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. Boomsma; J. 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

doi:10.1186/s12864-018-4482-7

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 journal › Article › Academic › peer-review

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 language	English
Article number	90
Number of pages	12
Journal	BMC Genomics
Volume	19
Issue number	90
DOIs	https://doi.org/10.1186/s12864-018-4482-7
Publication status	Published - 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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Yousefi, S., Abbassi-Daloii, T., Kraaijenbrink, T., Vermaat, M., Mei, H., van't Hof, P., van Iterson, M., Zhernakova, D. V., Claringbould, A., Franke, L., 't Hart, L. M., Slieker, R. C., van der Heijden, A., de Knijff, P., 't Hoen, P. A. C., BIOS Consortium, Jansen, R., van Meurs, J., Heijmans, B. T., ... Franke, L. (2018). A SNP panel for identification of DNA and RNA specimens. BMC Genomics, 19(90), Article 90. https://doi.org/10.1186/s12864-018-4482-7

@article{8e2be9a5c07a428486ed7ad656f7fb4a,

title = "A SNP panel for identification of DNA and RNA specimens",

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.",

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",

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

year = "2018",

month = jan,

day = "25",

doi = "10.1186/s12864-018-4482-7",

language = "English",

volume = "19",

journal = "BMC Genomics",

issn = "1471-2164",

publisher = "BioMed Central Ltd",

number = "90",

}

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, Jansen, R, van Meurs, J, Heijmans, BT, Boomsma, DI, van Dongen, J, Hottenga, J-J, Slagboom, PE, Suchiman, HED, van Iterson, M, van Zwet, EW, 't Hoen, P, Pool, R, van Greevenbroek, M , Stehouwer, C , van der Kallen, C , Schalkwijk, C, Wijmenga, C, Zhernakova, A, Tigchelaar, EF, Beekman, M, Deelen, J, van Heemst, D, Veldink, JH, van den Berg, LH, van Duijn, CM, Hofman, BA, Uitterlinden, AG, Jhamai, PM, Verbiest, M, Verkerk, M, van der Breggen, R, van Rooij, J, Lakenberg, N, Mei, H, Bot, J, Zhernakova, DV, Van't Hof, P, Deelen, P, Nooren, I, Moed, M, Vermaat, M, Bonder, MJ, van Dijk, F, van Galen, M, Arindrarto, W, Kielbasa, SM, Swertz, MA, Isaacs, A & Franke, L 2018, 'A SNP panel for identification of DNA and RNA specimens', BMC Genomics, vol. 19, no. 90, 90. https://doi.org/10.1186/s12864-018-4482-7

TY - JOUR

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 - Jansen, R.

AU - van Meurs, J.

AU - Heijmans, B.T.

AU - Boomsma, D.I.

AU - van Dongen, J.

AU - Hottenga, Jouke-Jan

AU - Slagboom, P.E.

AU - Suchiman, H. Eka D.

AU - van Iterson, Maarten

AU - van Zwet, Erik W.

AU - 't Hoen, P.

AU - Pool, R.

AU - van Greevenbroek, Marleen

AU - Stehouwer, Coen

AU - van der Kallen, Carla

AU - Schalkwijk, Casper

AU - Wijmenga, C.

AU - Zhernakova, A.

AU - Tigchelaar, E.F.

AU - Beekman, M

AU - Deelen, J

AU - van Heemst, D.

AU - Veldink, J H.

AU - van den Berg, L.H.

AU - van Duijn, C.M.

AU - Hofman, B. A.

AU - Uitterlinden, A. G.

AU - Jhamai, P. Mila

AU - Verbiest, M.

AU - Verkerk, M.

AU - van der Breggen, Ruud

AU - van Rooij, J.

AU - Lakenberg, N.

AU - Mei, H.

AU - Bot, J.

AU - Zhernakova, D. V.

AU - Van't Hof, P.

AU - Deelen, P.

AU - Nooren, I.

AU - Moed, M.

AU - Vermaat, M.

AU - Bonder, M.J.

AU - van Dijk, F.

AU - van Galen, M.

AU - Arindrarto, Wibowo

AU - Kielbasa, Szymon M.

AU - Swertz, Morris A.

AU - Isaacs, A.

AU - Franke, L.

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 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.

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 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.

KW - Genetic variation

KW - Sample tracking

KW - Mix up samples

KW - Biobanking

KW - Forensics

KW - CODIS CORE LOCI

KW - INDIVIDUAL IDENTIFICATION

KW - FORENSIC IDENTIFICATION

KW - MESSENGER-RNA

KW - UNITED-STATES

KW - POPULATIONS

KW - MARKERS

KW - MULTIPLEX

KW - BLOOD

KW - VALIDATION

U2 - 10.1186/s12864-018-4482-7

DO - 10.1186/s12864-018-4482-7

M3 - Article

C2 - 29370748

SN - 1471-2164

VL - 19

JO - BMC Genomics

JF - BMC Genomics

IS - 90

M1 - 90

ER -