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Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions


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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Figure 1: The LACHESIS scaffolding method.
Figure 2: Clustering and ordering mammalian sequences with LACHESIS.
Figure 3: LACHESIS ordering of scaffolds in a de novo human assembly.
Figure 4: Detection of chromosome fusions in HeLa S3 using Hi-C data.

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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 DGE-0718124 from the National Science Foundation (to A.A. and J.O.K.); and grant T32HG000035 from the NHGRI (to J.N.B.).

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Authors and Affiliations



J.N.B., A.A., J.O.K. and J.S. conceived and designed the study. J.N.B. designed and wrote the LACHESIS software. J.N.B. and R.P.P. performed the de novo assemblies. R.Q. conducted the HeLa Hi-C experiments. A.A. analyzed the HeLa Hi-C data. J.N.B., A.A. and J.S. prepared the manuscript, with input from all authors. J.S. supervised the study.

Corresponding authors

Correspondence to Joshua N Burton or Jay Shendure.

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Competing interests

The authors have fieled a provisional patent application on this method. J.S. is a member of the scientific advisory board or serves as a consultant for Adaptive Biotechnologies, Ariosa Diagnostics, Stratos Genomics, GenePeeks, Gen9, Good Start Genetics, Ingenuity Systems and Rubicon Genomics.

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Supplementary Figures 1–13 and Supplementary Tables 1–6 (PDF 4599 kb)

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LACHESIS.tar.gz (ZIP 43465 kb)

Supplementary Data 2

README.txt (TXT 13 kb)

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Burton, J., Adey, A., Patwardhan, R. et al. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat Biotechnol 31, 1119–1125 (2013).

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