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Inference of Chromosome-length Haplotypes Using Genomic Data of Three to Five Single Gametes

By Ruidong Li, Han Qu, Jinfeng Chen, Shibo Wang, John M. Chater, Le Zhang, Julong Wei, Yuan-Ming Zhang, Chenwu Xu, Wei-De Zhong, Jianguo Zhu, Jianming Lu, Renyuan Ma, Sergio Pietro Ferrante, Mikeal L. Roose, Zhenyu Jia

Posted 04 Jul 2018
bioRxiv DOI: 10.1101/361873

Knowledge of chromosome-length haplotypes will not only advance our understanding of the relationship between DNA and phenotypes, but also promote a variety of genetic applications. Here we present Hapi, an innovative method for chromosomal haplotype inference using only 3 to 5 gametes. Hapi outperformed all existing haploid-based phasing methods in terms of accuracy, reliability, and cost efficiency in both simulated and real gamete datasets. This highly cost-effective phasing method will make large-scale haplotype studies feasible to facilitate human disease studies and plant/animal breeding. In addition, Hapi can detect meiotic crossovers in gametes, which has promise in the diagnosis of abnormal recombination activity in human reproductive cells.

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