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CaClust: linking genotype to transcriptional heterogeneity of follicular lymphoma using BCR and exomic variants CaClust：利用 BCR 和外显子变异将滤泡淋巴瘤的基因型与转录异质性联系起来
IF 12.3 1区 生物学
Genome Biology Pub Date : 2024-11-05 DOI: 10.1186/s13059-024-03417-1
Kazimierz Oksza-Orzechowski, Edwin Quinten, Shadi Shafighi, Szymon M. Kiełbasa, Hugo W. van Kessel, Ruben A. L. de Groen, Joost S. P. Vermaat, Julieta H. Sepúlveda Yáñez, Marcelo A. Navarrete, Hendrik Veelken, Cornelis A. M. van Bergen, Ewa Szczurek
{"title":"CaClust: linking genotype to transcriptional heterogeneity of follicular lymphoma using BCR and exomic variants","authors":"Kazimierz Oksza-Orzechowski, Edwin Quinten, Shadi Shafighi, Szymon M. Kiełbasa, Hugo W. van Kessel, Ruben A. L. de Groen, Joost S. P. Vermaat, Julieta H. Sepúlveda Yáñez, Marcelo A. Navarrete, Hendrik Veelken, Cornelis A. M. van Bergen, Ewa Szczurek","doi":"10.1186/s13059-024-03417-1","DOIUrl":"https://doi.org/10.1186/s13059-024-03417-1","url":null,"abstract":"Tumours exhibit high genotypic and transcriptional heterogeneity. Both affect cancer progression and treatment, but have been predominantly studied separately in follicular lymphoma. To comprehensively investigate the evolution and genotype-to-phenotype maps in follicular lymphoma, we introduce CaClust, a probabilistic graphical model integrating deep whole exome, single-cell RNA and B-cell receptor sequencing data to infer clone genotypes, cell-to-clone mapping, and single-cell genotyping. CaClust outperforms a state-of-the-art model on simulated and patient data. In-depth analyses of single cells from four samples showcase effects of driver mutations, follicular lymphoma evolution, possible therapeutic targets, and single-cell genotyping that agrees with an independent targeted resequencing experiment.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"35 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142580334","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
TDFPS-Designer: an efficient toolkit for barcode design and selection in nanopore sequencing TDFPS-Designer：纳米孔测序中条形码设计和选择的高效工具包
IF 12.3 1区 生物学
Genome Biology Pub Date : 2024-11-04 DOI: 10.1186/s13059-024-03423-3
Junhai Qi, Zhengyi Li, Yao-zhong Zhang, Guojun Li, Xin Gao, Renmin Han
{"title":"TDFPS-Designer: an efficient toolkit for barcode design and selection in nanopore sequencing","authors":"Junhai Qi, Zhengyi Li, Yao-zhong Zhang, Guojun Li, Xin Gao, Renmin Han","doi":"10.1186/s13059-024-03423-3","DOIUrl":"https://doi.org/10.1186/s13059-024-03423-3","url":null,"abstract":"Oxford Nanopore Technologies (ONT) offers ultrahigh-throughput multi-sample sequencing but only provides barcode kits that enable up to 96-sample multiplexing. We present TDFPS-Designer, a new toolkit for nanopore sequencing barcode design, which creates significantly more barcodes: 137 with a length of 20 base pairs, 410 at 24 bp, and 1779 at 30 bp, far surpassing ONT’s offerings. It includes GPU-based acceleration for ultra-fast demultiplexing and designs robust barcodes suitable for high-error ONT data. TDFPS-Designer outperforms current methods, improving the demultiplexing recall rate by 20% relative to Guppy, without a reduction in precision.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"142 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142574464","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Benchmarking and building DNA binding affinity models using allele-specific and allele-agnostic transcription factor binding data 利用等位基因特异性和等位基因不确定性转录因子结合数据制定基准并构建 DNA 结合亲和力模型
IF 12.3 1区 生物学
Genome Biology Pub Date : 2024-10-31 DOI: 10.1186/s13059-024-03424-2
Xiaoting Li, Lucas A. N. Melo, Harmen J. Bussemaker
{"title":"Benchmarking and building DNA binding affinity models using allele-specific and allele-agnostic transcription factor binding data","authors":"Xiaoting Li, Lucas A. N. Melo, Harmen J. Bussemaker","doi":"10.1186/s13059-024-03424-2","DOIUrl":"https://doi.org/10.1186/s13059-024-03424-2","url":null,"abstract":"Transcription factors (TFs) bind to DNA in a highly sequence-specific manner. This specificity manifests itself in vivo as differences in TF occupancy between the two alleles at heterozygous loci. Genome-scale assays such as ChIP-seq currently are limited in their power to detect allele-specific binding (ASB) both in terms of read coverage and representation of individual variants in the cell lines used. This makes prediction of allelic differences in TF binding from sequence alone desirable, provided that the reliability of such predictions can be quantitatively assessed. We here propose methods for benchmarking sequence-to-affinity models for TF binding in terms of their ability to predict allelic imbalances in ChIP-seq counts. We use a likelihood function based on an over-dispersed binomial distribution to aggregate evidence for allelic preference across the genome without requiring statistical significance for individual variants. This allows us to systematically compare predictive performance when multiple binding models for the same TF are available. To facilitate the de novo inference of high-quality models from paired-end in vivo binding data such as ChIP-seq, ChIP-exo, and CUT&Tag without read mapping or peak calling, we introduce an extensible reimplementation of our biophysically interpretable machine learning framework named PyProBound. Explicitly accounting for assay-specific bias in DNA fragmentation rate when training on ChIP-seq yields improved TF binding models. Moreover, we show how PyProBound can leverage our threshold-free ASB likelihood function to perform de novo motif discovery using allele-specific ChIP-seq counts. Our work provides new strategies for predicting the functional impact of non-coding variants.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"8 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142555785","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Response to "Neglecting normalization impact in semi-synthetic RNA-seq data simulation generates artificial false positives" and "Winsorization greatly reduces false positives by popular differential expression methods when analyzing human population samples" 对 "在半合成 RNA-seq 数据模拟中忽略归一化的影响会产生人为的假阳性 "和 "在分析人类群体样本时，采用流行的差异表达方法进行反向归一化可大大降低假阳性 "的回应
IF 12.3 1区 生物学
Genome Biology Pub Date : 2024-10-30 DOI: 10.1186/s13059-024-03232-8
Xinzhou Ge, Yumei Li, Wei Li, Jingyi Jessica Li
{"title":"Response to \"Neglecting normalization impact in semi-synthetic RNA-seq data simulation generates artificial false positives\" and \"Winsorization greatly reduces false positives by popular differential expression methods when analyzing human population samples\"","authors":"Xinzhou Ge, Yumei Li, Wei Li, Jingyi Jessica Li","doi":"10.1186/s13059-024-03232-8","DOIUrl":"https://doi.org/10.1186/s13059-024-03232-8","url":null,"abstract":"Two correspondences raised concerns or comments about our analyses regarding exaggerated false positives found by differential expression (DE) methods. Here, we discuss the points they raise and explain why we agree or disagree with these points. We add new analysis to confirm that the Wilcoxon rank-sum test remains the most robust method compared to the other five DE methods (DESeq2, edgeR, limma-voom, dearseq, and NOISeq) in two-condition DE analyses after considering normalization and winsorization, the data preprocessing steps discussed in the two correspondences.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"15 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142541575","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Neglecting the impact of normalization in semi-synthetic RNA-seq data simulations generates artificial false positives 在半合成 RNA-seq 数据模拟中忽略归一化的影响会产生人为假阳性结果
IF 12.3 1区 生物学
Genome Biology Pub Date : 2024-10-30 DOI: 10.1186/s13059-024-03231-9
Boris P. Hejblum, Kalidou Ba, Rodolphe Thiébaut, Denis Agniel
{"title":"Neglecting the impact of normalization in semi-synthetic RNA-seq data simulations generates artificial false positives","authors":"Boris P. Hejblum, Kalidou Ba, Rodolphe Thiébaut, Denis Agniel","doi":"10.1186/s13059-024-03231-9","DOIUrl":"https://doi.org/10.1186/s13059-024-03231-9","url":null,"abstract":"A recent study reported exaggerated false positives by popular differential expression methods when analyzing large population samples. We reproduce the differential expression analysis simulation results and identify a caveat in the data generation process. Data not truly generated under the null hypothesis led to incorrect comparisons of benchmark methods. We provide corrected simulation results that demonstrate the good performance of dearseq and argue against the superiority of the Wilcoxon rank-sum test as suggested in the previous study.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"66 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142541577","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Winsorization greatly reduces false positives by popular differential expression methods when analyzing human population samples 在分析人类群体样本时，Winsorization 可大大降低流行的差异表达方法的误报率
IF 12.3 1区 生物学
Genome Biology Pub Date : 2024-10-30 DOI: 10.1186/s13059-024-03230-w
Lu Yang, Xianyang Zhang, Jun Chen
{"title":"Winsorization greatly reduces false positives by popular differential expression methods when analyzing human population samples","authors":"Lu Yang, Xianyang Zhang, Jun Chen","doi":"10.1186/s13059-024-03230-w","DOIUrl":"https://doi.org/10.1186/s13059-024-03230-w","url":null,"abstract":"A recent study found severely inflated type I error rates for DESeq2 and edgeR, two dominant tools used for differential expression analysis of RNA-seq data. Here, we show that by properly addressing the outliers in the RNA-Seq data using winsorization, the type I error rate of DESeq2 and edgeR can be substantially reduced, and the power is comparable to Wilcoxon rank-sum test for large datasets. Therefore, as an alternative to Wilcoxon rank-sum test, they may still be applied for differential expression analysis of large RNA-Seq datasets.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"5 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142541438","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
pan-Draft: automated reconstruction of species-representative metabolic models from multiple genomes pan-Draft：从多个基因组自动重建物种代表性代谢模型
IF 12.3 1区 生物学
Genome Biology Pub Date : 2024-10-25 DOI: 10.1186/s13059-024-03425-1
Nicola De Bernardini, Guido Zampieri, Stefano Campanaro, Johannes Zimmermann, Silvio Waschina, Laura Treu
{"title":"pan-Draft: automated reconstruction of species-representative metabolic models from multiple genomes","authors":"Nicola De Bernardini, Guido Zampieri, Stefano Campanaro, Johannes Zimmermann, Silvio Waschina, Laura Treu","doi":"10.1186/s13059-024-03425-1","DOIUrl":"https://doi.org/10.1186/s13059-024-03425-1","url":null,"abstract":"The accurate reconstruction of genome-scale metabolic models (GEMs) for unculturable species poses challenges due to the incomplete and fragmented genetic information typical of metagenome-assembled genomes (MAGs). While existing tools leverage sequence homology from single genomes, this study introduces pan-Draft, a pan-reactome-based approach exploiting recurrent genetic evidence to determine the solid core structure of species-level GEMs. By comparing MAGs clustered at the species-level, pan-Draft addresses the issues due to the incompleteness and contamination of individual genomes, providing high-quality draft models and an accessory reactions catalog supporting the gapfilling step. This approach will improve our comprehension of metabolic functions of uncultured species.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"15 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142489403","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Plant conservation in the age of genome editing: opportunities and challenges 基因组编辑时代的植物保护：机遇与挑战
IF 12.3 1区 生物学
Genome Biology Pub Date : 2024-10-24 DOI: 10.1186/s13059-024-03399-0
Kangquan Yin, Mi Yoon Chung, Bo Lan, Fang K. Du, Myong Gi Chung
{"title":"Plant conservation in the age of genome editing: opportunities and challenges","authors":"Kangquan Yin, Mi Yoon Chung, Bo Lan, Fang K. Du, Myong Gi Chung","doi":"10.1186/s13059-024-03399-0","DOIUrl":"https://doi.org/10.1186/s13059-024-03399-0","url":null,"abstract":"Numerous plant taxa are threatened by habitat destruction or overexploitation. To overcome these threats, new methods are urgently needed for rescuing threatened and endangered plant species. Here, we review the genetic consequences of threats to species populations. We highlight potential advantages of genome editing for mitigating negative effects caused by new pathogens and pests or climate change where other approaches have failed. We propose solutions to protect threatened plants using genome editing technology unless absolutely necessary. We further discuss the challenges associated with genome editing in plant conservation to mitigate the decline of plant diversity.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"110 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142488635","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
STASCAN deciphers fine-resolution cell distribution maps in spatial transcriptomics by deep learning STASCAN 通过深度学习解译空间转录组学中的精细分辨率细胞分布图
IF 12.3 1区 生物学
Genome Biology Pub Date : 2024-10-22 DOI: 10.1186/s13059-024-03421-5
Ying Wu, Jia-Yi Zhou, Bofei Yao, Guanshen Cui, Yong-Liang Zhao, Chun-Chun Gao, Ying Yang, Shihua Zhang, Yun-Gui Yang
{"title":"STASCAN deciphers fine-resolution cell distribution maps in spatial transcriptomics by deep learning","authors":"Ying Wu, Jia-Yi Zhou, Bofei Yao, Guanshen Cui, Yong-Liang Zhao, Chun-Chun Gao, Ying Yang, Shihua Zhang, Yun-Gui Yang","doi":"10.1186/s13059-024-03421-5","DOIUrl":"https://doi.org/10.1186/s13059-024-03421-5","url":null,"abstract":"Spatial transcriptomics technologies have been widely applied to decode cellular distribution by resolving gene expression profiles in tissue. However, sequencing techniques still limit the ability to create a fine-resolved spatial cell-type map. To this end, we develop a novel deep-learning-based approach, STASCAN, to predict the spatial cellular distribution of captured or uncharted areas where only histology images are available by cell feature learning integrating gene expression profiles and histology images. STASCAN is successfully applied across diverse datasets from different spatial transcriptomics technologies and displays significant advantages in deciphering higher-resolution cellular distribution and resolving enhanced organizational structures.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"13 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142486679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A comprehensive study of genetic regulation and disease associations of plasma circulatory microRNAs using population-level data 利用人群水平数据对血浆循环微RNA的遗传调控和疾病相关性进行综合研究
IF 12.3 1区 生物学
Genome Biology Pub Date : 2024-10-21 DOI: 10.1186/s13059-024-03420-6
Rima Mustafa, Michelle M. J. Mens, Arno van Hilten, Jian Huang, Gennady Roshchupkin, Tianxiao Huan, Linda Broer, Joyce B. J. van Meurs, Paul Elliott, Daniel Levy, M. Arfan Ikram, Marina Evangelou, Abbas Dehghan, Mohsen Ghanbari
{"title":"A comprehensive study of genetic regulation and disease associations of plasma circulatory microRNAs using population-level data","authors":"Rima Mustafa, Michelle M. J. Mens, Arno van Hilten, Jian Huang, Gennady Roshchupkin, Tianxiao Huan, Linda Broer, Joyce B. J. van Meurs, Paul Elliott, Daniel Levy, M. Arfan Ikram, Marina Evangelou, Abbas Dehghan, Mohsen Ghanbari","doi":"10.1186/s13059-024-03420-6","DOIUrl":"https://doi.org/10.1186/s13059-024-03420-6","url":null,"abstract":"MicroRNAs (miRNAs) are small non-coding RNAs that post-transcriptionally regulate gene expression. Perturbations in plasma miRNA levels are known to impact disease risk and have potential as disease biomarkers. Exploring the genetic regulation of miRNAs may yield new insights into their important role in governing gene expression and disease mechanisms. We present genome-wide association studies of 2083 plasma circulating miRNAs in 2178 participants of the Rotterdam Study to identify miRNA-expression quantitative trait loci (miR-eQTLs). We identify 3292 associations between 1289 SNPs and 63 miRNAs, of which 65% are replicated in two independent cohorts. We demonstrate that plasma miR-eQTLs co-localise with gene expression, protein, and metabolite-QTLs, which help in identifying miRNA-regulated pathways. We investigate consequences of alteration in circulating miRNA levels on a wide range of clinical conditions in phenome-wide association studies and Mendelian randomisation using the UK Biobank data (N = 423,419), revealing the pleiotropic and causal effects of several miRNAs on various clinical conditions. In the Mendelian randomisation analysis, we find a protective causal effect of miR-1908-5p on the risk of benign colon neoplasm and show that this effect is independent of its host gene (FADS1). This study enriches our understanding of the genetic architecture of plasma miRNAs and explores the signatures of miRNAs across a wide range of clinical conditions. The integration of population-based genomics, other omics layers, and clinical data presents opportunities to unravel potential clinical significance of miRNAs and provides tools for novel miRNA-based therapeutic target discovery.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"33 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142452047","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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