Resolving the complexity of the human genome using single-molecule sequencing

By Mark J. P. Chaisson, J. Huddleston, M. Dennis, Peter Sudmant, Maika Malig, Fereydoun Hormozdiari, F. Antonacci, U. Surti, R. Sandstrom, Matthew Boitano and 5 more. Nature, 2014

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The human genome is arguably the most complete mammalian reference assembly, yet more than 160 euchromatic gaps remain and aspects of its structural variation remain poorly understood ten years after its completion. To identify missing sequence and genetic variation, here we sequence and analyse a haploid human genome (CHM1) using single-molecule, real-time DNA sequencing. We close or extend 55% of the remaining interstitial gaps in the human GRCh37 reference genome—78% of which carried long runs of degenerate short tandem repeats, often several kilobases in length, embedded within (G+C)-rich genomic regions. We resolve the complete sequence of 26,079 euchromatic structural variants at the base-pair level, including inversions, complex insertions and long tracts of tandem repeats. Most have not been previously reported, with the greatest increases in sensitivity occurring for events less than 5 kilobases in size. Compared to the human reference, we find a significant insertional bias (3:1) in regions corresponding to complex insertions and long short tandem repeats. Our results suggest a greater complexity of the human genome in the form of variation of longer and more complex repetitive DNA that can now be largely resolved with the application of this longer-read sequencing technology.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/6abd3ae8d4f287c66746d5777f1afe13dc32bde2

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Citations in the corpus

Oxford Nanopore MinION Sequencing and Genome Assembly (2016, positive): “…signiﬁcant performance improvements in assembling bacterial genomes [43,44], middle-sized Drosophila melanogaster and Arabidopsis thaliana genomes [45], and more recently human genomes [46,47], thanks to the implementation of a new, faster algorithm called MinHash alignment process (MHAP) [45].”
From telomere to telomere: the transcriptional and epigenetic state of human repeat elements (2021, background): “GRCh18, GRCh38) that have been developed over the last two decades still contained large gaps and collapsed repeats (11), rendering a comprehensive repeat annotation for the entire human genome impossible.”
SVIM: structural variant identification using mapped long reads (2018, methodology): “We did not compare against short read SV callers because they have been shown to exhibit lower recall than methods relying on long reads [13, 12, 21].”
Opportunities and challenges in long-read sequencing data analysis (2020, background): “Even relatively short (5 kb) SMRT reads can identify structural variants in the human genome that were previously missed by short-read technologies [79].”
ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter (2016, neutral): “Although longer (albeit noisier) sequences from Pacific Biosciences (Menlo Park, CA) instruments are proven to yield high quality de novo human genome assemblies (Chaisson et al. 2014; Pendleton et al. 2015), they come at a higher price relative to Illumina reads.”
Haplotype-resolved diverse human genomes and integrated analysis of structural variation (2021, background): “When we considered structural polymorphisms that arise from perfect triplet repeats, expansions outnumbered contractions 3 to 1 (271 expansions, 88 contractions), which is consistent with such regions being systematically underrepresented in the original reference (8, 28).”
De novo assembly of haplotype-resolved genomes with trio binning (2018, neutral): “Retrospective application of the automated thresholding method selected similar thresholds of {[25,143], [27,147]} and {[10,57], [10,67]} for H.”
PacBio Sequencing and Its Applications (2015, background): “closed 50 of the 164 gaps in GRCh37 and shortened 40 other gaps [32].”
WhatsHap: fast and accurate read-based phasing (2016, background): “Sequencing haploid cell lines, like CHM1, a hydatidiform mole, can also be considered to fall in this category [7, 8].”
The Third Revolution in Sequencing Technology. (2018, background): “and tens of thousands of structural variants were resolved [30,31].”
High-Throughput Sequencing Technologies (2015, background): “Reconstructing structural variation (SV) in the genome (Chaisson et al., 2015) and isoform usage in the transcriptome (Sharon et al.”