SXTestPlate is a Windows program for evaluating the performance of a SNPlex™ genotyping platform by analyzing a test plate, which was typed with a control pool. The DNA samples on the test plate may be replicated multiple times. SXTestPlate determines automatically, how often a sample is replicated. It is recommended to use the SNPlex™ System gDNA Plates Kit (Applied Biosystems) with the SNPlex™ System Control Pool Kit (Applied Biosystems), but custom plates and control pools are being supported as well. SXTestPlate loads the genotypes of the test plate and the reference genotypes into a database and compares them to each other. It shows the callrate and concordance for each DNA and SNP. In addition it shows the genotype discrepancies in detail.

SXTestPlate is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. SXTestPlate is not for commercial use.

When using please cite the following publication:
Teuber M, Wenz MH, Schreiber S, Franke A (2009).
GMFilter and SXTestPlate: software tools for improving the SNPlex(TM) genotyping system.
BMC Bioinformatics 10(1):81
PubMed (PMID:19267942)

 

Requirements

SXTestPlate runs on Windows 2000 and XP. It has not been tested under Windows Vista.


Important notes:

• GeneMapper®: check Duplicate homozygous alleles under Tools/Options
• GeneMapper®: load the SXTestPlate table setting (see below) before exporting the genotypes table

File format for genotypes and reference:

• files must be tab or comma delimited (.txt or .csv)
• files must have a header row
• the columns must be called: Sample Name, SNP, Allele 1, Allele 2 (case sensitive)
• the maximum length for Sample Name and SNP is 20 characters
• the maximum length for Allele 1 and Allele 2 is one character
• no-calls must be included in the genotype file
• for no-calls Allele 1 and Allele 2 must be an empty string or "0" (zero)
• rows where Sample Name is an empty string or "0" (zero) will be ignored (this can be used for control wells)
• rows where SNP is an empty string will be ignored

Installation

First you need to install the free database SQL Server 2005 Express Edition from Microsoft including the free management tool SQL Server Management Studio Express. Afterwards you can run the SXTestPlate installer (see Download section).

Using SQL Server Management Studio Express:

• set the server authentication mode of your SQL Server Express to SQL Server and Windows Authentication mode (see Server Properties/Security)
• create a new database
• connect to the new database as a user who has sufficient rights (db_owner)
• execute the SQL script 'database.sql' which is located in the installation folder of SXTestPlate

Finally you can start SXTestPlate. Log on as a user who belongs to the bulkadmin or sysadmin fixed server role. Use your computer name as server name.
 

Download

SXTestPlate installer (includes the application, online help, sample data and source code):
SXTestPlate_1_0_0_setup.exe (3,2 MB)

table setting for GeneMapper®:
SXTestPlate.xml
 

Screenshot