Literature DB >> 26720812

EuroForMix: An open source software based on a continuous model to evaluate STR DNA profiles from a mixture of contributors with artefacts.

Øyvind Bleka1, Geir Storvik2, Peter Gill3.   

Abstract

We have released a software named EuroForMix to analyze STR DNA profiles in a user-friendly graphical user interface. The software implements a model to explain the allelic peak height on a continuous scale in order to carry out weight-of-evidence calculations for profiles which could be from a mixture of contributors. Through a properly parameterized model we are able to do inference on mixture proportions, the peak height properties, stutter proportion and degradation. In addition, EuroForMix includes models for allele drop-out, allele drop-in and sub-population structure. EuroForMix supports two inference approaches for likelihood ratio calculations. The first approach uses maximum likelihood estimation of the unknown parameters. The second approach is Bayesian based which requires prior distributions to be specified for the parameters involved. The user may specify any number of known and unknown contributors in the model, however we find that there is a practical computing time limit which restricts the model to a maximum of four unknown contributors. EuroForMix is the first freely open source, continuous model (accommodating peak height, stutter, drop-in, drop-out, population substructure and degradation), to be reported in the literature. It therefore serves an important purpose to act as an unrestricted platform to compare different solutions that are available. The implementation of the continuous model used in the software showed close to identical results to the R-package DNAmixtures, which requires a HUGIN Expert license to be used. An additional feature in EuroForMix is the ability for the user to adapt the Bayesian inference framework by incorporating their own prior information.
Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Keywords:  Forensic statistics; Open-source software; STR DNA interpretation

Mesh:

Substances:

Year:  2015        PMID: 26720812     DOI: 10.1016/j.fsigen.2015.11.008

Source DB:  PubMed          Journal:  Forensic Sci Int Genet        ISSN: 1872-4973            Impact factor:   4.882


  24 in total

1.  Towards developing forensically relevant single-cell pipelines by incorporating direct-to-PCR extraction: compatibility, signal quality, and allele detection.

Authors:  Nidhi Sheth; Harish Swaminathan; Amanda J Gonzalez; Ken R Duffy; Catherine M Grgicak
Journal:  Int J Legal Med       Date:  2021-01-23       Impact factor: 2.686

Review 2.  Separation/extraction, detection, and interpretation of DNA mixtures in forensic science (review).

Authors:  Ruiyang Tao; Shouyu Wang; Jiashuo Zhang; Jingyi Zhang; Zihao Yang; Xiang Sheng; Yiping Hou; Suhua Zhang; Chengtao Li
Journal:  Int J Legal Med       Date:  2018-05-25       Impact factor: 2.686

3.  Estimation of the number of contributors to mixed samples of DNA by mitochondrial DNA analyses using massively parallel sequencing.

Authors:  Hiroaki Nakanishi; Koji Fujii; Hiroaki Nakahara; Natsuko Mizuno; Kazumasa Sekiguchi; Katsumi Yoneyama; Masaaki Hara; Aya Takada; Kazuyuki Saito
Journal:  Int J Legal Med       Date:  2019-11-12       Impact factor: 2.686

4.  Enhanced mixture interpretation with macrohaplotypes based on long-read DNA sequencing.

Authors:  Jianye Ge; Jonathan King; Sammed Mandape; Bruce Budowle
Journal:  Int J Legal Med       Date:  2021-08-11       Impact factor: 2.686

5.  Estimating individual mtDNA haplotypes in mixed DNA samples by combining MinION and MiSeq.

Authors:  Hiroaki Nakanishi; Katsumi Yoneyama; Masaaki Hara; Aya Takada; Kentaro Sakai; Kazuyuki Saito
Journal:  Int J Legal Med       Date:  2022-01-10       Impact factor: 2.686

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

Authors:  Mitchell M Holland; Teresa M Tiedge; Abigail J Bender; Sidney A Gaston-Sanchez; Jennifer A McElhoe
Journal:  Int J Legal Med       Date:  2022-01-29       Impact factor: 2.686

7.  Four model variants within a continuous forensic DNA mixture interpretation framework: Effects on evidential inference and reporting.

Authors:  Harish Swaminathan; Muhammad O Qureshi; Catherine M Grgicak; Ken Duffy; Desmond S Lun
Journal:  PLoS One       Date:  2018-11-20       Impact factor: 3.240

8.  Massively parallel sequencing analysis of nondegraded and degraded DNA mixtures using the ForenSeq™ system in combination with EuroForMix software.

Authors:  Hsiao-Lin Hwa; Ming-Yih Wu; Wan-Chia Chung; Tsang-Ming Ko; Chih-Peng Lin; Hsiang-I Yin; Tsui-Ting Lee; James Chun-I Lee
Journal:  Int J Legal Med       Date:  2018-10-29       Impact factor: 2.686

9.  Report from the STRAND Working Group on the 2019 STR sequence nomenclature meeting.

Authors:  Katherine Butler Gettings; David Ballard; Martin Bodner; Lisa A Borsuk; Jonathan L King; Walther Parson; Christopher Phillips
Journal:  Forensic Sci Int Genet       Date:  2019-09-21       Impact factor: 4.882

Review 10.  The diversity of shedder tests and a novel factor that affects DNA transfer.

Authors:  Max Schwender; Malte Bamberg; Lisa Dierig; Sebastian N Kunz; Peter Wiegand
Journal:  Int J Legal Med       Date:  2021-03-30       Impact factor: 2.686

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