This page contains links to all of the data associated with the paper describing our low-cost, open-source SNP (Single Nucleotide Polymorphism) genotyping platform:

Macdonald, S.J., T. Pastinen, A. Genissel, T. W. Cornforth, and A.D. Long. 2005. A low-cost open-source SNP genotyping platform for association mapping applications. Genome Biology 6: R105.

Also, we are continuing to develop and improve our technology, and will distribute any updates to the protocols, software, or robotics directly from this site.

		Protocols
		Software
		Robotics

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Protocols

Our SNP genotyping technology is based around three robust techniques: the PCR (Polymerase Chain Reaction), the OLA (Oligonucleotide Ligation Assay), and hybridization. In the PDF below we provide step-by-step details of all of the procedures we use to generate the genotype data.

Protocols (220 KB PDF) posted 9 February 2006

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Software

We have written several pieces of software to automate various aspects of our genotyping system, and these are provided below. Please note that in some instances other software or packages may be required for these scripts to run correctly. Check the notes within the files for details.

SNPatron (32 KB perlscript) posted 9 February 2006
Extracts data on all polymorphic SNPs and insertion/deletion polymorphisms from a standard multiple-sequence aligned FASTA file.

Arrayatron (12 KB perlscript) posted 9 February 2006
Arrayatron (12 KB perlscript) posted 9 February 2006 LATEST
Script to allow our custom-built Cartesian arraying robot to be controlled from a PC. The ARRAYATRON script controls robot during sample arraying.

Adjustatron (8 KB perlscript) posted 9 February 2006
Script to allow our custom-built Cartesian arraying robot to be controlled from a PC. The ADJUSTATRON script allows more precise control of the robot head, permitting correct positioning of plates and membranes prior to arraying.

Genotype Calling (24 KB R code) posted 9 February 2006
In order to assign a genotype to each individual, we have written a script for freely-available statistical programming language R.

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Robotics

Genotyping reactions are printed onto nylon macroarrays using a custom-built Cartesian arraying robot. Below we provide a PDF describing the parts and construction of this robot.

Robot construction (3.3 MB PDF) posted 9 February 2006