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, D.I. Boomsma, J. van Dongen, J.J. Hottenga, R. Pool

Research output: Contribution to journalArticle

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 × 10- 20 when assuming no family relations and 1.2 × 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.

LanguageEnglish
Pages90
JournalBMC Genomics
Volume19
Issue number1
DOIs
StatePublished - 25 Jan 2018

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Single Nucleotide Polymorphism
RNA
DNA
Genotype
RNA Sequence Analysis
Genetic Research
Linkage Disequilibrium
Crime
Gene Frequency
Biomedical Research
Coloring Agents

Keywords

  • Journal Article

Cite this

Yousefi, S., Abbassi-Daloii, T., Kraaijenbrink, T., Vermaat, M., Mei, H., van 't Hof, P., ... Pool, R. (2018). A SNP panel for identification of DNA and RNA specimens. BMC Genomics, 19(1), 90. DOI: 10.1186/s12864-018-4482-7
Yousefi, Soheil ; Abbassi-Daloii, Tooba ; Kraaijenbrink, Thirsa ; Vermaat, Martijn ; Mei, Hailiang ; van 't Hof, Peter ; van Iterson, Maarten ; Zhernakova, Daria V ; Claringbould, Annique ; Franke, Lude ; 't Hart, Leen M ; Slieker, Roderick C ; van der Heijden, Amber ; de Knijff, Peter ; 't Hoen, Peter A C ; BIOS consortium ; Boomsma, D.I. ; van Dongen, J. ; Hottenga, J.J. ; Pool, R./ A SNP panel for identification of DNA and RNA specimens. In: BMC Genomics. 2018 ; Vol. 19, No. 1. pp. 90
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Yousefi, S, Abbassi-Daloii, T, Kraaijenbrink, T, Vermaat, M, Mei, H, van 't Hof, P, van Iterson, M, Zhernakova, DV, Claringbould, A, Franke, L, 't Hart, LM, Slieker, RC, van der Heijden, A, de Knijff, P, 't Hoen, PAC, BIOS consortium, Boomsma, DI, van Dongen, J, Hottenga, JJ & Pool, R 2018, 'A SNP panel for identification of DNA and RNA specimens' BMC Genomics, vol 19, no. 1, pp. 90. DOI: 10.1186/s12864-018-4482-7

A SNP panel for identification of DNA and RNA specimens. / Yousefi, Soheil; Abbassi-Daloii, Tooba; Kraaijenbrink, Thirsa; Vermaat, Martijn; Mei, Hailiang; van 't Hof, Peter; van Iterson, Maarten; Zhernakova, Daria V; Claringbould, Annique; Franke, Lude; 't Hart, Leen M; Slieker, Roderick C; van der Heijden, Amber; de Knijff, Peter; 't Hoen, Peter A C; BIOS consortium ; Boomsma, D.I.; van Dongen, J.; Hottenga, J.J.; Pool, R.

In: BMC Genomics, Vol. 19, No. 1, 25.01.2018, p. 90.

Research output: Contribution to journalArticle

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T1 - A SNP panel for identification of DNA and RNA specimens

AU - Yousefi,Soheil

AU - Abbassi-Daloii,Tooba

AU - Kraaijenbrink,Thirsa

AU - Vermaat,Martijn

AU - Mei,Hailiang

AU - van 't Hof,Peter

AU - van Iterson,Maarten

AU - Zhernakova,Daria V

AU - Claringbould,Annique

AU - Franke,Lude

AU - 't Hart,Leen M

AU - Slieker,Roderick C

AU - van der Heijden,Amber

AU - de Knijff,Peter

AU - 't Hoen,Peter A C

AU - BIOS consortium

AU - Boomsma,D.I.

AU - van Dongen,J.

AU - Hottenga,J.J.

AU - Pool,R.

PY - 2018/1/25

Y1 - 2018/1/25

N2 - 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 × 10- 20 when assuming no family relations and 1.2 × 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.

AB - 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 × 10- 20 when assuming no family relations and 1.2 × 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.

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Yousefi S, Abbassi-Daloii T, Kraaijenbrink T, Vermaat M, Mei H, van 't Hof P et al. A SNP panel for identification of DNA and RNA specimens. BMC Genomics. 2018 Jan 25;19(1):90. Available from, DOI: 10.1186/s12864-018-4482-7