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Infinium Assay for Large-scale SNP Genotyping Applications
Published on: November 19, 2013
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A SNP panel for identification of DNA and RNA specimens
Soheil Yousefi1, Tooba Abbassi-Daloii1, Thirsa Kraaijenbrink1
1Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC, Leiden, The Netherlands.
BMC Genomics
|January 27, 2018
Summary
A novel 50 single-nucleotide polymorphism (SNP) panel uniquely identifies individuals using both DNA and RNA. This genetic tool aids in preventing sample mix-ups in research and forensic applications.
Area of Science:
- Genetics
- Forensic Science
- Molecular Biology
Background:
- Single-nucleotide polymorphism (SNP) panels are crucial for genetic and forensic research.
- Existing SNP panels primarily use DNA profiles and intragenic SNPs.
- Growing interest in RNA expression profiles necessitates a SNP panel for both DNA and RNA genotyping.
Purpose of the Study:
- To establish a SNP panel capable of uniquely identifying individuals from both DNA and RNA data.
- To determine a minimal set of SNPs with maximal discriminative power for dual-level genotyping.
Main Methods:
- Genotype calls were generated from DNA and blood-derived RNA sequencing data of Dutch individuals.
- SNPs were selected based on criteria including call rate, minor allele frequency, Hardy-Weinberg equilibrium, and linkage disequilibrium.
- A panel of 50 SNPs was optimized and validated on an independent population dataset.
Main Results:
- A panel of 50 SNPs achieved unique individual identification with a probability of identity of 6.9 × 10^-20 (unrelated individuals) and 1.2 × 10^-10 (full sibs).
- The SNP panel demonstrated effectiveness in uniquely identifying individuals at both DNA and RNA levels.
- The panel is most effective for individuals of European descent, with reduced power for non-Europeans.
- Most selected SNPs are located in genes expressed across various tissues, though optimization for non-blood tissues is needed.
Conclusions:
- This novel DNA/RNA SNP panel is the first of its kind.
- The panel can identify sample mix-ups in biomedical research.
- It is applicable for assigning DNA and RNA evidence from crime scenes to unique individuals.
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