The board of the International Society of Forensic Genetics (ISFG) and the editors of Forensic Science International: Genetics and International Journal of Legal Medicine invited EMPOP to logistically organize and perform quality control (QC) of mtDNA sequences in the course of manuscript preparations for the journals. Before mtDNA population papers are put forward to the editors for review, the authors are requested to submit the data to EMPOP. After positive evaluation, the authors will be contacted by EMPOP with the respective EMPOP accession numbers that serve as indicator of successful QC for the editors and reviewers. The necessary steps for submission of mtDNA sequences to EMPOP are outlined below.
STEP 1
Prepare your sequence data as shown in the tutorial. An example can be downloaded from the EMPOP webpage here that can also be used as template. The emp-file is a tab delimited text file that can be created using standard text software or MS Excel (then, safe file under .txt format and rename "txt" by "emp"). The first 2 lines specify individual details of the dataset and origin of the samples. Further lines list the mtDNA haplotypes headed by their sequence range(s). Note that a given sequence range is applied to all mtDNA haplotypes following this range until a new range is defined (range lines are defined by "#!"). Text lines, e.g. for individual comments, need to be identified using the "#" symbol.
STEP 2
Submit your file to EMPOP by Email to EMPOP. The data will be quality checked for format, clerical error, sequence range violation, reference error, designation of indels, phantom mutation using in-house software and NETWORK.
The sequence data should be submitted in a file containing the following notation: Author_country_number of samples.emp (e.g. Parson_AUT_273.emp)
Line 1 should contain the title of the study and an author name with Email address for contact.
Line 2 should indicate the detailed geographic background of the haplotypes together with the appropriate metapopulation affiliation. Also use regional characterization if appropriate (see example).
Line 3 should indicate the sequence range, e.g. 16024-16365 or 16024-16400 73-340 or 16024-576, etc... (don't forget to exclude the primer sequences from the range!). Please note that every line indicating a sequence range needs the "#!" designation, so that the software recognizes it as sequence range.
Line 4 and below: list of the individual haplotypes. Note that sequences with different sequence ranges can be loaded on a single file by separating the different sequence ranges.
Please note the following format rules:
It is imperative that mtDNA sequences are reported as individual haplotypes (not condensed haplotypes) using a unique name for each mtDNA sequence in the dataset. The names will not be shown in the search output but are necessary for correspondence.
The file lists the haplotypes in columns with the following contents.
Column A: Sequence name: don't use blank space or special characters (allowed characters are letters (except umlauts ä, ö, ü), numbers, "-", "_", "/")
Column B: Haplogroup (hg) status: indicate hg, if unknown, use "?"
Column C: Frequency of haplotype: in this context this is always "1" because of individual sequence notation
Column D: Annotation of the haplotype relative to the rCRS. Separate differences by tabs (or use individual cells in MS Excel). Use forensic notation of sequences as outlined in the ISFG recommendations for mtDNA typing (Carracedo et al (2000)), e.g. 16311C, 249DEL (also 249Del, 249del, 249-), 315.1C, 524.1A 524.2C, etc...
Text lines can be included everywhere in the file for comments or description. They need to be marked with "#".
Avoid blank lines (except when marked with "#")
STEP 3
After EMPOP evaluation communication may follow with respect to individual sequences. Once your data passed QC you will receive the emp-file of your data together with the EMPOP accession number(s) for your data. Please provide accession number(s) together with your manuscript to the editor of the journal.
STEP 4
Upon publication your data will be uploaded onto EMPOP.
