Implementation and validation of an improved allele specific stutter filtering method for electropherogram interpretation

Kalafut, Tim; Schuerman, Curt; Sutton, Joel; Faris, Tom; Armogida, Luigi; Bright, Jo‐Anne; Buckleton, John; Taylor, Duncan

doi:10.1016/j.fsigen.2018.03.016

Cited by 17 publications

(8 citation statements)

References 8 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Profiles were analyzed using OSIRIS (version 2.9) with channel‐dependent analytical thresholds from 50‐90 rfu. ArmedXpert™ (version 3.0.8.6) was used to finalize all allele calls and prepare input tables for interpretation and LR calculation by STRmix™ (version 2.4.06) . All profiles were deconvoluted assigning the apparent number of contributors to the profile based on allele peak heights, and all LRs were calculated using the recommended STRmix™ settings of 8 chains, 100,000 burn‐in accepts per chain and 50,000 post‐burn‐in accepts per chain.…”

Section: Methodsmentioning

confidence: 99%

Using the Nondonor Distribution to Improve Communication and Inform Decision Making for Low LRs from Minor Contributors in Mixed DNA Profiles

Schuerman

Kalafut

Buchanan

et al. 2020

Journal of Forensic Sciences

Self Cite

View full text Add to dashboard Cite

The reporting of a likelihood ratio (LR) calculated from probabilistic genotyping software has become more popular since 2015 and has allowed for the use of more complex mixtures at court. The meaning of “inconclusive” LRs and how to communicate the significance of low LRs at court is now important. We present a method here using the distribution of LRs obtained from nondonors. The nondonor distribution is useful for examining calibration and discrimination for profiles that have produced LRs less than about 104. In this paper, a range of mixed DNA profiles of varying quantity were constructed and the LR distribution considering the minor contributor for a number of nondonors was compared to the expectation given a calibrated system. It is demonstrated that conditioning genotypes should be used where reasonable given the background information to decrease the rate of nondonor LRs above 1. In all 17 cases examined, the LR for the minor donor was higher than the nondonor LRs, and in 12 of the 17 cases, the 99.9 percentile of the nondonor distribution was lower when appropriate conditioning information was used. The output of the tool is a graph that can show the position of the LR for the person of interest set against the nondonor LR distribution. This may assist communication between scientists and the court.

show abstract

Section: Methodsmentioning

confidence: 99%

Using the Nondonor Distribution to Improve Communication and Inform Decision Making for Low LRs from Minor Contributors in Mixed DNA Profiles

Schuerman

Kalafut

Buchanan

et al. 2020

Journal of Forensic Sciences

Self Cite

View full text Add to dashboard Cite

show abstract

“…For the 3SD method, stutter was filtered in FaSTR DNA using per allele stutter models that were calibrated to a subset of the PROVEDIt data. Following Kalafut et al [5] stutter was filtered with a threshold using the expected stutter ratio plus three standard deviations.…”

Section: Analysis and Filteringmentioning

confidence: 99%

“…Allele counting has also been shown to be unreliable when alleles from one or more contributors have dropped out from the profile or when low level alleles from contributors are below the analytical threshold (AT) [3]. Uncertainty in NoC may also be an issue in the presence of a major contributor where trace peaks may be artefactual (for example, stutter) or alleles from a trace contributor [4], where it is not known which peaks in the profile are truly allelic peaks and which are artefacts such as stutters [5].…”

Section: Introductionmentioning

confidence: 99%

“…For instance, the MAC method requires all stutters to be removed and failing to remove a single stutter peak can easily lead to an overestimate of NoC. Models for stutter rates are well characterised and rates have been shown to be stable over a range of different platforms for the same kit and cycle number [5,17,18].…”

Section: Introductionmentioning

confidence: 99%

“…1 Using a combination of the Kalafut et al [5] method to automatically filter allelic specific stutter from DNA profiles with a threshold of three standard deviations and manual DNA profile analysis. Referred to as '3SD'.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Estimating the number of contributors to a DNA profile using decision trees

Kruijver

Kelly

Cheng

et al. 2021

Forensic Science International: Genetics

Self Cite

View full text Add to dashboard Cite

The interpretation of DNA profiles typically starts with an assessment of the number of contributors. In the last two decades, several methods have been proposed to assist with this assessment. We describe a relatively simple method using decision trees, that is fast to run and fully transparent to a forensic analyst. We use mixtures from the publicly available PROVEDIt dataset to demonstrate the performance of the method. We show that the performance of the method crucially depends on the performance of filters for stutter and other artefacts. We compare the performance of the decision tree method with other published methods for the same dataset.

show abstract

MaSTR™: an effective probabilistic genotyping tool for interpretation of STR mixtures associated with differentially degraded DNA

et al. 2022

View full text Add to dashboard Cite

Implementation and validation of an improved allele specific stutter filtering method for electropherogram interpretation

Cited by 17 publications

References 8 publications

Using the Nondonor Distribution to Improve Communication and Inform Decision Making for Low LRs from Minor Contributors in Mixed DNA Profiles

Using the Nondonor Distribution to Improve Communication and Inform Decision Making for Low LRs from Minor Contributors in Mixed DNA Profiles

Estimating the number of contributors to a DNA profile using decision trees

MaSTR™: an effective probabilistic genotyping tool for interpretation of STR mixtures associated with differentially degraded DNA

Contact Info

Product

Resources

About