Olerup SSP version of ®
Version 5.x Troubleshooting and Frequently Asked Questions
Version 5.x / September 2012
Installation and User Administration Problem
Where do I get the lab code requested upon registration?
Solution The lab code is something you choose by yourself. It is preferable that all users within a lab are using the same lab code. A suggestion is to use the name of your institution, lab or company. It is necessary to register in order to have your lab information on the print out. In addition, if linked to the internet, you will be automatically informed by SCORE™ of new essential program releases.
I cannot login into SCORE™ for the very first time as a new user.
User name or password is incorrect: 1. Password is case sensitive
When a user has been created, the password can be changed by clicking on “User > Change password”.
2. If you are the Administrator default user name and password are: admin 3.If your Administrator has created you’re a local user for you, ask your Administrator for your user name. By default, the password is the same as the user ID. SCORE™ does not fit on the screen, i.e. the scrolling bars on the right do not fit.
Minimum screen resolution for SCORE™ is 1024 x 724 pixel, small font.
Increase screen resolution.
I am not allowed to open and review an old typing result.
Individual access authorization.
Ask you administrator for access. Go to “User > User Administration Tool” and activate this feature.
What is the difference between “short cut version” and “standard version”?
In the new SCORE™ version 5.x the user can choose between a “short cut version” and “standard version”. The short cut version allows a fast way from the data input to the result. Advanced functions like “SSP”, “Typing kits” and “SSP details” are hidden to the user.
You can switch between “short cut version” and “standard version” by clicking on “configuration” and “General options”.
Is it possible to work with SCORE™ on multiple workstations?
Yes. SCORE™ needs to be locally installed on all workstations. Then shift your main user -, allele databaseand archive vdas to server based and link the paths of the locally installed programs to these files.
SCORE™ cannot find the user.vda or archive.vda.
An incorrect path has been chosen.
Go to “Files > Linked Files” and chose correct path.
I have imported wrong and not used kits in SCORE™.
Go to “import typing kit”, chose the latest typing kit database and open it. Here you will find a button “remove unused kits”. By selecting this, all kits which are not connected with a patient and sample will be deleted.
The kit you want to import does not appear in the list.
1. The user is not using the latest kit database (if the kit is new).
1. Make sure that you have the correct typing kit database.
2. Incorrect locus selected in the display list.
2. Select the correct locus.
3. Only kits which are not expired are listed.
3. Uncheck the box “no expired typing kits”.
I can’t find the gel picture for You have not selected a an old typing result. sample.
Select the sample for the patient.
I want to analyze KIR Genotyping kit, but can’t find this kit in SCORE™.
Use the lot specific worksheet to perform a manual analysis.
SCORE™ only contains HLAkits, and since the KIR Genotyping kit is targeted to the KIR genes and not HLA, it is not included in SCORE™.
I have inserted the wrong typing kit in my virtual gel. I would like to name my gels myself, is this possible?
Please go to “edit typing kit” and delete the typing kit from the gel. Default setting for gel naming is yymmdd_time.
My gel does not look like the default gel configuration of the virtual gel, can this setting be changed?
Default setting can be changed under “Configuration > Gel configuration”, check box to activate user-defined gel naming. Default setting can be changed under “Configuration > Gel configuration”, use “Gel type”, “Pipetting order” and “Strip order” to define your gels as you wish.
How do I enter a drop out in my typing on the virtual gel?
Solution Remove the internal positive control band in the virtual gel. SCORE™ will interpret this result as having no available information for this primer mix. Hence, both the options of a positive and negative reaction will be considered in analysis. For more information on result entering, refer to SCORE™ 5.x User Manual section 5.6.4.
I want to mark weak bands on the virtual gel to reflect what I am seeing on my gel. How will this affect my analysis?
You have not selected a sample.
A weak band is in analysis regarded as “no information” available. That is, both the options of a positive and negative reaction will be considered in the analysis. We advise you to refer to the batch specific footnotes for expected results. If a primer mix is noted as weak by a footnote, please do not overuse the possibility to assign bands as weak in the virtual gel. For more information on result entering, refer to SCORE™ 5.x User Manual section 5.6.4.
Enter and utilize amplification sizes: The sizes of bands where multiple amplifications are possible do not correspond to the actual sizes.
Due to limited resolution of agarose gels, SCORE™ uses a binning function displaying bands in default representative band sizes to reflect laboratory environment using standard agarose gel and visual read out (SCORE™ 5.x User Manual section 5.6.6).
Enter and utilize amplification sizes: Can I enter multiple bands in one lane?
This feature (ie. Enter and utilize information of multiple amplification sizes) needs to be activated under the menu “configuration” and “typing options”.
This feature (ie. Enter and utilize information of multiple amplification sizes) needs to be activated under the menu “configuration” and “typing options”. After you have entered one band, press the control key and right click to select an additional band size.
Improved presentation of B*27 u.d/bulk and B*57:01 kit results in SCORE™.
The presentation of results in the SCORE™ 5.x version it is improved to screen for target alleles where applicable. This applies to the B*27 u.d/bulk kits and B*57:01 kit.
Analysis and Result Presentation Problem
No high res result is provided Analyze mode for DRB3/4/5 for DRB3/4/5. high res inactivated.
Check the box “analyse DRB3/4/5” in the left side menu of the Analysis window, and reanalyze the sample.
“Unexplained” tolerance due Can be caused by a cross to a false positive amplifica- amplification. tion in Class I.
Activate the tick box “cross reactivity” and reanalyze the sample. In case of cross reactivity information will appear in the text box “mismatches, contradicting results”.
Homozygous result appears with an alternative heterozygous ambiguity listed.
Hidden alleles (by definition alleles which cannot be detected by the kit in use). SCORE™ is listing all available options and since hidden alleles are not reacting with any reagent applied on the sample the hidden allele(s) is a theoretically available option for a heterozygous combination.
Go to “Configuration > Typing Options” and tick the box “omit alleles that are not covered by any SSO/P of the typing kits used”. Reanalyze the sample. Hidden alleles will not be removed from the result list, but will be listed in the sample information text box.
No separation of common Default filter function to discombinations and rare alleles tinguish common combinapreferred. tions and rare alleles based on allele frequency.
Go to “Configuration > Typing Options” and activate “List all alleles as common alleles”. Reanalyze the sample.
Why do I get a different ambiguous result when I analyze with SCORE™ compared to when doing a manual analysis?
SCORE™ is continuously updated with new alleles, while the product insert and interpretation table are not. For this reason it is important to import every monthly typing kit database.
I can’t get a high resolution result after having assigned band sizes for the low resolution typing.
The size calling in SCORE™ Do not use size calling for is not primarily designed for low resolution and combi the low resolution and combi kits. kits. If you have done this it could complicate the analysis once you start inserting high resolution kits.
Allele(s) not listed in the batch specific paper documentation are displayed as possible results in SCORE™.
The new alleles were not included in the IMGT/HLA database at the time the kit was being produced, and could therefore not be taken into consideration when designing the primers. The new alleles are however still possible results.
There are multiple analysis settings available at “Configuration > Typing Options > Use AlleleDb”. Please note however that the new alleles are in theory still possible typing results.
Analysis and Result Presentation Problem
Strange display of typing results: for example DRB1*15XX.
You have selected pre-2010 nomenclature (3.x) and the typing result contains at least one allele that was assigned after the nomenclature change in April 2010.
Using the nomenclature switch, select to display results in the new nomenclature.
Is it possible to combine previous typing result from another method?
Go to “Analysis Screen” and type in your previous typing result in box labeled “Previous Typing results”. Please use the official nomenclature- with”*” and “:”.
I want to see a typing result for example only the low resolution (if there is already a high resolution result in combination).
Go to “Analysis Screen” and use the “Select” function in the left hand menu to select which kit(s) in the specific sample that analysis should be based on.
I want to reduce your result to 4 digits.
Go to “Configuration > General options” and click on “Omit silent mutations”.
How do you switch between the short cut and standard version during analysis?
You can return to the main starting menu by clicking on the “Olerup SSP logo” on the top left of the screen. From there you can switch between the versions. Alternatively you can switch between the standard version and short cut version by clicking on “Configuration > general options” and checking “use SCORE™ short cut version”. This will retain any new data entered.
I want to know the expected band size of a certain allele, where do I find this information?
Solution In the standard version of SCORE™ you can find this information if you go to the “Typing kits” page, select a kit and double click on the mix you are interested in. This will take you to the “SSP details” page, where size information for the alleles is listed.
SCORE™ does not seem to have stored a certain typing result.
You have forgotten the sample number or name.
Minimal information requirement for SCORE™ is Patient ID + Sample ID or First Name, Family Name + sample ID.
SCORE™ automatically stores all entered user data in the user.vda file.
Please note, Patient ID and sample ID can be identical. I cannot reproduce a problematic typing result.
One common reason is that the user has inserted two typing kits instead of one. Even if no reactivity was edited SCORE™ takes all typing kits applied to the sample into account when analyzing – a negative result is also a result for SCORE™.
Go to “Gel window” and remove the faulty inserted typing kit. In addition, check that the correct typing kit – and allele databases are in use.
How do I print out updated worksheets from SCORE™?
Go to Typing kits window and “Print” in the left hand menu. Choose your batch of interest and use function “Print worksheet”.
Typing result or information is missing on print out.
You haven’t chosen the cor- Choose the corresponding responding kit or the needed kit(s) or/and information on information in the print the print form. form.
How I can validate a new SCORE™ version and/or a new monthly update?
We are offering a validation sample for the validation.
On which publication is designation of common and rare alleles in SCORE™ based on?
Please contact your local distributor and you will receive a “transfer validation. vda”. Designation of common alleles is based on the publication: Pedro Cano et al. Common and Well- Documented HLA Alleles. Hum Immun., 68, 392-417
On which publication is serological equivalents in SCORE™ based on?
Designation of serological equivalents is based on the publication: R. Holdsworth, C.K. Hurley, S.G.E. Marsh, et al. The HLA Dictionary 2008: Tissue Antigens (2009) 73:95-170
Where I can find an overview of the old – new nomenclature and in addition: serology, G-groups and P-groups?
Short-cut version: Go to “Tools > Nomenclature and Conversion”.
Do I need to archive data? How do I do that?
It is not necessary to archive any items at all. If you see that your user.vda file steadily increases in size and the performance starts to drop, the first option is to compact your user.vda. However, if this does not make any substantial difference, or you do not want to be confronted with long lists of data that you do not use, archiving the data is the right option. For information on the archiving procedure, refer to SCORE™ 5.x User Manual section 5.13.
How often shall I “repair, compact and quit” when exiting SCORE?
Standard version: Go to “Conversion” in the left hand menu of Main/ Analysis or SSP details screen. Alternatively, go to “Tools > Nomenclature and Conversion”.
This function reduces the size of the user-vda file which has an upper size limit.
It is optional, but we suggest that labs do this once per week and after each archivation.
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