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

• Published in: PloS one Vol. 9; no. 2; p. e88163
• Main Authors: Miller, Jessica K, Buchner, Nicholas, Timms, Lee, Tam, Shirley, Luo, Xuemei, Brown, Andrew M K, Pasternack, Danielle, Bristow, Robert G, Fraser, Michael, Boutros, Paul C, McPherson, John D
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 13.02.2014; Public Library of Science (PLoS)
• Subjects: Amplification; Analysis; Base pairs; Biology; Biophysics; Biotechnology industries; Deoxyribonucleic acid; DNA; DNA sequencing; DNA, Neoplasm - genetics; DNA, Neoplasm - isolation & purification; Fixatives; Forensic science; Formaldehyde; Gene sequencing; Genetic Markers; Genetic testing; Genomes; Genotyping; Genotyping Techniques; Humans; Identification; Identification methods; Male; Medical research; Medicine; Microsatellite Repeats; Multiplexing; Paraffin; Paraffin Embedding; Polymerase chain reaction; Polymorphism, Single Nucleotide; Prostate cancer; Prostatic Neoplasms - diagnosis; Prostatic Neoplasms - genetics; Quality Control; Quality management; Quality standards; Sampling methods; Short tandem repeats; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Tissues; Tumors
• DOI: 10.1371/journal.pone.0088163
• ISSN: 1932-6203

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.