TY - JOUR
T1 - Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions
AU - Burton, Joshua N.
AU - Adey, Andrew
AU - Patwardhan, Rupali P.
AU - Qiu, Ruolan
AU - Kitzman, Jacob O.
AU - Shendure, Jay
N1 - Funding Information:
We thank F. Ay, E. Eichler, J. Felsenstein, P. Green, L. Hillier, M. van Min, W. Noble, R. Waterston and members of the Shendure lab for helpful discussions. Some of the sequencing data used in this research were derived from a HeLa cell line. Henrietta Lacks, and the HeLa cell line that was established from her tumor cells without her knowledge or consent in 1951, have made significant contributions to scientific progress and advances in human health. We are grateful to Henrietta Lacks, now deceased, and to her surviving family members for their contributions to biomedical research. Our work was supported by grant HG006283 from the National Human Genome Research Institute (NHGRI; to J.S.); a graduate research fellowship DGE0718124 from the National Science Foundation (to A.A. and J.O.K.); and grant T32HG000035 from the NHGRI (to J.N.B.).
PY - 2013/12
Y1 - 2013/12
N2 - Genomes assembled de novo from short reads are highly fragmented relative to the finished chromosomes of Homo sapiens and key model organisms generated by the Human Genome Project. To address this problem, we need scalable, cost-effective methods to obtain assemblies with chromosome-scale contiguity. Here we show that genome-wide chromatin interaction data sets, such as those generated by Hi-C, are a rich source of long-range information for assigning, ordering and orienting genomic sequences to chromosomes, including across centromeres. To exploit this finding, we developed an algorithm that uses Hi-C data for ultra-long-range scaffolding of de novo genome assemblies. We demonstrate the approach by combining shotgun fragment and short jump mate-pair sequences with Hi-C data to generate chromosome-scale de novo assemblies of the human, mouse and Drosophila genomes, achieving - for the human genome - 98% accuracy in assigning scaffolds to chromosome groups and 99% accuracy in ordering and orienting scaffolds within chromosome groups. Hi-C data can also be used to validate chromosomal translocations in cancer genomes.
AB - Genomes assembled de novo from short reads are highly fragmented relative to the finished chromosomes of Homo sapiens and key model organisms generated by the Human Genome Project. To address this problem, we need scalable, cost-effective methods to obtain assemblies with chromosome-scale contiguity. Here we show that genome-wide chromatin interaction data sets, such as those generated by Hi-C, are a rich source of long-range information for assigning, ordering and orienting genomic sequences to chromosomes, including across centromeres. To exploit this finding, we developed an algorithm that uses Hi-C data for ultra-long-range scaffolding of de novo genome assemblies. We demonstrate the approach by combining shotgun fragment and short jump mate-pair sequences with Hi-C data to generate chromosome-scale de novo assemblies of the human, mouse and Drosophila genomes, achieving - for the human genome - 98% accuracy in assigning scaffolds to chromosome groups and 99% accuracy in ordering and orienting scaffolds within chromosome groups. Hi-C data can also be used to validate chromosomal translocations in cancer genomes.
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U2 - 10.1038/nbt.2727
DO - 10.1038/nbt.2727
M3 - Article
C2 - 24185095
AN - SCOPUS:84890034912
SN - 1087-0156
VL - 31
SP - 1119
EP - 1125
JO - Nature biotechnology
JF - Nature biotechnology
IS - 12
ER -