A SNP panel for identification of DNA and RNA specimens

• Published in: BMC genomics Vol. 19; no. 1; p. 90
• Main Authors: 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
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 25.01.2018; BioMed Central; BMC
• Subjects: Analysis; Biobanking; Diagnostic specimens; DNA; DNA - analysis; DNA - genetics; DNA Fingerprinting; Ethnic Groups - genetics; Forensics; Gene Frequency; Genetic Testing; Genetic variation; Genetics, Population; Genotype; High-Throughput Nucleotide Sequencing; Humans; Individuality; Linkage Disequilibrium; Mix up samples; Patient Identification Systems - methods; Polymorphism, Single Nucleotide; RNA; RNA - analysis; RNA - genetics; Sample tracking; Single nucleotide polymorphisms; Sample tracking; Biobanking; Forensics; Genetic variation; Mix up samples
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-018-4482-7

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. 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 when assuming no family relations and 1.2 × 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. 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.