STR profiling and Copy Number Variation analysis on single, preserved cells using current Whole Genome Amplification methods

Abstract The growing interest in liquid biopsies for cancer research and cell-based non-invasive prenatal testing (NIPT) invigorates the need for improved single cell analysis. In these applications, target cells are extremely rare and fragile in peripheral circulation, which makes the genetic analy...

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Autores principales:	Ann-Sophie Vander Plaetsen, Lieselot Deleye, Senne Cornelis, Laurentijn Tilleman, Filip Van Nieuwerburgh, Dieter Deforce
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e01b2b8da70542ac943ce8b4e70398e9
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spelling	oai:doaj.org-article:e01b2b8da70542ac943ce8b4e70398e92021-12-02T15:06:05ZSTR profiling and Copy Number Variation analysis on single, preserved cells using current Whole Genome Amplification methods10.1038/s41598-017-17525-52045-2322https://doaj.org/article/e01b2b8da70542ac943ce8b4e70398e92017-12-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-17525-5https://doaj.org/toc/2045-2322Abstract The growing interest in liquid biopsies for cancer research and cell-based non-invasive prenatal testing (NIPT) invigorates the need for improved single cell analysis. In these applications, target cells are extremely rare and fragile in peripheral circulation, which makes the genetic analysis very challenging. To overcome these challenges, cell stabilization and unbiased whole genome amplification are required. This study investigates the performance of four WGA methods on single or a limited number of cells after 24 hour of Streck Cell-Free DNA BCT preservation. The suitability of the DNA, amplified with Ampli1, DOPlify, PicoPLEX and REPLI-g, was assessed for both short tandem repeat (STR) profiling and copy number variant (CNV) analysis after shallow whole genome massively parallel sequencing (MPS). Results demonstrate that Ampli1, DOPlify and PicoPLEX perform well for both applications, with some differences between the methods. Samples amplified with REPLI-g did not result in suitable STR or CNV profiles, indicating that this WGA method is not able to generate high quality DNA after Streck Cell-Free DNA BCT stabilization of the cells.Ann-Sophie Vander PlaetsenLieselot DeleyeSenne CornelisLaurentijn TillemanFilip Van NieuwerburghDieter DeforceNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-9 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ann-Sophie Vander Plaetsen Lieselot Deleye Senne Cornelis Laurentijn Tilleman Filip Van Nieuwerburgh Dieter Deforce STR profiling and Copy Number Variation analysis on single, preserved cells using current Whole Genome Amplification methods
description	Abstract The growing interest in liquid biopsies for cancer research and cell-based non-invasive prenatal testing (NIPT) invigorates the need for improved single cell analysis. In these applications, target cells are extremely rare and fragile in peripheral circulation, which makes the genetic analysis very challenging. To overcome these challenges, cell stabilization and unbiased whole genome amplification are required. This study investigates the performance of four WGA methods on single or a limited number of cells after 24 hour of Streck Cell-Free DNA BCT preservation. The suitability of the DNA, amplified with Ampli1, DOPlify, PicoPLEX and REPLI-g, was assessed for both short tandem repeat (STR) profiling and copy number variant (CNV) analysis after shallow whole genome massively parallel sequencing (MPS). Results demonstrate that Ampli1, DOPlify and PicoPLEX perform well for both applications, with some differences between the methods. Samples amplified with REPLI-g did not result in suitable STR or CNV profiles, indicating that this WGA method is not able to generate high quality DNA after Streck Cell-Free DNA BCT stabilization of the cells.
format	article
author	Ann-Sophie Vander Plaetsen Lieselot Deleye Senne Cornelis Laurentijn Tilleman Filip Van Nieuwerburgh Dieter Deforce
author_facet	Ann-Sophie Vander Plaetsen Lieselot Deleye Senne Cornelis Laurentijn Tilleman Filip Van Nieuwerburgh Dieter Deforce
author_sort	Ann-Sophie Vander Plaetsen
title	STR profiling and Copy Number Variation analysis on single, preserved cells using current Whole Genome Amplification methods
title_short	STR profiling and Copy Number Variation analysis on single, preserved cells using current Whole Genome Amplification methods
title_full	STR profiling and Copy Number Variation analysis on single, preserved cells using current Whole Genome Amplification methods
title_fullStr	STR profiling and Copy Number Variation analysis on single, preserved cells using current Whole Genome Amplification methods
title_full_unstemmed	STR profiling and Copy Number Variation analysis on single, preserved cells using current Whole Genome Amplification methods
title_sort	str profiling and copy number variation analysis on single, preserved cells using current whole genome amplification methods
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/e01b2b8da70542ac943ce8b4e70398e9
work_keys_str_mv	AT annsophievanderplaetsen strprofilingandcopynumbervariationanalysisonsinglepreservedcellsusingcurrentwholegenomeamplificationmethods AT lieselotdeleye strprofilingandcopynumbervariationanalysisonsinglepreservedcellsusingcurrentwholegenomeamplificationmethods AT sennecornelis strprofilingandcopynumbervariationanalysisonsinglepreservedcellsusingcurrentwholegenomeamplificationmethods AT laurentijntilleman strprofilingandcopynumbervariationanalysisonsinglepreservedcellsusingcurrentwholegenomeamplificationmethods AT filipvannieuwerburgh strprofilingandcopynumbervariationanalysisonsinglepreservedcellsusingcurrentwholegenomeamplificationmethods AT dieterdeforce strprofilingandcopynumbervariationanalysisonsinglepreservedcellsusingcurrentwholegenomeamplificationmethods
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STR profiling and Copy Number Variation analysis on single, preserved cells using current Whole Genome Amplification methods

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