A ranking index for quality assessment of forensic DNA profiles

Background: Assessment of DNA profile quality is vital in forensic DNA analysis, both in order to determine the evidentiary value of DNA results and to compare the performance of different DNA analysis protocols. Generally the quality assessment is performed through manual examination of the DNA profiles based on empirical knowledge, or by comparing the intensities (allelic peak heights) of the capillary electrophoresis electropherograms. Results: We recently developed a ranking index for unbiased and quantitative quality assessment of forensic DNA profiles, the forensic DNA profile index (FI) (Hedman et al. Improved forensic DNA analysis through the use of alternative DNA polymerases and statistical modeling of DNA profiles, Biotechniques 47 (2009) 951-958). FI uses electropherogram data to combine the intensities of the allelic peaks with the balances within and between loci, using Principal Components Analysis. Here we present the construction of FI. We explain the mathematical and statistical methodologies used and present details about the applied data reduction method. Thereby we show how to adapt the ranking index for any Short Tandem Repeat-based forensic DNA typing system through validation against a manual grading scale and calibration against a specific set of DNA profiles. Conclusions: The developed tool provides unbiased quality assessment of forensic DNA profiles. It can be applied for any DNA profiling system based on Short Tandem Repeat markers. Apart from crime related DNA analysis, FI can therefore be used as a quality tool in paternal or familial testing as well as in disaster victim identification. Background The object of forensic DNA analysis is to generate individual-specific DNA profiles from crime scene stains and reference samples, thereby linking perpetrators to crimes. The analytical process includes sampling, DNA extraction/purification, and amplification of certain genetic markers (Short Tandem Repeats, STR) using the polymerase chain reaction (PCR). The actual DNA profile is generated by capillary electrophoresis separation of DNA fragments and detection using fluorescently labeled primers. An electropherogram (EPG) is produced where the intensity of the allelic peaks corresponds to the amount of produced DNA fragments, and the balance between peaks gives information on the reliability of the DNA profile (Figure 1). The amount and purity of the DNA is determined by all steps in the analytical process and subsequently affect the quality of the EPG/DNA profile. Consequently, assessment of DNA profile quality is vital both for establishing the evidentiary value of a certain DNA profile and for comparing the relative performance of different DNA analysis protocols, e.g., in validation studies. In the last years, several statistical models and expert systems have been developed to streamline and simplify the routine evaluation of forensic DNA profiles [1-3], to aid in the interpretation of mixed DNA profiles [4,5] and to estimate the risk of encountering artifact peaks and/or allelic drop-outs [6-9]. However, assessment of DNA profile quality is generally not quantified or treated in an unbiased way. For example, in most studies comparing the performance of different forensic DNA analysis protocols, DNA profile quality is either assessed by manual examination based on empirical knowledge, and/or by comparing the intensities (allelic peak heights or areas) of the EPG/DNA profiles [10-14]. Manual examination has its apparent drawbacks in the difficulty for reproducibility and automation. The intensity is a * Correspondence: [email protected] Swedish National Laboratory of Forensic Science (SKL), SE-581 94 Linköping, Sweden Full list of author information is available at the end of the article Hedman et al. BMC Research Notes 2010, 3:290 http://www.biomedcentral.com/1756-0500/3/290 © 2010 Nordgaard et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Figure 1 Two EPGs/DNA profiles obtained from DNA analysis of a crime scene DNA sample using two different DNA polymerases. The DNA profiles were generated using A) standard AmpliTaq Gold DNA polymerase and B) an alternative DNA polymerase. The sample is a swab from a spoon found in a honey jar, with a DNA concentration of 0.09 ng/μl. Primers from the AmpFlSTR SGM Plus kit were used for both analyses. Peak heights are given in relative fluorescence units (rfu). Hedman et al. BMC Research Notes 2010, 3:290 http://www.biomedcentral.com/1756-0500/3/290 Page 2 of 10