A low-cost open-source SNP genotyping platform for association mapping applications

doi:10.1186/gb-2005-6-12-r105

Genome Biology
Volume 6
Issue 12

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Macdonald SJ
Pastinen T
Genissel A
Cornforth TW
Long AD

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Pastinen T
Genissel A
Cornforth TW
Long AD
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A low-cost open-source SNP genotyping platform for association mapping applications

Stuart J Macdonald¹ , Tomi Pastinen² , Anne Genissel¹^,3 , Theodore W Cornforth¹^,4 and Anthony D Long¹

¹Department of Ecology and Evolutionary Biology, University of California Irvine, CA 92697-2525, USA

²McGill University and Genome Québec Innovation Centre, 740 Docteur Penfield Avenue, Montreal, Québec H3A 1A4, Canada

³Section of Evolution and Ecology, University of California Davis, Davis, CA 95616, USA

⁴Institute of Neuroscience, 1254 University of Oregon, Eugene, Oregon 97403-1254, USA

author email corresponding author email

Genome Biology 2005, 6:R105doi:10.1186/gb-2005-6-12-r105


Published:	2 December 2005

Subject areas: Genome studies, Genetics

Additional files

Additional data file 1:

Detailed protocols for the presented SNP genotyping platform.

Format: PDF Size: 216KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional data file 2:

Oligonucleotide sequences for PCR, OLA genotyping, and sequencing.

Format: XLS Size: 84KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional data file 3:

Alignment of 16 resequenced Drosophila melanogaster alleles for the complete Enhancer of split gene complex.

Format: TXT Size: 747KB Download file

Additional data file 4:

Details of the 168 SNPs and insertion/deletion polymorphisms genotyped.

Format: XLS Size: 62KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional data file 5:

Passing a sequence alignment in FASTA format to the script will return tables of the SNPs and insertion/deletion polymorphisms present in the alignment, and a consensus sequence.

Format: TXT Size: 29KB Download file

Additional data file 6:

This includes a parts list, diagrams, and photographs of the system.

Format: PDF Size: 3.3MB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional data file 7:

This script allows the user to control the movement of our custom-built Cartesian arraying robot with a regular PC.

Format: TXT Size: 10KB Download file

Additional data file 8:

This script is written in the freely available statistical programming language R, and allows the user to take the intensity data for each allele of each spot from the hybridized membranes, and assign genotypes to each spot.

Format: TXT Size: 20KB Download file

Additional data file 9:

Each row represents a D. melanogaster individual, or a blank. The first column is the name of the individual (or blank), the second column identifies the replicate spot (spot 1), and the remaining columns hold the intensity data, with alleles from the same polymorphism in consecutive columns. The column names for the intensity data are constructed from the amplicon within which the site resides, its position (in base pairs) in a sequence alignment, the SNP allele, and the barcode marking the allele.

Format: TXT Size: 7MB Download file

Additional data file 10:

Each row represents a D. melanogaster individual, or a blank. The first column is the name of the individual (or blank), the second column identifies the replicate spot (spot 2), and the remaining columns hold the intensity data, with alleles from the same polymorphism in consecutive columns. The column names for the intensity data are constructed from the amplicon within which the site resides, its position (in base pairs) in a sequence alignment, the SNP allele, and the barcode marking the allele.

Format: TXT Size: 7MB Download file

Additional data file 11:

The first column is the individual name, and the remaining columns hold genotype data (NA, no genotype assigned; 0, minor allele homozygote; 1, heterozygote; 2, major allele homozygote). The column names for the genotype data are constructed from the amplicon within which the site resides, the major allele, the position (in base pairs) of the site in a sequence alignment, and the minor allele.

Format: TXT Size: 1014KB Download file

Additional data file 12:

Each plot displays approximately 2,000 points, representing single D. melanogaster individuals. The points representing individuals assigned genotypes by an OLA assay and by sequencing are colored and large, while the remaining individuals are shown as smaller gray points. Red, major allele homozygote in both OLA and sequencing; black, heterozygote in both OLA and sequencing; green, minor allele homozygote in both OLA and sequencing; yellow, OLA and sequencing yield different genotypes.

Format: PDF Size: 2.1MB Download file

This file can be viewed with: Adobe Acrobat Reader