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GeneMapperToFamilias Developed by Antonio Vozmediano and Lourdes Prieto
DNA Laboratory, Comisaria General de Policia Cientifica
(Spanish Forensic Police)
This software, freely available here, was created to facilitate transferring data from GeneMapper
program to Familias (1.97 or 3) program more quickly and safely. A Spanish version of this
document is also available. Input files for the example showed in this document as well as
additional files (kits configuration) are available here.
Improvements from previous versions are:
- Fits any commercial PCR kit.
- Genetic data (nuclear DNA profiles) that can be imported from Genemapper
have increased from 8 to 9 profiles.
- Available in two languages: English or Spanish.
- The txt file generated by GeneMapper can be used directly.
- The name of genetic markers, alleles and their frequencies are imported as
in previous versions (Excel file xls/x). In previous versions an Excel file for
each PCR kit was necessary. In this version you can keep your population
data in only one Excel file, using one sheet for each kit (5 sheets t
maximum).
The steps to follow are:
1. Select the txt file containing the configuration of the PCR kit you have
used to analyze the samples.
2. Create an Excel (xls / x) file containing the allele frequencies of your
population (name of genetic markers, alleles and their frequencies).
3. Generate a txt file from GeneMapper.
4. Open the executable and follow the instructions.
1. Select the “Kit configuration” file (txt)
“Kit configuration” files are available for the following PCR kits: Cofiler, PowerPlex Fusion,
Globalfiler, Identifiler, Minifiler, NGM, NGM-Select, PowerPlex-16, PowerPlex-21, Profiler,
ProfilerPlus, SEfiler, SGM-Plus and Verifiler. You can download them here (zipped “kit
config” folder)
If you are using a different kit you can also create the “kit configuration” txt file as follows:
- Open a new txt file. To move from one line to next one return key should be
used.
- Write the name of the kit in the first line.
- Add the number of genetic markers that your kit contains in the second line.
- Add the number of genetic markers that are not involved in the calculation
in the third line (amelogenin, Y chromosome, etc.).
- Add the position of Amelogenin in the kit in the fourth line.
- Add the position/s where the rest of genetic markers that are not related to
calculation are located in the kit (one number per line)
- Save the file as “kitname_config.txt” (e.g., globalfiler_config.txt)
See the picture as an example for Globalfiler: 24 markers, 3 markers not involved in the
calculations (Y-indel, Amel and DYS391), amel located at position 7th, other markers located in
positions 6th and 11
th.
2. Create an Excel (xls/x) containing the population database
This works as in previous versions but it has been improved. The order of markers in the
population database has to be the same as the ones generated in the GeneMapper txt.
GeneMappertoFamilias does not check the name of the markers, but only the order of markers
involved in the calculation.
In previous versions of GeneMappertoFamilias you needed an Excel population file per PCR
kit. Now you can create a single Excel file containing population data for several PCR kits by
adding each data for each PCR kit in one sheet of the file (5 worksheets at maximum).
See the picture as an example (note that Yindel, amelogenin and DYS391 are excluded):
3. Generate a txt file from GeneMapper
1. Open the Project of interest in GeneMapper
2. Go to the “Genotypes” tab
3. In the upper menu, go to “Table settings” and select “Traditional Allele Table”
4. In the upper menu select the “Export Table” button
5. Export the table in txt format and save it where you desire. This table contains the data
of all the samples that were analysed in the project (including Ladders, negative
controls, etc.)
4. Open the executable “GeneMappertoFamilias” and follow the steps.
The first screen of the executable allows you to select the language (English or Spanish).
Value 1 is Spanish.
Any other value or action is English.
Take into account that this option cannot be changed after this step.
Click OK.
A screen with three tabs ('Home', 'Import' and 'To Familias 1.97 or 3') will be opened:
4.1. HOME TAB
This tab contains 4 sections: kit configuration, Options, Individuals and Sheet
4.1.1. Kit configuration section (load txt file): Import the kit configuration txt file of
interest (e.g. Globalfiler_config). You cannot change this file during the following
steps (if you want to change the kit you will have to begin again)
4.1.2. Options section: you can choose here how the frequencies are going to be used in the
Familias application. “Rest allele” indicates that only the alleles involved in the
calculation are going to exported to Familias (and a “rest allele frequency” will be
also exported so that the sum is 1); and “all alleles” option means that all the alleles
frequencies of each marker will be exported to Familias.
4.1.3. Individuals section: select the number of individuals involved in the calculations
(individuals with known and unknown relationships)
4.1.4. Sheet section: you have to indicate here the sheet in the population Excel file where
your population data was stored and then upload the Excel file. The population Excel
file can be changed during the following steps. A button called “3.Next” will appear
after the upload of the population Excel file. This button allows you to move to the
'Import' tab (it does not work select 'Import' tab directly).
4.2. IMPORT TAB
In this tab you’ll be able to see a button called “4.Load txt Genemapper”. Click on this button
and select the Genemapper file you want to import (created on point 3 in this manual). This file
can be changed during following steps since several samples from the same case could be
analysed in different runs.
See the example:
Once the Genemapper.txt file is uploaded, a new screen showing the content of the file will be
opened. You will also see a cell in the upper part of the screen. Fill in this cell with the name of
the sample you wish (case sensitive) and click the button “Search sample name”. The first
marker of the sample of interest will be automatically located in the GeneMapper file. Write the
position of the first marker of your sample in the cell near button P# (green arrow) and click in
the P# button. The genetic profile will be stored at 'To Familias 1.97 or 3' tab. Repeat the
selection of samples procedure for each individual (you will see as much as P# buttons as the
number of individuals you have selected in the Home tab).
Note that new GeneMapper files can be imported and used for other relatives (P2, P3 and so on)
by using the button 'Load txt Genemapper'.
See the following example where 2 individuals are involved in the kinship: 337 is the position
where the first marker for the first sample of interest is located (individual P1) and 433 is the
one for the second individual (individual P2).
4.3. TO FAMILIAS TAB
Once you have completed the selection of the samples of interest go to the 'To Familias 1.97 or
3' tab directly. You will see a screen showing a table containing all the information loaded from
the previous tab.
You can edit/change any allele from the table (e.g. if OL instead of the desired allele was
imported).
If you want to remove the profiles, press Delete.
Press OK key to save the final txt file in your computer. This is the file you have to open in
Familias 1.97 or 3. Take into account that the selected profiles are now labelled as P1, P2, etc.
You can change these names in Familias (e.g. P1 is the alleged Father, P2 is the son, etc)
THIS IS A BETA VERSION (0.89) OF “GENEMAPPERTOFAMILIAS”. If you have
any comment or suggestions, please contact Antonio Vozmediano
([email protected]) or Lourdes Prieto ([email protected]). All your comments
will be very welcome!