Inference of Chromosome-Length Haplotypes Using Genomic Data of Three or a Few More Single Gametes.

Molecular Biology and Evolution
Ruidong LiZhenyu Jia

Abstract

Compared with genomic data of individual markers, haplotype data provide higher resolution for DNA variants, advancing our knowledge in genetics and evolution. Although many computational and experimental phasing methods have been developed for analyzing diploid genomes, it remains challenging to reconstruct chromosome-scale haplotypes at low cost, which constrains the utility of this valuable genetic resource. Gamete cells, the natural packaging of haploid complements, are ideal materials for phasing entire chromosomes because the majority of the haplotypic allele combinations has been preserved. Therefore, compared with the current diploid-based phasing methods, using haploid genomic data of single gametes may substantially reduce the complexity in inferring the donor's chromosomal haplotypes. In this study, we developed the first easy-to-use R package, Hapi, for inferring chromosome-length haplotypes of individual diploid genomes with only a few gametes. Hapi outperformed other phasing methods when analyzing both simulated and real single gamete cell sequencing data sets. The results also suggested that chromosome-scale haplotypes may be inferred by using as few as three gametes, which has pushed the boundary to its possible...Continue Reading

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Datasets Mentioned

BETA
SRP017516
SRP047362

Methods Mentioned

BETA
proximity ligation
genotyping

Software Mentioned

Hapi R package
Genome Analysis Toolkit ( GATK )
BWA
R
SpeedSeq
PHMM
Perl scripts
Hapi
WhatsHap
MPR

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