Laboratory Information Management System
We have developed since 2008 a new LIMS based on ABI SQL*LIMS platform self-customized for IARC High-throughput Genetic platform. It manages the whole laboratory workflows for:
- mutation screening by combination of High Resolution Melting Curve analysis and Sequencing
- genotyping by:
- High Resolution Melting Curve analysis
- GoldenGate with Illumina platform
- whole genome expression profiling
The LIMS which relies on an Oracle 10g database, enables strict follow-up of the laboratory processes by also communicating with all our instruments: from barcodes printers to sequencer through Beckman and Tecan pipetting robots, Lightscanner, Qiagen Biorobot, Taqman and Illumina platform.
(More information to follow...)
Reference:A Laboratory Information Management System (LIMS) for high throughput genetic platform aimed at candidate gene mutation screening
C Voegele; S.V Tavtigian; D de Silva; S Cuber; A Thomas; F Le Calvez-Kelm
Bioinformatics 2007; doi: 10.1093/bioinformatics/btm365
Abstract is available at this address:
ContextOver the past 30 years, family-based and association-based studies have enabled identification of susceptibility genes involved in human genetic disorders. For common diseases that have a strong element of inherited risk, an individual's susceptibility is often determined by a complex interaction of multiple genes. Because highly penetrant cancer susceptibility genes that have been identified account for a relative small fraction of the genetic component of cancer risk (15 to 25%) and because studies have failed to identify other highly penetrant cancer susceptibility genes (Thompson and Easton, 2004), it seems likely that the unexplained inherited risk results from interactions of many sequence variants, which individually have modest to moderate effect on attributable cancer risks. Thus, identification of genetic variants that confer susceptibility to cancer (genetic diseases) requires the screening of large numbers of individuals for many possible genetic variations. Advances in genomics technology have steadily increased the level of automation incorporated into laboratory genetics platforms, significantly reducing sample handling time and thereby allowing studies comprising larger numbers of samples. Furthermore, the sequencing of the human genome has, on one hand, markedly contributed to the identification of a large number of single-nucleotide polymorphisms (SNPs) and on the other hand, facilitated the design of new tests for the discovery of new genetic variants. One key challenge in the area of genome research is to manage the large amount of data generated during such genetic screening workflows. There is a need to organise and compute these data in an efficient system that tracks samples, captures data at various steps of the laboratory processes and ensures reliable storage, retrieval and analysis of the data generated.
We have therefore developed a platform independent LIMS for a laboratory workflow tailored to the search for new genetic variants in candidate genes. The workflow is based on a combination of a mutation scan by High Resolution Melting Curve Analysis and dye-primer re-sequencing of suggestive samples. The LIMS is based on a Client/Server architecture hosted on two servers, one for a MySQL relational database and one for the web application. Flexible, expansible and highly secure, the LIMS, by communicating with most of the laboratory instruments and robots, tracks every step of our workflow ending with the deposition of processed resequencing data in the database.
Source codes for the different LIMS modules are freely available for the scientific community.
|LIMS architecture||Click here|
|Servers configuration||Click here|
|Database model||Click here|
|Script for database tables creation||Click here|
|Overview of mutation screening workflow tracked in the LIMS||Click here|
|Application configuration||Click here|
|Whole JSP application (zip file)||Click here|
|Scripts for LIMS communication with the robots and instruments||Click here|
|Scripts for barcodes printing||Click here|
|Link to the underlying UBB interface (optional)||Click here|
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