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

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

PROVIDER: PRJNA210760 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR927079_1.fastq.gz	Fastqsanger.gz
	SRR927079_2.fastq.gz	Fastqsanger.gz
	SRR927080_1.fastq.gz	Fastqsanger.gz
	SRR927080_2.fastq.gz	Fastqsanger.gz
	SRR927081_1.fastq.gz	Fastqsanger.gz

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

Project description: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)

2013-11-03 | E-GEOD-48592 | biostudies-arrayexpress

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

2013-11-03 | GSE48592 | GEO

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

Project description: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 DNA variants on a homolog. Computational analysis of such data sets allows for accurate (?99.5%) reconstruction of chromosome-spanning haplotypes for ?95% of alleles in hybrid mouse cells with 30× sequencing coverage. To resolve haplotypes for a human genome, which has a low density of variants, we coupled HaploSeq with local conditional phasing to obtain haplotypes for ?81% of alleles with ?98% accuracy from just 17× sequencing. Whereas methods based on proximity ligation were originally designed to investigate spatial organization of genomes, our results lend support for their use as a general tool for haplotyping.

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Project description:We used one of the RNA-DNA proximity ligation approaches, RedC, for the analysis of an RNA-DNA interactome of microbial cells. We assess the distribution of main RNA types — mRNA, tRNA and rRNA — along the genomes of E.coli, B.subtilis, and thermophilic archaea T. adornatum.

2023-04-07 | GSE209901 | GEO

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Project description:RNA-DNA interactome of a prokaryotic cell uncovered by proximity ligation

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Mapping of Long-Range Chromatin Interactions using Proximity Ligation Assisted ChIP-seq

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Project description:Proof-of-concept of a new method involving the limited digestion and subsequent ligation of intramolecular RNA structures in situ followed by deep sequencing

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RNA Proximity Ligation to Resolve Intramolecular RNA Structures in situ

Project description:Proof-of-concept of a new method involving the limited digestion and subsequent ligation of intramolecular RNA structures in situ followed by deep sequencing Proof-of-concept of RPL in S. cerevisiae and H. sapiens tissue culture

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