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  Haplotype inference from unphased SNP data in heterozygous polyploids based on SAT

Neigenfind, J., Gyetvai, G., Basekow, R., Diehl, S., Achenbach, U., Gebhardt, C., et al. (2008). Haplotype inference from unphased SNP data in heterozygous polyploids based on SAT. BMC Genomics, 9, 356. doi:10.1186/1471-2164-9-356.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-26F2-0 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0019-1AFA-3
Genre: Journal Article

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 Creators:
Neigenfind, J.1, Author              
Gyetvai, G.2, Author
Basekow, R.2, Author
Diehl, S.2, Author
Achenbach, U.2, Author
Gebhardt, C.2, Author
Selbig, J.3, Author              
Kersten, B.1, Author              
Affiliations:
1BioinformaticsCIG, Infrastructure Groups and Service Units, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753303              
2External Organizations, ou_persistent22              
3BioinformaticsCRG, Cooperative Research Groups, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753315              

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Free keywords: *Computational Biology Computer Simulation *Haplotypes Heterozygote Models, Genetic *Polymorphism, Single Nucleotide *Polyploidy *Software Solanum tuberosum/genetics
 Abstract: ABSTRACT: BACKGROUND: Haplotype inference based on unphased SNP markers is an important task in population genetics. Although there are different approaches to the inference of haplotypes in diploid species, the existing software is not suitable for inferring haplotypes from unphased SNP data in polyploid species, such as the cultivated potato (Solanum tuberosum). Potato species are tetraploid and highly heterozygous. RESULTS: Here we present the software SATlotyper which is able to handle polyploid and polyallelic data. SATlotyper uses the Boolean satisfiability problem to formulate Haplotype Inference by Pure Parsimony. The software excludes existing haplotype inferences, thus allowing for calculation of alternative inferences. As it is not known which of the multiple haplotype inferences are best supported by the given unphased data set, we use a bootstrapping procedure that allows for scoring of alternative inferences. Finally, by means of the bootstrapping scores, it is possible to optimise the phased genotypes belonging to a given haplotype inference. The program is evaluated with simulated and experimental SNP data generated for heterozygous tetraploid populations of potato. We show that, instead of taking the first haplotype inference reported by the program, we can significantly improve the quality of the final result by applying additional methods that include scoring of the alternative haplotype inferences and genotype optimisation. For a sub-population of nineteen individuals, the predicted results computed by SATlotyper were directly compared with results obtained by experimental haplotype inference via sequencing of cloned amplicons. Prediction and experiment gave similar results regarding the inferred haplotypes and phased genotypes. CONCLUSIONS: Our results suggest that Haplotype Inference by Pure Parsimony can be solved efficiently by the SAT approach, even for data sets of unphased SNP from heterozygous polyploids. SATlotyper is freeware and is distributed as a Java JAR file. The software can be downloaded from the webpage of the GABI Primary Database at http://www.gabipd.org/projects/satlotyper/. The application of SATlotyper will provide haplotype information, which can be used in haplotype association mapping studies of polyploid plants.

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Language(s): eng - English
 Dates: 2008-07-302008
 Publication Status: Published in print
 Pages: -
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 Table of Contents: -
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Title: BMC Genomics
Source Genre: Journal
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Publ. Info: BioMed Central
Pages: - Volume / Issue: 9 Sequence Number: - Start / End Page: 356 Identifier: ISSN: 1471-2164
CoNE: https://pure.mpg.de/cone/journals/resource/111000136905010