SuperSelective primer pairs for sensitive detection of rare somatic mutations

Abstract SuperSelective primers, by virtue of their unique design, enable the selective exponential amplification of rare DNA fragments containing somatic mutations in the presence of abundant closely related wild-type DNA fragments. However, when a SuperSelective primer is used in conjunction with...

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Autores principales:	Fred Russell Kramer, Diana Yaneth Vargas
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/43b039342e344c4eb3331baf1432c5c1
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spelling	oai:doaj.org-article:43b039342e344c4eb3331baf1432c5c12021-11-21T12:16:17ZSuperSelective primer pairs for sensitive detection of rare somatic mutations10.1038/s41598-021-00920-42045-2322https://doaj.org/article/43b039342e344c4eb3331baf1432c5c12021-11-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-00920-4https://doaj.org/toc/2045-2322Abstract SuperSelective primers, by virtue of their unique design, enable the selective exponential amplification of rare DNA fragments containing somatic mutations in the presence of abundant closely related wild-type DNA fragments. However, when a SuperSelective primer is used in conjunction with a conventional reverse primer, linear amplification of the abundant wild-type fragments occurs, and this may lead to a late arising signal that can be confused with the late arising signal from the rare mutant fragments. We have discovered that the use of a pair of SuperSelective primers, one specific for the target mutation in a plus strand, and the other specific for the same mutation in the complementary minus strand, but both possessing 3′-terminal nucleotides that are complementary to the mutation, significantly suppresses the linear amplification of the related wild-type sequence, and prevents the generation of false mutant sequences due to mis-incorporation by the DNA polymerase. As a consequence, the absence of mutant fragments in a sample does not give rise to a false-positive signal, and the presence of mutant fragments in a sample is clearly distinguishable as a true-positive signal. The use of SuperSelective primer pairs should enhance the sensitivity of multiplex PCR assays that identify and quantitate somatic mutations in liquid biopsies obtained from patients with cancer, thereby enabling the choice of a targeted therapy, the determination of its effectiveness over time, and the substitution of a more appropriate therapy as new mutations arise.Fred Russell KramerDiana Yaneth VargasNature 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 Fred Russell Kramer Diana Yaneth Vargas SuperSelective primer pairs for sensitive detection of rare somatic mutations
description	Abstract SuperSelective primers, by virtue of their unique design, enable the selective exponential amplification of rare DNA fragments containing somatic mutations in the presence of abundant closely related wild-type DNA fragments. However, when a SuperSelective primer is used in conjunction with a conventional reverse primer, linear amplification of the abundant wild-type fragments occurs, and this may lead to a late arising signal that can be confused with the late arising signal from the rare mutant fragments. We have discovered that the use of a pair of SuperSelective primers, one specific for the target mutation in a plus strand, and the other specific for the same mutation in the complementary minus strand, but both possessing 3′-terminal nucleotides that are complementary to the mutation, significantly suppresses the linear amplification of the related wild-type sequence, and prevents the generation of false mutant sequences due to mis-incorporation by the DNA polymerase. As a consequence, the absence of mutant fragments in a sample does not give rise to a false-positive signal, and the presence of mutant fragments in a sample is clearly distinguishable as a true-positive signal. The use of SuperSelective primer pairs should enhance the sensitivity of multiplex PCR assays that identify and quantitate somatic mutations in liquid biopsies obtained from patients with cancer, thereby enabling the choice of a targeted therapy, the determination of its effectiveness over time, and the substitution of a more appropriate therapy as new mutations arise.
format	article
author	Fred Russell Kramer Diana Yaneth Vargas
author_facet	Fred Russell Kramer Diana Yaneth Vargas
author_sort	Fred Russell Kramer
title	SuperSelective primer pairs for sensitive detection of rare somatic mutations
title_short	SuperSelective primer pairs for sensitive detection of rare somatic mutations
title_full	SuperSelective primer pairs for sensitive detection of rare somatic mutations
title_fullStr	SuperSelective primer pairs for sensitive detection of rare somatic mutations
title_full_unstemmed	SuperSelective primer pairs for sensitive detection of rare somatic mutations
title_sort	superselective primer pairs for sensitive detection of rare somatic mutations
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/43b039342e344c4eb3331baf1432c5c1
work_keys_str_mv	AT fredrussellkramer superselectiveprimerpairsforsensitivedetectionofraresomaticmutations AT dianayanethvargas superselectiveprimerpairsforsensitivedetectionofraresomaticmutations
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SuperSelective primer pairs for sensitive detection of rare somatic mutations

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