Jasmine and Iris: population-scale structural variant comparison and analysis

Kirsche, Melanie; Prabhu, Gautam; Sherman, Rachel M.; Ni, Bohan; Battle, Alexis; Aganezov, Sergey; Schatz, Michael C.

doi:10.1038/s41592-022-01753-3

Cited by 56 publications

(44 citation statements)

References 64 publications

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“…The three SV sets were then merged together using Jasmine version 1.1.5 (Kirsche et al., 2023), which integrates various information including chromosome, position, end, size and type to determine whether SV calls from different files or samples refer to the same SV or not. We ran Jasmine with parameters “‐‐mutual_distance ‐‐max_dist_linear = 0.25”, so that the maximum allowed distance required between two SVs for them to be merged is correlated with their size.…”

Section: Methodsmentioning

confidence: 99%

“…We ran Sniffles 2.0.7 (Sedlazeck, Rescheneder, et al., 2018; Smolka et al., 2022) (default settings and “‐‐output‐rnames ‐‐combine‐consensus” options) on each sample and filtered for PASS and PRECISE calls. We then refined alternate allele sequences and breakpoints for insertions, deletions and some duplications by running Iris (Kirsche et al., 2023): we first preprocessed each sample's VCF with Jasmine (“‐‐dup_to_ins ‐‐preprocess_only”), and ran Iris with parameters “‐‐keep_long_variants ‐‐also_deletions”. The four samples' refined VCFs were merged together using Jasmine ‐‐ignore_strand ‐‐mutual_distance ‐‐allow_intrasample ‐‐output_genotypes, and refined SVs were then converted back to their original type with Jasmine ‐‐dup_to_ins ‐‐postprocess_only.…”

Section: Methodsmentioning

confidence: 99%

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Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations

Lecomte,

Árnyasi,

Ferchaud

et al. 2024

Evolutionary Applications

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Genomic structural variants (SVs) are now recognized as an integral component of intraspecific polymorphism and are known to contribute to evolutionary processes in various organisms. However, they are inherently difficult to detect and genotype from readily available short‐read sequencing data, and therefore remain poorly documented in wild populations. Salmonid species displaying strong interpopulation variability in both life history traits and habitat characteristics, such as Atlantic salmon (Salmo salar), offer a prime context for studying adaptive polymorphism, but the contribution of SVs to fine‐scale local adaptation has yet to be explored. Here, we performed a comparative analysis of SVs, single nucleotide polymorphisms (SNPs) and small indels (<50 bp) segregating in the Romaine and Puyjalon salmon, two putatively locally adapted populations inhabiting neighboring rivers (Québec, Canada) and showing pronounced variation in life history traits, namely growth, fecundity, and age at maturity and smoltification. We first catalogued polymorphism using a hybrid SV characterization approach pairing both short‐ (16X) and long‐read sequencing (20X) for variant discovery with graph‐based genotyping of SVs across 60 salmon genomes, along with characterization of SNPs and small indels from short reads. We thus identified 115,907 SVs, 8,777,832 SNPs and 1,089,321 short indels, with SVs covering 4.8 times more base pairs than SNPs. All three variant types revealed a highly congruent population structure and similar patterns of FST and density variation along the genome. Finally, we performed outlier detection and redundancy analysis (RDA) to identify variants of interest in the putative local adaptation of Romaine and Puyjalon salmon. Genes located near these variants were enriched for biological processes related to nervous system function, suggesting that observed variation in traits such as age at smoltification could arise from differences in neural development. This study therefore demonstrates the feasibility of large‐scale SV characterization and highlights its relevance for salmonid population genomics.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations

Lecomte,

Árnyasi,

Ferchaud

et al. 2024

Evolutionary Applications

View full text Add to dashboard Cite

show abstract

“…To prove the validity of our somatic INSs, we collected all available long-read whole-genome sequencing (WGS) data (generated on the ONT platform) from the 1000 Genomes Project [37] and identified insertions and duplications using Sniffles. We also downloaded a germline SV dataset (generated on the ONT platform) from 405 unrelated healthy Chinese individuals [89]. The SVs from the two projects were pooled together to be employed as an ONT platform-based ‘Panel of Normals (PONs)’.…”

Section: Methods Detailsmentioning

confidence: 99%

Landscape of Large-Scale Somatic Genomic Insertions in Non-Small Cell Lung Carcinoma Revealed by Nanopore Sequencing

Xie,

Xia,

Wang

et al. 2023

Preprint

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Previous NSCLC genomic studies were mostly based on the next-generation sequencing of short reads, which is an efficient approach for identifying single nucleotide variants and small indels but ineffective for identifying structural variants, especially large-scale insertions. Here, we studied 151 lung adenocarcinoma (LUAD) and 106 lung squamous cell carcinoma (LUSC) samples and paired blood samples using nanopore sequencing technology. We developed a rigorous computational pipeline and characterized the landscape of large-scale somatic insertions in NSCLC. Combining other omics data, we report three findings: 1. we identified an LUSC-enriched somatic simple repeat expansion shared by approximately 40% of LUSC patients that regulatesPTPRZ1gene expression through distal enhancers; 2. the somatic insertion of transposable elements (TEs) in NSCLC were mostly ‘complex TEs’ consisting of multiple TE elements; and 3. the insertion of short interspersed nuclear elements, especially from the Alu family in young lineages, is a frequent somatic mutation type that shapes the transcriptome of NSCLC through the expression of these elements.

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“…We, therefore, developed a new comparison tool called Minda, which is agnostic to SV types and is better suited for analysis of somatic SVs represented as junctions. Minda can also be used for multiway call sets comparison and merging (Jeffares et al 2017;Kirsche et al 2023). Benchmarking long-read tools using the GIAB HG002 germline SV set.…”

Section: Overview Of the Severus Algorithmmentioning

confidence: 99%

Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads

Keskus,

Bryant,

Ahmad

et al. 2024

Preprint

Self Cite

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Most current studies rely on short-read sequencing to detect somatic structural variation (SV) in cancer genomes. Long-read sequencing offers the advantage of better mappability and long-range phasing, which results in substantial improvements in germline SV detection. However, current long-read SV detection methods do not generalize well to the analysis of somatic SVs in tumor genomes with complex rearrangements, heterogeneity, and aneuploidy. Here, we present Severus: a method for the accurate detection of different types of somatic SVs using a phased breakpoint graph approach. To benchmark various short- and long-read SV detection methods, we sequenced five tumor/normal cell line pairs with Illumina, Nanopore, and PacBio sequencing platforms; on this benchmark Severus showed the highest F1 scores (harmonic mean of the precision and recall) as compared to long-read and short-read methods. We then applied Severus to three clinical cases of pediatric cancer, demonstrating concordance with known genetic findings as well as revealing clinically relevant cryptic rearrangements missed by standard genomic panels.

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Jasmine and Iris: population-scale structural variant comparison and analysis

Cited by 56 publications

References 64 publications

Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations

Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations

Landscape of Large-Scale Somatic Genomic Insertions in Non-Small Cell Lung Carcinoma Revealed by Nanopore Sequencing

Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads

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