Dataset Information


Whole-genome Haplotype Reconstruction using Proximity-ligation and Shotgun Sequencing

ABSTRACT: Rapid advances in high-throughput DNA sequencing technologies are accelerating the pace of research into personalized medicine. While methods for variant discovery and genotyping from whole genome sequencing (WGS) datasets have been well established, linking variants together into a single haplotype remains a challenge. An understanding of complete haplotypes of an individual will help clarify the consequences of inheriting multiple alleles in combination, identify novel disease associations, and augment studies of gene regulation. Although numerous methods have been developed to reconstruct haplotypes from WGS data, chromosome-span haplotypes at high resolution have been difficult to obtain. Here we present a novel method to accurately reconstruct chromosome-span haplotypes from proximity-ligation and DNA shotgun sequencing. We demonstrate the utility of this approach in producing high-resolution chromosome-span haplotype phasing in mouse and human. While proximity-ligation based methods were originally designed to investigate spatial organization of the genome, our results lend support for their use as a general tool for haplotyping in the future. Hi-C experiments in two replicates of Human GM12878 Lymphoblastoid cells and two replicates of F123 mouse ES cells (4 total samples)


ORGANISM(S): Homo Sapiens Mus Musculus

SUBMITTER: Jesse R Dixon   Bing Ren  Siddarth Selvaraj 

PROVIDER: E-GEOD-48592 | ArrayExpress | 2013-11-03


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Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing.

Selvaraj Siddarth S   R Dixon Jesse J   Bansal Vikas V   Ren Bing B  

Nature biotechnology 20131103 12

Rapid advances in high-throughput sequencing facilitate variant discovery and genotyping, but linking variants into a single haplotype remains challenging. Here we demonstrate HaploSeq, an approach for assembling chromosome-scale haplotypes by exploiting the existence of 'chromosome territories'. We use proximity ligation and sequencing to show that alleles on homologous chromosomes occupy distinct territories, and therefore this experimental protocol preferentially recovers physically linked DN  ...[more]

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