthew
Thyagarajan, Bharat
author_facet Hartman, Paige
Beckman, Kenneth
Silverstein, Kevin
Yohe, Sophia
Schomaker, Matthew
Henzler, Christine
Onsongo, Getiria
Lam, Ham Ching
Munro, Sarah
Daniel, Jerry
Billstein, Bradley
Deshpande, Archana
Hauge, Adam
Mroz, Pawel
Lee, Whiwon
Holle, Jennifer
Wiens, Katie
Karnuth, Kylene
Kemmer, Teresa
Leary, Michaela
Michel, Stephen
Pohlman, Laurie
Thayanithy, Venugopal
Nelson, Andrew
Bower, Matthew
Thyagarajan, Bharat
author_sort Hartman, Paige
collection PubMed
description Clinical laboratories have adopted next generation sequencing (NGS) as a gold standard for the diagnosis of hereditary disorders because of its analytic accuracy, high throughput, and potential for cost-effectiveness. We describe the implementation of a single broad-based NGS sequencing assay to meet the genetic testing needs at the University of Minnesota. A single hybrid capture library preparation was used for each test ordered, data was informatically blinded to clinically-ordered genes, and identified variants were reviewed and classified by genetic counselors and molecular pathologists. We performed 2509 sequencing tests from August 2012 till December 2017. The diagnostic yield has remained steady at 25%, but the number of variants of uncertain significance (VUS) included in a patient report decreased over time with 50% of the patient reports including at least one VUS in 2012 and only 22% of the patient reports reporting a VUS in 2017 (p = .002). Among the various clinical specialties, the diagnostic yield was highest in dermatology (60% diagnostic yield) and ophthalmology (42% diagnostic yield) while the diagnostic yield was lowest in gastrointestinal diseases and pulmonary diseases (10% detection yield in both specialties). Deletion/duplication analysis was also implemented in a subset of panels ordered, with 9% of samples having a diagnostic finding using the deletion/duplication analysis. We have demonstrated the feasibility of this broad-based NGS platform to meet the needs of our academic institution by aggregating a sufficient sample volume from many individually rare tests and providing a flexible ordering for custom, patient-specific panels.
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spelling pubmed-64034472019-03-19 Next generation sequencing for clinical diagnostics: Five year experience of an academic laboratory Hartman, Paige Beckman, Kenneth Silverstein, Kevin Yohe, Sophia Schomaker, Matthew Henzler, Christine Onsongo, Getiria Lam, Ham Ching Munro, Sarah Daniel, Jerry Billstein, Bradley Deshpande, Archana Hauge, Adam Mroz, Pawel Lee, Whiwon Holle, Jennifer Wiens, Katie Karnuth, Kylene Kemmer, Teresa Leary, Michaela Michel, Stephen Pohlman, Laurie Thayanithy, Venugopal Nelson, Andrew Bower, Matthew Thyagarajan, Bharat Mol Genet Metab Rep Research Paper Clinical laboratories have adopted next generation sequencing (NGS) as a gold standard for the diagnosis of hereditary disorders because of its analytic accuracy, high throughput, and potential for cost-effectiveness. We describe the implementation of a single broad-based NGS sequencing assay to meet the genetic testing needs at the University of Minnesota. A single hybrid capture library preparation was used for each test ordered, data was informatically blinded to clinically-ordered genes, and identified variants were reviewed and classified by genetic counselors and molecular pathologists. We performed 2509 sequencing tests from August 2012 till December 2017. The diagnostic yield has remained steady at 25%, but the number of variants of uncertain significance (VUS) included in a patient report decreased over time with 50% of the patient reports including at least one VUS in 2012 and only 22% of the patient reports reporting a VUS in 2017 (p = .002). Among the various clinical specialties, the diagnostic yield was highest in dermatology (60% diagnostic yield) and ophthalmology (42% diagnostic yield) while the diagnostic yield was lowest in gastrointestinal diseases and pulmonary diseases (10% detection yield in both specialties). Deletion/duplication analysis was also implemented in a subset of panels ordered, with 9% of samples having a diagnostic finding using the deletion/duplication analysis. We have demonstrated the feasibility of this broad-based NGS platform to meet the needs of our academic institution by aggregating a sufficient sample volume from many individually rare tests and providing a flexible ordering for custom, patient-specific panels. Elsevier 2019-03-01 /pmc/articles/PMC6403447/ /pubmed/30891420 http://dx.doi.org/10.1016/j.ymgmr.2019.100464 Text en © 2019 The Authors http://creativecommons.org/licenses/by/4.0/ This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Research Paper
Hartman, Paige
Beckman, Kenneth
Silverstein, Kevin
Yohe, Sophia
Schomaker, Matthew
Henzler, Christine
Onsongo, Getiria
Lam, Ham Ching
Munro, Sarah
Daniel, Jerry
Billstein, Bradley
Deshpande, Archana
Hauge, Adam
Mroz, Pawel
Lee, Whiwon
Holle, Jennifer
Wiens, Katie
Karnuth, Kylene
Kemmer, Teresa
Leary, Michaela
Michel, Stephen
Pohlman, Laurie
Thayanithy, Venugopal
Nelson, Andrew
Bower, Matthew
Thyagarajan, Bharat
Next generation sequencing for clinical diagnostics: Five year experience of an academic laboratory
title Next generation sequencing for clinical diagnostics: Five year experience of an academic laboratory
title_full Next generation sequencing for clinical diagnostics: Five year experience of an academic laboratory
title_fullStr Next generation sequencing for clinical diagnostics: Five year experience of an academic laboratory
title_full_unstemmed Next generation sequencing for clinical diagnostics: Five year experience of an academic laboratory
title_short Next generation sequencing for clinical diagnostics: Five year experience of an academic laboratory
title_sort next generation sequencing for clinical diagnostics: five year experience of an academic laboratory
topic Research Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6403447/
https://www.ncbi.nlm.nih.gov/pubmed/30891420
http://dx.doi.org/10.1016/j.ymgmr.2019.100464
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