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Laboratory information management software for genotyping workflows: Applications in high throughput crop genotyping

Jayashree, B. and Reddy, P.T. and Leeladevi, Y. and Crouch, J.H. and Mahalakshmi, V. and Buhariwalla, H.K. and Eshwar, K.E. and Mace, E. and Folksterma, R. and Senthilvel, S. and Varshney, R.K. and Seetha, K. and Rajalakshmi, R. and Prasanth, V.P. and Chandra, S. and Swarupa, L. and SriKalyani, P. and Hoisington, D.A. (2006) Laboratory information management software for genotyping workflows: Applications in high throughput crop genotyping. BMC Bioinformatics, 7 . p. 383.

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Article Link(s): http://dx.doi.org/10.1186/1471-2105-7-383

Publisher URL: http://www.biomedcentral.com/

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.

Conclusions: 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/bt-software-d-lims.htm

Item Type:Article
Business groups:Agri-Science, Crop and Food Science
Additional Information:© Jayashree et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Keywords:Plant genotyping; AGL-LIMS (Applied Genomics Laboratory - LIMS); crops; legumes; cereal; genotypic data.
Subjects:Technology > Technology (General)
Science > Biology > Genetics
Deposited On:19 Feb 2009 05:17
Last Modified:25 Oct 2011 04:08

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