Use of Sequenom sample ID Plus® SNP genotyping in identification of FFPE tumor samples.

Short tandem repeat (STR) analysis, such as the AmpFlSTR® Identifiler® Plus kit, is a standard, PCR-based human genotyping method used in the field of forensics. Misidentification of cell line and tissue DNA can be costly if not detected early; therefore it is necessary to have quality control measu...

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Autores principales:	Jessica K Miller, Nicholas Buchner, Lee Timms, Shirley Tam, Xuemei Luo, Andrew M K Brown, Danielle Pasternack, Robert G Bristow, Michael Fraser, Paul C Boutros, John D McPherson
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/294f29ce8aa6499fb83e2cc5958f7c8d
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spelling	oai:doaj.org-article:294f29ce8aa6499fb83e2cc5958f7c8d2021-11-18T08:32:40ZUse of Sequenom sample ID Plus® SNP genotyping in identification of FFPE tumor samples.1932-620310.1371/journal.pone.0088163https://doaj.org/article/294f29ce8aa6499fb83e2cc5958f7c8d2014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24551080/?tool=EBIhttps://doaj.org/toc/1932-6203Short tandem repeat (STR) analysis, such as the AmpFlSTR® Identifiler® Plus kit, is a standard, PCR-based human genotyping method used in the field of forensics. Misidentification of cell line and tissue DNA can be costly if not detected early; therefore it is necessary to have quality control measures such as STR profiling in place. A major issue in large-scale research studies involving archival formalin-fixed paraffin embedded (FFPE) tissues is that varying levels of DNA degradation can result in failure to correctly identify samples using STR genotyping. PCR amplification of STRs of several hundred base pairs is not always possible when DNA is degraded. The Sample ID Plus® panel from Sequenom allows for human DNA identification and authentication using SNP genotyping. In comparison to lengthy STR amplicons, this multiplexing PCR assay requires amplification of only 76-139 base pairs, and utilizes 47 SNPs to discriminate between individual samples. In this study, we evaluated both STR and SNP genotyping methods of sample identification, with a focus on paired FFPE tumor/normal DNA samples intended for next-generation sequencing (NGS). The ability to successfully validate the identity of FFPE samples can enable cost savings by reducing rework.Jessica K MillerNicholas BuchnerLee TimmsShirley TamXuemei LuoAndrew M K BrownDanielle PasternackRobert G BristowMichael FraserPaul C BoutrosJohn D McPhersonPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 2, p e88163 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jessica K Miller Nicholas Buchner Lee Timms Shirley Tam Xuemei Luo Andrew M K Brown Danielle Pasternack Robert G Bristow Michael Fraser Paul C Boutros John D McPherson Use of Sequenom sample ID Plus® SNP genotyping in identification of FFPE tumor samples.
description	Short tandem repeat (STR) analysis, such as the AmpFlSTR® Identifiler® Plus kit, is a standard, PCR-based human genotyping method used in the field of forensics. Misidentification of cell line and tissue DNA can be costly if not detected early; therefore it is necessary to have quality control measures such as STR profiling in place. A major issue in large-scale research studies involving archival formalin-fixed paraffin embedded (FFPE) tissues is that varying levels of DNA degradation can result in failure to correctly identify samples using STR genotyping. PCR amplification of STRs of several hundred base pairs is not always possible when DNA is degraded. The Sample ID Plus® panel from Sequenom allows for human DNA identification and authentication using SNP genotyping. In comparison to lengthy STR amplicons, this multiplexing PCR assay requires amplification of only 76-139 base pairs, and utilizes 47 SNPs to discriminate between individual samples. In this study, we evaluated both STR and SNP genotyping methods of sample identification, with a focus on paired FFPE tumor/normal DNA samples intended for next-generation sequencing (NGS). The ability to successfully validate the identity of FFPE samples can enable cost savings by reducing rework.
format	article
author	Jessica K Miller Nicholas Buchner Lee Timms Shirley Tam Xuemei Luo Andrew M K Brown Danielle Pasternack Robert G Bristow Michael Fraser Paul C Boutros John D McPherson
author_facet	Jessica K Miller Nicholas Buchner Lee Timms Shirley Tam Xuemei Luo Andrew M K Brown Danielle Pasternack Robert G Bristow Michael Fraser Paul C Boutros John D McPherson
author_sort	Jessica K Miller
title	Use of Sequenom sample ID Plus® SNP genotyping in identification of FFPE tumor samples.
title_short	Use of Sequenom sample ID Plus® SNP genotyping in identification of FFPE tumor samples.
title_full	Use of Sequenom sample ID Plus® SNP genotyping in identification of FFPE tumor samples.
title_fullStr	Use of Sequenom sample ID Plus® SNP genotyping in identification of FFPE tumor samples.
title_full_unstemmed	Use of Sequenom sample ID Plus® SNP genotyping in identification of FFPE tumor samples.
title_sort	use of sequenom sample id plus® snp genotyping in identification of ffpe tumor samples.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/294f29ce8aa6499fb83e2cc5958f7c8d
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Use of Sequenom sample ID Plus® SNP genotyping in identification of FFPE tumor samples.

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