Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

By Valerie A. Schneider, Tina A. Graves-Lindsay, Kerstin Howe, Nathan Bouk, Hsiu-Chuan Chen, P. Kitts, T. Murphy, Kim D. Pruitt, Françoise Thibaud-Nissen, Derek Albracht and 28 more. bioRxiv, 2016

1,005 citations recorded by the source corpus.

The human reference genome assembly plays a central role in nearly all aspects of today’s basic and clinical research. GRCh38 is the first coordinate-changing assembly update since 2009 and reflects the resolution of roughly 1000 issues and encompasses modifications ranging from thousands of single base changes to megabase-scale path reorganizations, gap closures and localization of previously orphaned sequences. We developed a new approach to sequence generation for targeted base updates and used data from new genome mapping technologies and single haplotype resources to identify and resolve larger assembly issues. For the first time, the reference assembly contains sequence-based representations for the centromeres. We also expanded the number of alternate loci to create a reference that provides a more robust representation of human population variation. We demonstrate that the updates render the reference an improved annotation substrate, alter read alignments in unchanged regions and impact variant interpretation at clinically relevant loci. We additionally evaluated a collection of new de novo long-read haploid assemblies and conclude that while the new assemblies compare favorably to the reference with respect to continuity, error rate, and gene completeness, the reference still provides the best representation for complex genomic regions and coding sequences. We assert that the collected updates in GRCh38 make the newer assembly a more robust substrate for comprehensive analyses that will promote our understanding of human biology and advance our efforts to improve health.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/3c8b248c2b96107333b21b6a06a693ac65591ea4

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Citations in the corpus

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome (2019, background): “%) at 15 kb read length would double the current contiguity, which already matches the best published de novo assemblies 46 .”
The design and construction of reference pangenome graphs with minigraph (2020, background): “Meanwhile, the advances in long-read sequencing technologies make it possible to assemble a human individual to a quality comparable to GRCh38 [1, 5].”
Integrating Hi-C links with assembly graphs for chromosome-scale assembly (2018, methodology): “We masked sequences in GRCh38 which matched known structural variants from a previous assembly of NA12878 (Pendleton et al., 2015) to avoid counting true variations as scaffolding errors.”
The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000 (2018, background): “Examples of such errors can be found in the best available reference genomes for many species (Robert B. Norgren 2013; Shearer et al. 2014; Tang et al. 2014; Chen et al. 2015; Davey et al. 2016; Utsunomiya et al. 2016; Schneider et al. 2017; Korlach et al. 2017).”
GENCODE reference annotation for the human and mouse genomes (2018, methodology): “Over the last two years mouse annotation has been dominated by the clone-by-clone approach while the human genome has been refined entirely via targeted reannotation except for the annotation of human assembly patches and haplotypes released by the Genome Reference Consortium (15), which take a clon”
The International Genome Sample Resource (IGSR) collection of open human genomic variation resources (2019, methodology): “Phase three of the 1000 Genomes Project used the GRCh37 reference assembly based on its availability at the start of analysis, meaning its resources were not generated on the improved GRCh38 assembly (8).”
Genome graphs and the evolution of genome inference (2017, methodology): “These graphs were then used to generate linear reference sequences for the two arrays (Miga et al. 2014), using a Markovian traversal, and have subsequently been used to define linear representations of the centro-meres that are included in GRCh38 (Schneider et al. 2017).”
HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads (2020, methodology): “To estimate the effect of SDs on the continuity of HiCanu assemblies, we aligned contigs from the CHM13 genome assemblies to the human reference genome (GRCh38) and tested if the ends of contigs mapped within SDs. Compared with the Canu, Peregrine, or ONT assemblies, HiCanu had the fewest contig bre”
De novo assembly of haplotype-resolved genomes with trio binning (2018, neutral): “Switch error between the haplotypes was roughly estimated at 0.68% using independent Hi-C data from the F1 ( Supplementary Note and Supplementary Table 9).”
Nanopore sequencing and assembly of a human genome with ultra-long reads (2017, neutral): “4) 25 .”