Use of sequenom sample ID plus® SNP genotyping in identification of FFPE tumor samples

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 Douglas Mcpherson

Research output: Contribution to journalArticle

11 Citations (Scopus)

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.

Original languageEnglish (US)
Article numbere88163
JournalPLoS One
Volume9
Issue number2
DOIs
StatePublished - Feb 13 2014
Externally publishedYes

Fingerprint

formalin
Paraffin
Microsatellite Repeats
alkanes
Formaldehyde
genotyping
Single Nucleotide Polymorphism
Tumors
neoplasms
microsatellite repeats
DNA
Neoplasms
Base Pairing
Polymerase Chain Reaction
Amplification
sampling
Tissue
reworks
Forensic Anthropology
Cost Savings

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Use of sequenom sample ID plus® SNP genotyping in identification of FFPE tumor samples. / 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 Douglas.

In: PLoS One, Vol. 9, No. 2, e88163, 13.02.2014.

Research output: Contribution to journalArticle

Miller, JK, Buchner, N, Timms, L, Tam, S, Luo, X, Brown, AMK, Pasternack, D, Bristow, RG, Fraser, M, Boutros, PC & Mcpherson, JD 2014, 'Use of sequenom sample ID plus® SNP genotyping in identification of FFPE tumor samples', PLoS One, vol. 9, no. 2, e88163. https://doi.org/10.1371/journal.pone.0088163
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 Douglas. / Use of sequenom sample ID plus® SNP genotyping in identification of FFPE tumor samples. In: PLoS One. 2014 ; Vol. 9, No. 2.
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