@article {309046,
	title = {Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing.},
	journal = {Nat Biotechnol},
	volume = {31},
	year = {2013},
	note = {http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2728.html},
	month = {2013 Dec},
	pages = {1111-8},
	abstract = {<p>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 {\textquoteright}chromosome territories{\textquoteright}. 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{\texttimes} 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{\texttimes} 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.</p>},
	keywords = {Algorithms, Base Sequence, Chromosome Mapping, Genome, Human, Haplotypes, Humans, Molecular Sequence Data, Polymorphism, Single Nucleotide, Sequence Analysis, DNA},
	issn = {1546-1696},
	doi = {10.1038/nbt.2728},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/24185094},
	author = {Selvaraj, Siddarth and R Dixon, Jesse and Bansal, Vikas and Ren, Bing}
}
