Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes

Chin, Chen-Shan; Behera, Sairam; Khalak, Asif; Sedlazeck, Fritz J.; Sudmant, Peter H.; Wagner, Justin; Zook, Justin M.

doi:10.1038/s41592-023-01914-y

Cited by 22 publications

(10 citation statements)

References 66 publications

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“…The use of pangenomes for association testing has largely relied on presence/absence variation between groups (Brynildsrud et al, 2016; Leonard et al, 2022), decomposed graph genome variation (Chin et al, 2023), or genotypes obtained by mapping of short reads to pangenomes (Cochetel et al, 2023; Sirén et al, 2021). We have developed and applied an approach that compares path similarities and differences between assemblies of samples with divergent phenotypes.…”

Section: Discussionmentioning

confidence: 99%

Taurine pangenome uncovers a segmental duplication upstream ofKITassociated with depigmentation in white-headed cattle

Milia,

Leonard,

Mapel

et al. 2024

Preprint

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Cattle have been selectively bred for coat color, spotting, and depigmentation patterns. The assumed autosomal dominant inherited genetic variants underlying the characteristic white head of Fleckvieh, Simmental, and Hereford cattle have not been identified yet, although the contribution of structural variation upstream the KIT gene has been proposed. Here, we construct a graph pangenome from 24 haplotype assemblies representing seven taurine cattle breeds to identify and characterize the white head-associated locus for the first time based on long-read sequencing data. Through examining assembly path similarities within the graph, we reveal an association between two most likely serial alleles of a complex structural variant 66 kb upstream KIT and facial depigmentation. The complex structural variant contains a variable number of tandemly duplicated 14.3 kb repeats, consisting of LTRs, LINEs, and other repetitive elements, leading to misleading alignments of short and long reads when using a linear reference. We align 250 short-read sequencing samples spanning 15 cattle breeds to the pangenome graph, further validating that the alleles of the structural variant segregate with head depigmentation. We estimate an increased count of repeats in Hereford relative to Simmental and other white-headed cattle breeds from the graph alignment coverage, suggesting a large under-assembly in the current Hereford-based cattle reference genome which had fewer copies. We show that exploiting assembly path similarities within graph pangenomes can reveal trait-associated complex structural variants.

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Section: Discussionmentioning

confidence: 99%

Taurine pangenome uncovers a segmental duplication upstream ofKITassociated with depigmentation in white-headed cattle

Milia,

Leonard,

Mapel

et al. 2024

Preprint

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“…To characterize the structural diversity of the amylase locus, we first constructed a minimizer anchored pangenome graph (MAP-graph) 22 from 94 amylase haplotypes derived from 54 long-read, haplotype resolved genome assemblies recently sequenced by the Human Pangenome Reference Consortium (HPRC) 23 alongside GRCh38 and the newly sequenced T2T-CHM13 reference 24 ( Fig 2B , see methods). The MAP-graph captures large-scale sequence structures with vertices representing sets of homologous or paralogous sequences; thus, input haplotypes can be represented as paths through the graph.…”

Section: Mainmentioning

confidence: 99%

Global diversity, recurrent evolution, and recent selection on amylase structural haplotypes in humans

Bolognini,

Halgren,

Lou

et al. 2024

Preprint

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The adoption of agriculture, first documented ~12,000 years ago in the Fertile Crescent, triggered a rapid shift toward starch-rich diets in human populations. Amylase genes facilitate starch digestion and increased salivary amylase copy number has been observed in some modern human populations with high starch intake, though evidence of recent selection is lacking. Here, using 52 long-read diploid assemblies and short read data from ~5,600 contemporary and ancient humans, we resolve the diversity, evolutionary history, and selective impact of structural variation at the amylase locus. We find that both salivary and pancreatic amylase genes have higher copy numbers in populations with agricultural subsistence compared to fishing, hunting, and pastoral groups. We identify 28 distinct amylase structural architectures and demonstrate that identical structures have arisen independently multiple times throughout recent human history. Using a pangenome graph-based approach to infer structural haplotypes across thousands of humans, we identify extensively duplicated haplotypes present at higher frequencies in modern agricultural populations. Leveraging 534 ancient human genomes we find that duplication-containing haplotypes have increased in frequency more than seven-fold over the last 12,000 years providing evidence for recent selection in Eurasians at this locus comparable in magnitude to that at lactase. Together, our study highlights the strong impact of the agricultural revolution on human genomes and the importance of long-read sequencing in identifying signatures of selection at structurally complex loci.

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“…Genomic analysis has mainly been based on using a linear reference genome since the release of its initial draft in 2001 [1]. However, this approach is inadequate to represent the genetic diversity of a species [2][3][4][5]. Given the fact that the human reference genome (e.g., GRCh38) harbors only a single representative scaffold for each chromosome as the primary sequence, using it as a reference genome comes with severe limitations, including population-specific read mapping biases.…”

Section: Introductionmentioning

confidence: 99%

SVarp: pangenome-based structural variant discovery

Soylev,

Ebler,

Pani

et al. 2024

Preprint

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The linear human reference genome that we use today does not represent the haplotypic diversity of the global human population. This raises bias in genomic read alignment and limits our ability to call large structural variations (SV), especially at highly polymorphic loci. Thus, many SV alleles remain unresolved. Recent efforts to transition to a graph-based reference genome resulted in the generation of the first draft human pangenome reference, but tools to call SVs relative to the pangenome reference are presently lacking. In this study, we present the SVarp algorithm, aiming to discover haplotype resolved SVs on top of a pangenome reference using long sequencing reads. SVarp outputs local assemblies of SV alleles, termed svtigs, instead of a VCF file of SV breakpoints, which we propose as a general exchange format allowing for flexible downstream analyses. In order to assess the accuracy of svtigs, we used simulated and real human genomes. Simulations allowed us to make exact breakpoint comparisons against the true callsets. We observed ~96% recall with deletions, insertions and duplications larger than 1,000bp, showing that SVarp can reliably detect genomic structural variants not yet represented in the graph. On the other hand, we compared SVarp output for ONT sequencing data at 20X coverage against independent genome assemblies of the same samples and found that ~82% of our svtig predictions are validated by the assemblies by a match with more than 85% sequence identity. SVarp was implemented using C++ and its source code is available at https://github.com/asylvz/SVarp under MIT license.

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Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes

Cited by 22 publications

References 66 publications

Taurine pangenome uncovers a segmental duplication upstream ofKITassociated with depigmentation in white-headed cattle

Taurine pangenome uncovers a segmental duplication upstream ofKITassociated with depigmentation in white-headed cattle

Global diversity, recurrent evolution, and recent selection on amylase structural haplotypes in humans

SVarp: pangenome-based structural variant discovery

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