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Infinium Assay for Large-scale SNP Genotyping Applications
Published on: November 19, 2013
ISHAPE: new rapid and accurate software for haplotyping
Olivier Delaneau1, Cédric Coulonges, Pierre-Yves Boelle
1Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France. olivier.delaneau@gmail.com <olivier.delaneau@gmail.com>
BMC Bioinformatics
|June 19, 2007
Summary
A new haplotyping program, Ishape, combines an iterative EM algorithm and bootstrap resampling for faster and more accurate haplotype configuration analysis. It outperforms existing software in speed and accuracy for various SNP datasets.
Area of Science:
- Genetics and Genomics
- Computational Biology
- Bioinformatics
Background:
- Developed a novel haplotyping program, Ishape (Iterative Segmented HAPlotyping by Em).
- Combines iterative multiallelic EM algorithm (IEM), bootstrap resampling, and a pseudo Gibbs sampler.
- Employs a segmented approach for large SNP datasets (>30 SNPs) using a partition-ligation strategy.
Purpose of the Study:
- To evaluate the performance of the Ishape program.
- To compare Ishape against established haplotyping software like Phase, Fastphase, and PL-EM.
- To assess accuracy and computational speed across different SNP dataset types and sizes.
Main Methods:
- Utilized IEM-bootstrap procedure to reduce haplotype configuration space and computation time.
- Adapted a Gibbs sampler with a recombination model for accuracy on a restricted space.
- Tested two versions: Ishape1 (coalescence model) and Ishape2 (recombination model).
Main Results:
- Ishape2 demonstrated superior speed and accuracy for adjacent SNPs (high LD).
- For 5 Kb spaced SNPs (lower LD), Ishape2 achieved accuracy comparable to Phase2.1, outperforming other software.
- Ishape2 was significantly faster than Phase2.1, especially with larger SNP sets (up to 10x faster).
Conclusions:
- The Ishape heuristic approach offers a competitive balance of accuracy and speed.
- Ishape shows potential for widespread use in genetic and genomic studies.
- Further extensive evaluation is recommended for Ishape's broader application.
