Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping

Abstract

Background: With the advances in DNA sequencer-based technologies, it has become possible to automate several steps of the genotyping process leading to increased throughput. To efficiently handle the large amounts of genotypic data generated and help with quality control, there is a strong need for a software system that can help with the tracking of samples and capture and management of data at different steps of the process. Such systems, while serving to manage the workflow precisely, also encourage good laboratory practice by standardizing protocols, recording and annotating data from every step of the workflow.

Results: A laboratory information management system (LIMS) has been designed and implemented at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) that meets the requirements of a moderately high throughput molecular genotyping facility. The application is designed as modules and is simple to learn and use. The application leads the user through each step of the process from starting an experiment to the storing of output data from the genotype detection step with auto-binning of alleles; thus ensuring that every DNA sample is handled in an identical manner and all the necessary data are captured. The application keeps track of DNA samples and generated data. Data entry into the system is through the use of forms for file uploads. The LIMS provides functions to trace back to the electrophoresis gel files or sample source for any genotypic data and for repeating experiments. The LIMS is being presently used for the capture of high throughput SSR (simple-sequence repeat) genotyping data from the legume (chickpea, groundnut and pigeonpea) and cereal (sorghum and millets) crops of importance in the semi-arid tropics.

Conclusion: A laboratory information management system is available that has been found useful in the management of microsatellite genotype data in a moderately high throughput genotyping laboratory. The application with source code is freely available for academic users and can be downloaded from http://www.icrisat.org/gt-bt/lims/lims.asp.

Figure 1

LIMS modules and information flow. Dotted rectangles indicate the four LIMS modules. Rectangles indicate processes in the data flow chart, diamond indicates decision, and parallelogram indicates data storage steps. (PCR: Polymerase Chain Reaction, PAGE: Polyacrylamide Gel Electrophoresis, CE: Capillary Electrophoresis)

Figure 2

LIMS modules and user interfaces. A: The LIMS user interface for Experimental Design. B: Protocols and Markers – Form uploads for information on markers. C: Reports – sample DNA localization in microtitre plates for DNA extraction. D: Sample Tracking – User interfaces to upload capillary electrophoresis output files. E & F: Output files from the allele-binning program.