Systematic comparison of two whole-genome amplification methods for targeted next-generation sequencing using frozen and FFPE normal and cancer tissues

Abstract Sequencing key cancer-driver genes using formalin-fixed, paraffin-embedded (FFPE) cancer tissues is becoming the standard for identifying the best treatment regimen. However, about 25% of all samples are rejected for genetic analyses for reasons that include too little tissue to extract eno...

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Autores principales:	Pedro Mendez, Li Tai Fang, David M. Jablons, Il-Jin Kim
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/ac0e0e205e9a4dbf83fc291cf8779024
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spelling	oai:doaj.org-article:ac0e0e205e9a4dbf83fc291cf87790242021-12-02T12:32:34ZSystematic comparison of two whole-genome amplification methods for targeted next-generation sequencing using frozen and FFPE normal and cancer tissues10.1038/s41598-017-04419-92045-2322https://doaj.org/article/ac0e0e205e9a4dbf83fc291cf87790242017-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-04419-9https://doaj.org/toc/2045-2322Abstract Sequencing key cancer-driver genes using formalin-fixed, paraffin-embedded (FFPE) cancer tissues is becoming the standard for identifying the best treatment regimen. However, about 25% of all samples are rejected for genetic analyses for reasons that include too little tissue to extract enough high quality DNA. One way to overcome this is to do whole-genome amplification (WGA) in clinical samples, but only limited studies have tested different WGA methods in FFPE cancer specimens using targeted next-generation sequencing (NGS). We therefore tested the two most commonly used WGA methods, multiple displacement amplification (MDA-Qiagen REPLI-g kit) and the hybrid or modified PCR-based method (Sigma/Rubicon Genomics Inc. GenomePlex kit) in FFPE normal and tumor tissue specimens. For the normalized copy number analysis, the FFPE process caused none or very minimal bias. Variations in copy number were minimal in samples amplified using the GenomePlex kit, but they were statistically significantly higher in samples amplified using the REPLI-g kit. The pattern was similar for variant allele frequencies across the samples, which was minimal for the GenomePlex kit but highly variable for the REPLI-g kit. These findings suggest that each WGA method should be tested thoroughly before using it for clinical cancer samples.Pedro MendezLi Tai FangDavid M. JablonsIl-Jin KimNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-10 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Pedro Mendez Li Tai Fang David M. Jablons Il-Jin Kim Systematic comparison of two whole-genome amplification methods for targeted next-generation sequencing using frozen and FFPE normal and cancer tissues
description	Abstract Sequencing key cancer-driver genes using formalin-fixed, paraffin-embedded (FFPE) cancer tissues is becoming the standard for identifying the best treatment regimen. However, about 25% of all samples are rejected for genetic analyses for reasons that include too little tissue to extract enough high quality DNA. One way to overcome this is to do whole-genome amplification (WGA) in clinical samples, but only limited studies have tested different WGA methods in FFPE cancer specimens using targeted next-generation sequencing (NGS). We therefore tested the two most commonly used WGA methods, multiple displacement amplification (MDA-Qiagen REPLI-g kit) and the hybrid or modified PCR-based method (Sigma/Rubicon Genomics Inc. GenomePlex kit) in FFPE normal and tumor tissue specimens. For the normalized copy number analysis, the FFPE process caused none or very minimal bias. Variations in copy number were minimal in samples amplified using the GenomePlex kit, but they were statistically significantly higher in samples amplified using the REPLI-g kit. The pattern was similar for variant allele frequencies across the samples, which was minimal for the GenomePlex kit but highly variable for the REPLI-g kit. These findings suggest that each WGA method should be tested thoroughly before using it for clinical cancer samples.
format	article
author	Pedro Mendez Li Tai Fang David M. Jablons Il-Jin Kim
author_facet	Pedro Mendez Li Tai Fang David M. Jablons Il-Jin Kim
author_sort	Pedro Mendez
title	Systematic comparison of two whole-genome amplification methods for targeted next-generation sequencing using frozen and FFPE normal and cancer tissues
title_short	Systematic comparison of two whole-genome amplification methods for targeted next-generation sequencing using frozen and FFPE normal and cancer tissues
title_full	Systematic comparison of two whole-genome amplification methods for targeted next-generation sequencing using frozen and FFPE normal and cancer tissues
title_fullStr	Systematic comparison of two whole-genome amplification methods for targeted next-generation sequencing using frozen and FFPE normal and cancer tissues
title_full_unstemmed	Systematic comparison of two whole-genome amplification methods for targeted next-generation sequencing using frozen and FFPE normal and cancer tissues
title_sort	systematic comparison of two whole-genome amplification methods for targeted next-generation sequencing using frozen and ffpe normal and cancer tissues
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/ac0e0e205e9a4dbf83fc291cf8779024
work_keys_str_mv	AT pedromendez systematiccomparisonoftwowholegenomeamplificationmethodsfortargetednextgenerationsequencingusingfrozenandffpenormalandcancertissues AT litaifang systematiccomparisonoftwowholegenomeamplificationmethodsfortargetednextgenerationsequencingusingfrozenandffpenormalandcancertissues AT davidmjablons systematiccomparisonoftwowholegenomeamplificationmethodsfortargetednextgenerationsequencingusingfrozenandffpenormalandcancertissues AT iljinkim systematiccomparisonoftwowholegenomeamplificationmethodsfortargetednextgenerationsequencingusingfrozenandffpenormalandcancertissues
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Systematic comparison of two whole-genome amplification methods for targeted next-generation sequencing using frozen and FFPE normal and cancer tissues

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