iXora: exact haplotype inferencing and trait association

BMC Genetics

Parida Laxmi⁴  David N Kuhn¹  Juan Carlos Motamayor³  Raymond J Schnell³  Stefan Royaert¹  Omar E Cornejo²  Donald Livingstone³  Niina Haiminen⁴  Filippo Utro⁴ 

[1] USDA-ARS SHRS, Miami, FL, USA;Stanford University, Stanford, CA, USA;MARS, Incorporated, Miami, FL, USA;Computational Biology Center, IBM T J Watson Research, Yorktown Heights, NY, USA

关键词: Randomization;    QTL;    Trait Association;    Phenotype Association;    Phasing;    Haplotype;   

Others  :  1087006
DOI  :  10.1186/1471-2156-14-48

 received in 2012-10-07, accepted in 2013-05-14,  发布年份 2013

【 摘 要 】

Background

We address the task of extracting accurate haplotypes from genotype data of individuals of large F₁ populations for mapping studies. While methods for inferring parental haplotype assignments on large F₁ populations exist in theory, these approaches do not work in practice at high levels of accuracy.

Results

We have designed iXora (Identifying crossovers and recombining alleles), a robust method for extracting reliable haplotypes of a mapping population, as well as parental haplotypes, that runs in linear time. Each allele in the progeny is assigned not just to a parent, but more precisely to a haplotype inherited from the parent. iXora shows an improvement of at least 15% in accuracy over similar systems in literature. Furthermore, iXora provides an easy-to-use, comprehensive environment for association studies and hypothesis checking in populations of related individuals.

Conclusions

iXora provides detailed resolution in parental inheritance, along with the capability of handling very large populations, which allows for accurate haplotype extraction and trait association. iXora is available for non-commercial use from http://researcher.ibm.com/project/3430 webcite.

【 授权许可】

   
2013 Utro et al.; licensee BioMed Central Ltd.

【 图 表 】

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