Single-copy detection of somatic variants from solid and liquid biopsy

Abstract Accurate detection of somatic variants, against a background of wild-type molecules, is essential for clinical decision making in oncology. Existing approaches, such as allele-specific real-time PCR, are typically limited to a single target gene and lack sensitivity. Alternatively, next-gen...

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Autores principales:	Ana-Luisa Silva, Paulina Klaudyna Powalowska, Magdalena Stolarek, Eleanor Ruth Gray, Rebecca Natalie Palmer, Bram Herman, Cameron Alexander Frayling, Barnaby William Balmforth
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/32a9deb4b5494e9b83600d66a2c7451b
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spelling	oai:doaj.org-article:32a9deb4b5494e9b83600d66a2c7451b2021-12-02T16:31:14ZSingle-copy detection of somatic variants from solid and liquid biopsy10.1038/s41598-021-85545-32045-2322https://doaj.org/article/32a9deb4b5494e9b83600d66a2c7451b2021-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-85545-3https://doaj.org/toc/2045-2322Abstract Accurate detection of somatic variants, against a background of wild-type molecules, is essential for clinical decision making in oncology. Existing approaches, such as allele-specific real-time PCR, are typically limited to a single target gene and lack sensitivity. Alternatively, next-generation sequencing methods suffer from slow turnaround time, high costs, and are complex to implement, typically limiting them to single-site use. Here, we report a method, which we term Allele-Specific PYrophosphorolysis Reaction (ASPYRE), for high sensitivity detection of panels of somatic variants. ASPYRE has a simple workflow and is compatible with standard molecular biology reagents and real-time PCR instruments. We show that ASPYRE has single molecule sensitivity and is tolerant of DNA extracted from plasma and formalin fixed paraffin embedded (FFPE) samples. We also demonstrate two multiplex panels, including one for detection of 47 EGFR variants. ASPYRE presents an effective and accessible method that simplifies highly sensitive and multiplexed detection of somatic variants.Ana-Luisa SilvaPaulina Klaudyna PowalowskaMagdalena StolarekEleanor Ruth GrayRebecca Natalie PalmerBram HermanCameron Alexander FraylingBarnaby William BalmforthNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-9 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ana-Luisa Silva Paulina Klaudyna Powalowska Magdalena Stolarek Eleanor Ruth Gray Rebecca Natalie Palmer Bram Herman Cameron Alexander Frayling Barnaby William Balmforth Single-copy detection of somatic variants from solid and liquid biopsy
description	Abstract Accurate detection of somatic variants, against a background of wild-type molecules, is essential for clinical decision making in oncology. Existing approaches, such as allele-specific real-time PCR, are typically limited to a single target gene and lack sensitivity. Alternatively, next-generation sequencing methods suffer from slow turnaround time, high costs, and are complex to implement, typically limiting them to single-site use. Here, we report a method, which we term Allele-Specific PYrophosphorolysis Reaction (ASPYRE), for high sensitivity detection of panels of somatic variants. ASPYRE has a simple workflow and is compatible with standard molecular biology reagents and real-time PCR instruments. We show that ASPYRE has single molecule sensitivity and is tolerant of DNA extracted from plasma and formalin fixed paraffin embedded (FFPE) samples. We also demonstrate two multiplex panels, including one for detection of 47 EGFR variants. ASPYRE presents an effective and accessible method that simplifies highly sensitive and multiplexed detection of somatic variants.
format	article
author	Ana-Luisa Silva Paulina Klaudyna Powalowska Magdalena Stolarek Eleanor Ruth Gray Rebecca Natalie Palmer Bram Herman Cameron Alexander Frayling Barnaby William Balmforth
author_facet	Ana-Luisa Silva Paulina Klaudyna Powalowska Magdalena Stolarek Eleanor Ruth Gray Rebecca Natalie Palmer Bram Herman Cameron Alexander Frayling Barnaby William Balmforth
author_sort	Ana-Luisa Silva
title	Single-copy detection of somatic variants from solid and liquid biopsy
title_short	Single-copy detection of somatic variants from solid and liquid biopsy
title_full	Single-copy detection of somatic variants from solid and liquid biopsy
title_fullStr	Single-copy detection of somatic variants from solid and liquid biopsy
title_full_unstemmed	Single-copy detection of somatic variants from solid and liquid biopsy
title_sort	single-copy detection of somatic variants from solid and liquid biopsy
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/32a9deb4b5494e9b83600d66a2c7451b
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Single-copy detection of somatic variants from solid and liquid biopsy

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