Validation - Experimental Design and Analysis using STR-validator

Validation of new STR typing kits are often time consuming which can delay implementation of new technology. STR-validator is a free open-source software tool designed to help forensic genetic laboratories evaluate the data. Lectures and demonstrations will exemplify experimental design and efficient evaluation. Examples will highlight quality control of the data and result. The goal is to introduce STR-validator as an efficient tool to analyze validation data in accordance to ENFSI recommendations and SWGDAM guidelines.

Learning Outcomes

• Understanding the STR-validator framework and its possibilities.

• Experimental design and analysis according to ENFSI recommendations and SWGDAM guidelines.

• Documentation and interpretation of the validation result.

• Demonstration of automated analysis and report generation using R markdown.

Course Level

This workshop is suitable for DNA analysts/technicians, QA/QC managers, consultants, and other interested individuals. A minimal background in forensic human identification testing would be beneficial. Programming or statistical background is helpful but not required.

Prepare for the workshop

In order to get the most out of this workshop, you will need to bring your own laptop. STR-validator is developed on a Windows 10 system, but should work on any system where R/RStudio can be installed.

To prepare for the workshop you should download the input_files.zip from the Drive folder below, and unzip it to a folder of your choice on your local machine. The files contain the input files for the exercises. In addition you must download and install:

1. The statistical software R: https://cloud.r-project.org/

2. The integrated development environment RStudio Desktop: https://www.rstudio.com/products/rstudio/download/#download

3. The R package strvalidator version 2.4.0. NB! At the time of writing this instruction (28th of august), the current version on CRAN is 2.3.0. I will do my best to get version 2.4.0 published on CRAN before the workshop begins. Alternatively you must install the latest developer version available from GitHub, where the code is hosted.

Open Rstudio that you installed in step 2. In the lower left there is a tab named “Console”.

a) To install from CRAN:

i. Install the strvalidator package from CRAN by typing this in the Console window (press Enter to execute the command):

install.packages("strvalidator", dependencies = TRUE)   

b) To install from GitHub:

i. Install the devtools package from CRAN by typing this in the Console window (press Enter to execute the command):

install.packages("devtools", dependencies = TRUE)   

ii. Load the devtools package and install the strvalidator package from GitHub:

library(devtools)

install_github("OskarHansson/strvalidator")

c) Confirm successful installation by typing:

library(strvalidator)

## STR-validator 2.4.0 loaded!

d) To open the graphical user interface type (The window may open “behind” RStudio):

strvalidator()   

Links to course material

This Presentation was created using R markdown code in isfg_2022_strvalidator_presentation.Rmd

These Exercises were created using R markdown code in isfg_2022_exercises.Rmd (minor corrections since Exercises version 3, Exercises version 2, and Exercises version 1).

This Automated Kit Comparison Using R markdown report was created using the code in automated_kit_comparison.Rmd

ISFG 2022 official site