A SNP panel for identification of DNA and RNA specimens

Soheil Yousefi, Tooba Abbassi-Daloii, Thirsa Kraaijenbrink, Martijn Vermaat, Hailiang Mei, Peter van't Hof, Maarten van Iterson, Daria V. Zhernakova, Annique Claringbould, Lude Franke, Leen M. 't Hart, Roderick C. Slieker, Amber van der Heijden, Peter de Knijff, Peter A. C. 't Hoen*, BIOS Consortium, R. Jansen, J. van Meurs, B.T. Heijmans, D.I. BoomsmaJ. van Dongen, Jouke-Jan Hottenga, P.E. Slagboom, H. Eka D. Suchiman, Maarten van Iterson, Erik W. van Zwet, P. 't Hoen, R. Pool, Marleen van Greevenbroek, Coen Stehouwer, Carla van der Kallen, Casper Schalkwijk, C. Wijmenga, A. Zhernakova, E.F. Tigchelaar, M Beekman, J Deelen, D. van Heemst, J H. Veldink, L.H. van den Berg, C.M. van Duijn, B. A. Hofman, A. G. Uitterlinden, P. Mila Jhamai, M. Verbiest, M. Verkerk, Ruud van der Breggen, J. van Rooij, N. Lakenberg, H. Mei, J. Bot, D. V. Zhernakova, P. Van't Hof, P. Deelen, I. Nooren, M. Moed, M. Vermaat, M.J. Bonder, F. van Dijk, M. van Galen, Wibowo Arindrarto, Szymon M. Kielbasa, Morris A. Swertz, A. Isaacs, L. Franke

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

17 Citations (Web of Science)

Abstract

Background: SNP panels that uniquely identify an individual are useful for genetic and forensic research. Previously recommended SNP panels are based on DNA profiles and mostly contain intragenic SNPs. With the increasing interest in RNA expression profiles, we aimed for establishing a SNP panel for both DNA and RNA-based genotyping.

Results: To determine a small set of SNPs with maximally discriminative power, genotype calls were obtained from DNA and blood-derived RNA sequencing data belonging to healthy, geographically dispersed, Dutch individuals. SNPs were selected based on different criteria like genotype call rate, minor allele frequency, Hardy-Weinberg equilibrium and linkage disequilibrium. A panel of 50 SNPs was sufficient to identify an individual uniquely: the probability of identity was 6.9 x 10(-20) when assuming no family relations and 1.2 x 10(-10) when accounting for the presence of full sibs. The ability of the SNP panel to uniquely identify individuals on DNA and RNA level was validated in an independent population dataset. The panel is applicable to individuals from European descent, with slightly lower power in non-Europeans. Whereas most of the genes containing the 50 SNPs are expressed in various tissues, our SNP panel needs optimization for other tissues than blood.

Conclusions: This first DNA/RNA SNP panel will be useful to identify sample mix-ups in biomedical research and for assigning DNA and RNA stains in crime scenes to unique individuals.

Original languageEnglish
Article number90
Number of pages12
JournalBMC Genomics
Volume19
Issue number90
DOIs
Publication statusPublished - 25 Jan 2018

Keywords

  • Genetic variation
  • Sample tracking
  • Mix up samples
  • Biobanking
  • Forensics
  • CODIS CORE LOCI
  • INDIVIDUAL IDENTIFICATION
  • FORENSIC IDENTIFICATION
  • MESSENGER-RNA
  • UNITED-STATES
  • POPULATIONS
  • MARKERS
  • MULTIPLEX
  • BLOOD
  • VALIDATION

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