A SNP panel for identification of DNA and RNA specimens

Bios Consortium ,Soheil Yousefi,Hailiang Mei,Peter De Knijff,Daria V Zhernakova,Leen M ‘T Hart,Amber Van Der Heijden,Thirsa Kraaijenbrink,Roderick C Slieker,Maarten Van Iterson,Martijn Vermaat,Peter Van ‘T Hof,Annique Claringbould,Tooba Abbassi-Daloii,Lude Franke,Peter A C ’T Hoen

doi:10.1186/s12864-018-4482-7

Abstract

BackgroundSNP 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.ResultsTo 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.ConclusionsThis 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.

Highlights

Single Nucleotide Polymorphisms (SNPs) panels that uniquely identify an individual are useful for genetic and forensic research
Data and SNP identification In previous studies, most of the recommended individual identification SNP panels were generated based on DNA profiles and they mostly contain intragenic SNPs
In this study both DNA and RNA-based genotype calls were used to find a small set of SNPs that can be used for identification of individuals

Summary

Introduction

SNP panels that uniquely identify an individual are useful for genetic and forensic research. Yousefi et al BMC Genomics (2018) 19:90 populations [9,10,11] Despite their high discriminatory power, they have some limitations such as required large amplicon sizes, high mutation rates, and the presence of artefacts, which can negatively influence the downstream analysis [12, 13]. To overcome these limitations, SNPs have been more recently introduced for individual identification [14]

Methods

Results

Discussion

Conclusion