Quality Control

Typical errors found in STR datasets and strategies how to avoid them are described in Bodner M & Parson W: The STRidER Report on Two Years of Quality Control of Autosomal STR Population Datasets. Genes 2020, 11(8): 901 (doi: 10.3390/genes11080901).

STRidER provides quality control of autosomal STR datasets. STRidER is accepting datasets from diverse worldwide populations and forensically relevant autosomal STR markers that comply with ethical standards. Minimum requirements of journals might apply when datasets are intended for peer-reviewed publication. A suite of software tools has been developed to scrutinize STR population data and thus increase the quality of datasets to ensure reliable allele frequency estimates. The Executive Board of the International Society of Forensic Genetics (ISFG) and the editors of Forensic Science International: Genetics invited STRidER to logistically organize and perform quality control (QC) of autosomal STR population data in the course of manuscript preparations for the journal 1. Before STR population papers are put forward to the editors for review, the authors are requested to submit the data to STRidER. After positive evaluation, the authors will be contacted with the respective STRidER accession numbers that serve as indicator of successful QC for the editors and reviewers. The necessary steps for submission of CE-based STR data to STRidER are outlined below. Please contact STRidER in case you want to submit STR sequence data or for any comments concerning your submission.

Step 1

Prepare your STR data file as shown in the example file that can be downloaded and used as template. It is a tab-delimited text file that can be created using standard text software or MS Excel (then, save file under .txt format). The minimum requirements for population datasets for STRidER are 15 autosomal STR loci typed in 100 samples. Up to 1,000 samples can be accepted per dataset. The minimum requirements for population datasets for Forensic Science International: Genetics 1 are 15 autosomal STR loci typed in 500 samples (for exceptional populations, the latter number can be smaller, please directly contact the editors of Forensic Science International: Genetics before a submission intended for publication in this journal).

The initial lines (identified using the "#" symbol) specify details of the dataset and origin of the samples. Line 1 must contain a description of population(s) reported (e.g., the title of the study), number of samples, geographic origin, and the number of STR loci. Line 2 must indicate the contact author’s name with email address. Further text lines marked with "#" can be included for comments or description of the detailed geographic background and the appropriate metapopulation affiliation of the genotypes. Lines below these text lines list the original STR genotypes including amelogenin. Allele nomenclature criteria are applied as described in the “About” tab of this website. The order of loci does not matter. Alleles for the same locus have to be reported in adjacent columns. Loci names must not contain spaces. Report both alleles for homozygous loci. Use "." instead of "," for incomplete alleles, e.g. "9.3" not "9,3". Note that only complete genotypes are accepted. It is imperative that STR genotypes are reported individually and unshuffled using a unique identifier for each genotype in the dataset. The names are necessary for correspondence. The STR data file should be named Author_country_number of samples.txt (e.g. Parson_AUT_573.txt).

Step 2

Enter accompanying information per dataset in the online submission form and upload your STR data file (Step 1). This information is necessary for evaluation of the dataset. Keep raw data files available for any later inquiries. Inspection may be necessary for quality control purposes. By submitting the data, you confirm that informed consent and ethics approval for data generation and publication have been granted according to your national laws. You also confirm that you are submitting unshuffled (original) genotypes and that complete raw data is available for all genotypes for quality control purposes. By submitting, you agree that allele frequencies will be uploaded onto the STRidER database when QC is passed.

The data will be immediately checked for plausibility as outlined in 2 using in-house software. When submission is complete, you will receive a confirmation by e-mail.

Step 3

During STRidER quality control and evaluation, communication with respect to individual genotypes may follow. Once your data passed QC you will receive the STRidER accession number(s) for your data together with allele frequencies calculated from the dataset(s). Please provide accession number(s) to the journal editor and cite STRidER 2 in your manuscript.

Step 4

Data that successfully passed QC will be uploaded onto the STRidER database.

References

1 Gusmão L, Butler JM, Linacre A, Parson W, Roewer L, Schneider PM, Carracedo A (2017) Revised guidelines for the publication of genetic population data; Forensic Sci Int Gen 30:160-163
2 Bodner M, Bastisch I, Butler JM, Fimmers R, Gill P, Gusmão L, Morling N, Phillips C, Prinz M, Schneider PM, Parson W (2016) Recommendations of the DNA Commission of the International Society for Forensic Genetics (ISFG) on quality control of autosomal Short Tandem Repeat allele frequency databasing (STRidER); Forensic Sci Int Gen 24:97-102