Fast P(RMNE): Fast forensic DNA probability of random man not excluded calculation

Steven Schwartz,Darrell O Ricke

doi:10.12688/f1000research.13349.2

Steven Schwartz, Darrell O Ricke

Open Access

https://doi.org/10.12688/f1000research.13349.2

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Abstract

High throughput sequencing (HTS) of DNA forensic samples is expanding from the sizing of short tandem repeats (STRs) to massively parallel sequencing (MPS). HTS panels are expanding from the FBI 20 core Combined DNA Index System (CODIS) loci to include SNPs. The calculation of random man not excluded, P(RMNE), is used in DNA mixture analysis to estimate the probability that a person is present in a DNA mixture. This calculation encounters calculation artifacts with expansion to larger panel sizes. Increasing the floating-point precision of the calculations allows for increased panel sizes but with a corresponding increase in computation time. The Taylor series higher precision libraries used fail on some input data sets leading to algorithm unreliability. Herein, a new formula is introduced for calculating P(RMNE) that scales to larger SNP panel sizes while being computationally efficient (patent pending).

Highlights

High throughput sequencing (HTS) of DNA single nucleotide polymorphism (SNP) panels have significant advantages for analysis of DNA mixtures and trace DNA profiles compared to sizing short tandem repeats (STRs)
When the panel size is increased to 3,000 SNPs, the Taylor methods are unable to calculate P(RMNE) values
A calculation artifact was observed for some datasets with the P(RMNE) method implemented in Sherlock’s Toolkit, see Figure 1

Summary

Introduction

High throughput sequencing (HTS) of DNA single nucleotide polymorphism (SNP) panels have significant advantages for analysis of DNA mixtures and trace DNA profiles compared to sizing STRs. Analysis of mixtures by sized STRs is limited to mixtures of two individuals within DNA ratios of 1:1 to 1:10. SNP-based methods offer the potential to analyze complex mixtures of 15 contributors or more[2]. The current method of calculating the significance of a match between a SNP DNA mixture and a reference profile is the random man not excluded P(RMNE) calculation[2] for forensic applications. Performance and precision issues are being observed with current implementations of the P(RMNE) calculations[2]. To address the calculation artifacts and performance issues, a novel P(RMNE) calculation method is presented

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Results

Conclusion