title: Use of Sequenom sample ID Plus® SNP genotyping in identification of FFPE tumor samples.
abstract: 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.
authors.affiliation: Department of Genome Technologies, Ontario Institute for Cancer Research, Toronto, Canada.
authors.forename: Jessica K
authors.initials: JK
authors.lastname: Miller
authors.affiliation: Department of Genome Technologies, Ontario Institute for Cancer Research, Toronto, Canada.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Buchner
authors.affiliation: Department of Genome Technologies, Ontario Institute for Cancer Research, Toronto, Canada.
authors.forename: Lee
authors.initials: L
authors.lastname: Timms
authors.affiliation: Department of Genome Technologies, Ontario Institute for Cancer Research, Toronto, Canada.
authors.forename: Shirley
authors.initials: S
authors.lastname: Tam
authors.affiliation: Department of Genome Technologies, Ontario Institute for Cancer Research, Toronto, Canada.
authors.forename: Xuemei
authors.initials: X
authors.lastname: Luo
authors.affiliation: Department of Genome Technologies, Ontario Institute for Cancer Research, Toronto, Canada.
authors.forename: Andrew M K
authors.initials: AM
authors.lastname: Brown
authors.affiliation: Department of Genome Technologies, Ontario Institute for Cancer Research, Toronto, Canada.
authors.forename: Danielle
authors.initials: D
authors.lastname: Pasternack
authors.affiliation: Ontario Cancer Institute/Princess Margaret Hospital, Toronto, Canada ; Department of Medical Biophysics, University of Toronto, Toronto, Canada.
authors.forename: Robert G
authors.initials: RG
authors.lastname: Bristow
authors.affiliation: Ontario Cancer Institute/Princess Margaret Hospital, Toronto, Canada.
authors.forename: Michael
authors.initials: M
authors.lastname: Fraser
authors.affiliation: Informatics & Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, Canada ; Department of Medical Biophysics, University of Toronto, Toronto, Canada ; Department of Pharmacology & Toxicology, University of Toronto, Toronto, Canada.
authors.forename: Paul C
authors.initials: PC
authors.lastname: Boutros
authors.affiliation: Department of Genome Technologies, Ontario Institute for Cancer Research, Toronto, Canada ; Department of Medical Biophysics, University of Toronto, Toronto, Canada.
authors.forename: John D
authors.initials: JD
authors.lastname: McPherson
mesh_terms: D004273:DNA, Neoplasm / Q000235:genetics / Q000302:isolation & purification*; D005404:Fixatives; D005557:Formaldehyde; D005819:Genetic Markers; D060005:Genotyping Techniques; D006801:Humans; D008297:Male; D018895:Microsatellite Repeats; D016612:Paraffin Embedding; D020641:Polymorphism, Single Nucleotide; D011471:Prostatic Neoplasms / Q000175:diagnosis / Q000235:genetics*; D011786:Quality Control
chemical_list: D004273:DNA, Neoplasm; D005404:Fixatives; D005819:Genetic Markers; D005557:Formaldehyde