Gaps and complex structurally variant loci in phased genome assemblies

Porubsky, D.; Vollger, M. R.; Harvey, W. T.; Rozanski, A. N.; Ebert, P.; Hickey, G.; Hasenfeld, P.; Sanders, A. D.; Stober, C.; Human Pangenome Reference Consortium (HPRC),; Korbel, J. O.; Paten, B.; Marschall, T.; Eichler, E. E.

doi:10.1101/2022.07.06.498874

bioRxiv · 10.1101/2022.07.06.498874

Gaps and complex structurally variant loci in phased genome assemblies

Porubsky, D.·Vollger, M. R.·Harvey, W. T.·Rozanski, A. N.·Ebert, P.·Hickey, G.·Hasenfeld, P.·Sanders, A. D.·Stober, C.·Human Pangenome Reference Consortium (HPRC),·Korbel, J. O.·Paten, B.·Marschall, T.·Eichler, E. E.

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Abstract

There has been tremendous progress in the production of phased genome assemblies by combining long-read data with parental information or linking read data. Nevertheless, a typical phased genome assembly generated by trio-hifiasm still generates more than ~140 gaps. We perform a detailed analysis of gaps, assembly breaks, and misorientations from 77 phased and assembled human genomes (154 unique haplotypes). We find that trio-based approaches using HiFi are the current gold standard although chromosome-wide phasing accuracy is comparable when using Strand-seq instead of parental data. We find two-thirds of defined contig ends cluster near the largest and most identical repeats [including segmental duplications (35.4%) or satellite DNA (22.3%) or to regions enriched in GA/AT rich DNA (27.4%)]. As a result, 1513 protein-coding genes overlap assembly gaps in at least one haplotype and 231 are recurrently disrupted or missing from five or more haplotypes. In addition, we estimate that 6-7 Mbp of DNA are incorrectly orientated per haplotype irrespective of whether trio-free or trio-based approaches are employed. 81% of such misorientations correspond to bona fide large inversion polymorphisms in the human species, most of which are flanked by large identical segmental duplications. In addition, we also identify large-scale alignment discontinuities consistent with an 11.9 Mbp deletion and 161.4 Mbp of insertion per human haploid genome. While 99% of this variation corresponds to satellite DNA, we identify 230 regions of the euchromatic DNA with frequent expansions and contractions, nearly half of which overlap with 197 protein-coding genes. Although not completely resolved, these regions include copy number polymorphic and biomedically relevant genic regions where complete resolution and a pangenome representation will be most useful, yet most challenging, to realize.

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Porubsky, D., Vollger, M. R., Harvey, W. T., Rozanski, A. N., Ebert, P., Hickey, G., Hasenfeld, P., Sanders, A. D., Stober, C., Human Pangenome Reference Consortium (HPRC),, Korbel, J. O., Paten, B., Marschall, T., Eichler, E. E.. 2022-07-06. Gaps and complex structurally variant loci in phased genome assemblies. https://doi.org/10.1101/2022.07.06.498874

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