ClearCNV: CNV calling from NGS panel data in the presence of ambiguity and noise

May, Vinzenz; Koch, L.J.; Fischer-Zirnsak, Björn; Horn, Denise; Gehle, Petra; Kornak, Uwe; Beule, Dieter; Holtgrewe, Manuel

doi:10.1093/bioinformatics/btac418

Cited by 4 publications

(2 citation statements)

References 18 publications

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“…While our results showed that 1061 retained a higher number of genes in silico (Table 2), the Illumina sequencing run of the 1272 probe set shows much higher locus retention and greater resolution than the 1061 probe set (Table 3). We hypothesize that the low loci retention in silico Moore-Pollard, Jones, Mandel 17 is a relic of read simulators not always capturing the variances of Illumina sequenced data since they cannot model noise or sequencing technology biases perfectly (May et al, 2022;Duncavage et al, 2023). Additionally, we suspect that having longer gene sequences in the probe set influences read simulator results, though we cannot confirm the validity of these suspicions.…”

Section: Discussionmentioning

confidence: 89%

Compositae-ParaLoss-1272: Complementary sunflower specific probe-set reduces issues with paralogs in complex systems

Moore-Pollard

Jones

Mandel

2023

Preprint

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Premise: The sunflower family specific probe set, Compositae-1061, has enabled family-wide phylogenomic studies and investigations at lower-taxonomic levels by targeting 1,000+ genes. However, it generally lacks resolution at the genus to species level, especially in groups with complex evolutionary histories including polyploidy and hybridization. Methods: In this study, we developed a new HybSeq probe set, Compositae-ParaLoss-1272, designed to target orthologous loci in Asteraceae family members. We tested its efficiency across the family by simulating target-enrichment sequencing in silico. Additionally, we tested its effectiveness at lower taxonomic levels in genus Packera which has a complex evolutionary and taxonomic history. We performed HybSeq with Compositae-ParaLoss-1272 for 19 taxa which were previously studied using the Compositae-1061 probe set. Sequences from both probe sets were used to generate phylogenies, compare topologies, and assess node support. Results: We report that Compositae-ParaLoss-1272 captured loci across all tested Asteraceae members. Additionally, Compositae-ParaLoss-1272 had less gene tree discordance, recovered considerably fewer paralogous sequences, and retained longer loci than Compositae-1061. Discussion: Given the complexity of plant evolutionary histories, assigning orthology for phylogenomic analyses will continue to be challenging. However, we anticipate this new probe set will provide improved resolution and utility for studies at lower-taxonomic levels and complex groups in the sunflower family.

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Section: Discussionmentioning

confidence: 89%

Compositae-ParaLoss-1272: Complementary sunflower specific probe-set reduces issues with paralogs in complex systems

Moore-Pollard

Jones

Mandel

2023

Preprint

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“…While our results showed that Comp‐1061 retained a higher number of genes in silico (Table 3 ), the Illumina sequencing run of the Comp‐ParaLoss‐1272 probe set shows much higher locus retention and greater resolution than the Comp‐1061 probe set (Table 3 ). We hypothesize that the low loci retention in silico is a relic of read simulators not always capturing the variances of Illumina‐sequenced data because they cannot perfectly model noise or sequencing technology biases (May et al, 2022 ; Duncavage et al, 2023 ). Additionally, we suspect that having longer gene sequences in the probe set influences read simulator results, although we cannot confirm the validity of these suspicions.…”

Section: Discussionmentioning

confidence: 99%

Compositae‐ParaLoss‐1272: A complementary sunflower‐specific probe set reduces paralogs in phylogenomic analyses of complex systems

Moore‐Pollard,

Jones,

Mandel

2024

Appl Plant Sci

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PremiseA family‐specific probe set for sunflowers, Compositae‐1061, enables family‐wide phylogenomic studies and investigations at lower taxonomic levels, but may lack resolution at genus to species levels, especially in groups complicated by polyploidy and hybridization.MethodsWe developed a Hyb‐Seq probe set, Compositae‐ParaLoss‐1272, that targets orthologous loci in Asteraceae. We tested its efficiency across the family by simulating target enrichment sequencing in silico. Additionally, we tested its effectiveness at lower taxonomic levels in the historically complex genus Packera. We performed Hyb‐Seq with Compositae‐ParaLoss‐1272 for 19 Packera taxa that were previously studied using Compositae‐1061. The resulting sequences from each probe set, plus a combination of both, were used to generate phylogenies, compare topologies, and assess node support.ResultsWe report that Compositae‐ParaLoss‐1272 captured loci across all tested Asteraceae members, had less gene tree discordance, and retained longer loci than Compositae‐1061. Most notably, Compositae‐ParaLoss‐1272 recovered substantially fewer paralogous sequences than Compositae‐1061, with only ~5% of the recovered loci reporting as paralogous, compared to ~59% with Compositae‐1061.DiscussionGiven the complexity of plant evolutionary histories, assigning orthology for phylogenomic analyses will continue to be challenging. However, we anticipate Compositae‐ParaLoss‐1272 will provide improved resolution and utility for studies of complex groups and lower taxonomic levels in the sunflower family.

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Detection of germline CNVs from gene panel data: benchmarking the state of the art

Munté,

Roca,

Del Valle

et al. 2024

Briefings in Bioinformatics

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Germline copy number variants (CNVs) play a significant role in hereditary diseases. However, the accurate detection of CNVs from targeted next-generation sequencing (NGS) gene panel data remains a challenging task. Several tools for calling CNVs within this context have been published to date, but the available benchmarks suffer from limitations, including testing on simulated data, testing on small datasets, and testing a small subset of published tools. In this work, we conducted a comprehensive benchmarking of 12 tools (Atlas-CNV, ClearCNV, ClinCNV, CNVkit, Cobalt, CODEX2, CoNVaDING, DECoN, ExomeDepth, GATK-gCNV, panelcn.MOPS, VisCap) on four validated gene panel datasets using their default parameters. We also assessed the impact of modifying 107 tool parameters and identified 13 parameter values that we suggest using to improve the tool F1 score. A total of 66 tool pair combinations were also evaluated to produce better meta-callers. Furthermore, we developed CNVbenchmarker2, a framework to help users perform their own evaluations. Our results indicated that in terms of F1 score, ClinCNV and GATK-gCNV were the best CNV callers. Regarding sensitivity, GATK-gCNV also exhibited particularly high performance. The results presented here provide an evaluation of the current state of the art in germline CNV detection from gene panel data and can be used as a reference resource when using any of the tools.

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ClearCNV: CNV calling from NGS panel data in the presence of ambiguity and noise

Cited by 4 publications

References 18 publications

Compositae-ParaLoss-1272: Complementary sunflower specific probe-set reduces issues with paralogs in complex systems

Compositae-ParaLoss-1272: Complementary sunflower specific probe-set reduces issues with paralogs in complex systems

Compositae‐ParaLoss‐1272: A complementary sunflower‐specific probe set reduces paralogs in phylogenomic analyses of complex systems

Detection of germline CNVs from gene panel data: benchmarking the state of the art

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