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DeepKINET: a deep generative model for estimating single-cell RNA splicing and degradation rates. DeepKINET:用于估计单细胞 RNA 剪接和降解率的深度生成模型。
IF 12.3 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-09-06 DOI: 10.1186/s13059-024-03367-8
Chikara Mizukoshi, Yasuhiro Kojima, Satoshi Nomura, Shuto Hayashi, Ko Abe, Teppei Shimamura

Messenger RNA splicing and degradation are critical for gene expression regulation, the abnormality of which leads to diseases. Previous methods for estimating kinetic rates have limitations, assuming uniform rates across cells. DeepKINET is a deep generative model that estimates splicing and degradation rates at single-cell resolution from scRNA-seq data. DeepKINET outperforms existing methods on simulated and metabolic labeling datasets. Applied to forebrain and breast cancer data, it identifies RNA-binding proteins responsible for kinetic rate diversity. DeepKINET also analyzes the effects of splicing factor mutations on target genes in erythroid lineage cells. DeepKINET effectively reveals cellular heterogeneity in post-transcriptional regulation.

信使 RNA 的剪接和降解对基因表达调控至关重要,其异常会导致疾病。以往估算动力学速率的方法有其局限性,即假设整个细胞的速率是一致的。DeepKINET 是一种深度生成模型,能根据 scRNA-seq 数据以单细胞分辨率估算剪接和降解率。DeepKINET 在模拟和代谢标记数据集上的表现优于现有方法。在应用于前脑和乳腺癌数据时,它能识别导致动力学速率多样性的 RNA 结合蛋白。DeepKINET 还分析了红系细胞中剪接因子突变对靶基因的影响。DeepKINET 能有效揭示转录后调控的细胞异质性。
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引用次数: 0
Seqrutinator: scrutiny of large protein superfamily sequence datasets for the identification and elimination of non-functional homologues. Sequrutinator:仔细检查大型蛋白质超家族序列数据集,以识别和消除无功能同源物。
IF 12.3 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-08-26 DOI: 10.1186/s13059-024-03371-y
Agustín Amalfitano, Nicolás Stocchi, Hugo Marcelo Atencio, Fernando Villarreal, Arjen Ten Have

Seqrutinator is an objective, flexible pipeline that removes sequences with sequencing and/or gene model errors and sequences from pseudogenes from complex, eukaryotic protein superfamilies. Testing Seqrutinator on major superfamilies BAHD, CYP, and UGT removes only 1.94% of SwissProt entries, 14% of entries from the model plant Arabidopsis thaliana, but 80% of entries from Pinus taeda's recent complete proteome. Application of Seqrutinator on crude BAHDomes, CYPomes, and UGTomes obtained from 16 plant proteomes shows convergence of the numbers of paralogues. MSAs, phylogenies, and particularly functional clustering improve drastically upon Seqrutinator application, indicating good performance.

Seqrutinator 是一个客观、灵活的管道,可从复杂的真核生物蛋白质超家族中移除存在测序和/或基因模型错误的序列以及来自假基因的序列。在主要超家族 BAHD、CYP 和 UGT 上测试 Seqrutinator,只移除了 1.94% 的 SwissProt 条目、14% 的模式植物拟南芥条目,但移除了 80% 的太田松近期完整蛋白质组条目。将 Seqrutinator 应用于从 16 个植物蛋白质组中获得的粗 BAHDomes、CYPomes 和 UGTomes,结果显示旁系物的数量趋于一致。应用 Seqrutinator 后,MSA、系统发育,特别是功能聚类得到了显著改善,显示出良好的性能。
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引用次数: 0
Systemic interindividual DNA methylation variants in cattle share major hallmarks with those in humans. 牛的系统性个体间 DNA 甲基化变异与人类具有相同的主要特征。
IF 12.3 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-07-15 DOI: 10.1186/s13059-024-03307-6
Wen-Jou Chang, Maria S Baker, Eleonora Laritsky, Chathura J Gunasekara, Uditha Maduranga, Justine C Galliou, Joseph W McFadden, Jessica R Waltemyer, Bruce Berggren-Thomas, Brianna N Tate, Hanxue Zhang, Benjamin D Rosen, Curtis P Van Tassell, George E Liu, Cristian Coarfa, Yi Athena Ren, Robert A Waterland

Background: We recently identified ~ 10,000 correlated regions of systemic interindividual epigenetic variation (CoRSIVs) in the human genome. These methylation variants are amenable to population studies, as DNA methylation measurements in blood provide information on epigenetic regulation throughout the body. Moreover, establishment of DNA methylation at human CoRSIVs is labile to periconceptional influences such as nutrition. Here, we analyze publicly available whole-genome bisulfite sequencing data on multiple tissues of each of two Holstein cows to determine whether CoRSIVs exist in cattle.

Results: Focusing on genomic blocks with ≥ 5 CpGs and a systemic interindividual variation index of at least 20, our approach identifies 217 cattle CoRSIVs, a subset of which we independently validate by bisulfite pyrosequencing. Similar to human CoRSIVs, those in cattle are strongly associated with genetic variation. Also as in humans, we show that establishment of DNA methylation at cattle CoRSIVs is particularly sensitive to early embryonic environment, in the context of embryo culture during assisted reproduction.

Conclusions: Our data indicate that CoRSIVs exist in cattle, as in humans, suggesting these systemic epigenetic variants may be common to mammals in general. To the extent that individual epigenetic variation at cattle CoRSIVs affects phenotypic outcomes, assessment of CoRSIV methylation at birth may become an important tool for optimizing agriculturally important traits. Moreover, adjusting embryo culture conditions during assisted reproduction may provide opportunities to tailor agricultural outcomes by engineering CoRSIV methylation profiles.

背景:我们最近在人类基因组中发现了约 10,000 个系统性个体间表观遗传变异相关区域(CoRSIVs)。这些甲基化变异可用于群体研究,因为血液中的 DNA 甲基化测量可提供全身表观遗传调控的信息。此外,人类 CoRSIVs 上 DNA 甲基化的建立不易受到围孕期影响(如营养)的影响。在这里,我们分析了公开的全基因组亚硫酸氢盐测序数据,分别对两头荷斯坦奶牛的多个组织进行了分析,以确定牛体内是否存在CoRSIVs:我们的方法以 CpGs ≥ 5 个且系统个体间变异指数至少为 20 的基因组区块为重点,识别出 217 个牛 CoRSIVs,我们通过亚硫酸氢盐热测序独立验证了其中的一部分。与人类的 CoRSIV 相似,牛的 CoRSIV 也与遗传变异密切相关。与人类一样,我们的研究表明,在辅助生殖过程中胚胎培养的背景下,牛CoRSIVs上DNA甲基化的建立对早期胚胎环境特别敏感:我们的数据表明,与人类一样,牛体内也存在 CoRSIVs,这表明这些系统性表观遗传变异可能是哺乳动物的共性。由于牛 CoRSIV 的个体表观遗传变异会影响表型结果,因此评估牛出生时的 CoRSIV 甲基化情况可能会成为优化重要农业性状的重要工具。此外,在辅助生殖过程中调整胚胎培养条件可能会提供机会,通过设计 CoRSIV 甲基化图谱来定制农业结果。
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引用次数: 0
TaqTth-hpRNA: a novel compact RNA-targeting tool for specific silencing of pathogenic mRNA. TaqTth-hpRNA:特异性沉默致病性 mRNA 的新型紧凑型 RNA 靶向工具。
IF 12.3 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-07-07 DOI: 10.1186/s13059-024-03326-3
Chong Xu, Jiyanuo Cao, Huanran Qiang, Yu Liu, Jialin Wu, Qiudan Luo, Meng Wan, Yujie Wang, Peiliang Wang, Qian Cheng, Guohua Zhou, Jian Sima, Yongjian Guo, Shu Xu

Pathogenic allele silencing is a promising treatment for genetic hereditary diseases. Here, we develop an RNA-cleaving tool, TaqTth-hpRNA, consisting of a small, chimeric TaqTth, and a hairpin RNA guiding probe. With a minimal flanking sequence-motif requirement, in vitro and in vivo studies show TaqTth-hpRNA cleaves RNA efficiently and specifically. In an Alzheimer's disease model, we demonstrate silencing of mutant APPswe mRNA without altering the wild-type APP mRNA. Notably, due to the compact size of TaqTth, we are able to combine with APOE2 overexpression in a single AAV vector, which results in stronger inhibition of pathologies.

致病等位基因沉默是治疗遗传性疾病的一种很有前景的方法。在这里,我们开发了一种 RNA 切割工具 TaqTth-hpRNA,它由小型嵌合 TaqTth 和发夹式 RNA 引导探针组成。体外和体内研究表明,TaqTth-hpRNA 只需要极少的侧翼序列-主题词,就能高效、特异地裂解 RNA。在阿尔茨海默氏症模型中,我们证明了对突变 APPswe mRNA 的沉默,而不改变野生型 APP mRNA。值得注意的是,由于 TaqTth 体积小巧,我们能够在单一 AAV 载体中结合 APOE2 的过表达,从而对病症产生更强的抑制作用。
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引用次数: 0
Tagging large CNV blocks in wheat boosts digitalization of germplasm resources by ultra-low-coverage sequencing. 通过超低覆盖率测序技术标记小麦中的大型 CNV 块,促进种质资源的数字化。
IF 12.3 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-07-01 DOI: 10.1186/s13059-024-03315-6
Jianxia Niu, Wenxi Wang, Zihao Wang, Zhe Chen, Xiaoyu Zhang, Zhen Qin, Lingfeng Miao, Zhengzhao Yang, Chaojie Xie, Mingming Xin, Huiru Peng, Yingyin Yao, Jie Liu, Zhongfu Ni, Qixin Sun, Weilong Guo

Background: The massive structural variations and frequent introgression highly contribute to the genetic diversity of wheat, while the huge and complex genome of polyploid wheat hinders efficient genotyping of abundant varieties towards accurate identification, management, and exploitation of germplasm resources.

Results: We develop a novel workflow that identifies 1240 high-quality large copy number variation blocks (CNVb) in wheat at the pan-genome level, demonstrating that CNVb can serve as an ideal DNA fingerprinting marker for discriminating massive varieties, with the accuracy validated by PCR assay. We then construct a digitalized genotyping CNVb map across 1599 global wheat accessions. Key CNVb markers are linked with trait-associated introgressions, such as the 1RS·1BL translocation and 2NvS translocation, and the beneficial alleles, such as the end-use quality allele Glu-D1d (Dx5 + Dy10) and the semi-dwarf r-e-z allele. Furthermore, we demonstrate that these tagged CNVb markers promote a stable and cost-effective strategy for evaluating wheat germplasm resources with ultra-low-coverage sequencing data, competing with SNP array for applications such as evaluating new varieties, efficient management of collections in gene banks, and describing wheat germplasm resources in a digitalized manner. We also develop a user-friendly interactive platform, WheatCNVb ( http://wheat.cau.edu.cn/WheatCNVb/ ), for exploring the CNVb profiles over ever-increasing wheat accessions, and also propose a QR-code-like representation of individual digital CNVb fingerprint. This platform also allows uploading new CNVb profiles for comparison with stored varieties.

Conclusions: The CNVb-based approach provides a low-cost and high-throughput genotyping strategy for enabling digitalized wheat germplasm management and modern breeding with precise and practical decision-making.

背景:小麦的大量结构变异和频繁的外源引入极大地促进了小麦的遗传多样性,而多倍体小麦庞大而复杂的基因组则阻碍了对丰富品种进行高效基因分型以实现种质资源的准确鉴定、管理和开发利用:我们开发了一种新的工作流程,在泛基因组水平上鉴定出小麦中的 1240 个高质量大拷贝数变异块(CNVb),证明 CNVb 可作为鉴别大量品种的理想 DNA 指纹标记,其准确性已通过 PCR 检测得到验证。然后,我们构建了一个涵盖全球 1599 个小麦品种的数字化 CNVb 基因分型图谱。关键的 CNVb 标记与性状相关的引种(如 1RS-1BL 易位和 2NvS 易位)以及有益等位基因(如最终使用品质等位基因 Glu-D1d (Dx5 + Dy10) 和半矮小 r-e-z 等位基因)相关联。此外,我们还证明了这些标记的 CNVb 标记可促进使用超低覆盖率测序数据评估小麦种质资源的稳定且经济高效的策略,可与 SNP 阵列竞争,应用于新品种评估、基因库藏品的高效管理以及小麦种质资源的数字化描述等。我们还开发了一个用户友好型交互平台--WheatCNVb ( http://wheat.cau.edu.cn/WheatCNVb/ ),用于探索不断增加的小麦种质资源的 CNVb 图谱,并提出了一种类似 QR 码的单个数字 CNVb 指纹表示法。该平台还允许上传新的 CNVb 图谱,以便与储存的品种进行比较:结论:基于 CNVb 的方法提供了一种低成本、高通量的基因分型策略,可实现数字化的小麦种质管理和现代育种,做出精确而实用的决策。
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引用次数: 0
RIBAP: a comprehensive bacterial core genome annotation pipeline for pangenome calculation beyond the species level. RIBAP:细菌核心基因组综合注释管道,用于物种水平以上的泛基因组计算。
IF 12.3 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-07-01 DOI: 10.1186/s13059-024-03312-9
Kevin Lamkiewicz, Lisa-Marie Barf, Konrad Sachse, Martin Hölzer

Microbial pangenome analysis identifies present or absent genes in prokaryotic genomes. However, current tools are limited when analyzing species with higher sequence diversity or higher taxonomic orders such as genera or families. The Roary ILP Bacterial core Annotation Pipeline (RIBAP) uses an integer linear programming approach to refine gene clusters predicted by Roary for identifying core genes. RIBAP successfully handles the complexity and diversity of Chlamydia, Klebsiella, Brucella, and Enterococcus genomes, outperforming other established and recent pangenome tools for identifying all-encompassing core genes at the genus level. RIBAP is a freely available Nextflow pipeline at github.com/hoelzer-lab/ribap and zenodo.org/doi/10.5281/zenodo.10890871.

微生物泛基因组分析可确定原核生物基因组中存在或不存在的基因。然而,目前的工具在分析序列多样性较高的物种或较高的分类次序(如属或科)时受到限制。Roary ILP 细菌核心注释管道(RIBAP)使用整数线性规划方法来完善 Roary 预测的基因簇,以确定核心基因。RIBAP 成功地处理了衣原体、克雷伯氏菌、布鲁氏菌和肠球菌基因组的复杂性和多样性,在属一级鉴定包罗万象的核心基因方面优于其他已有的和最新的泛基因组工具。RIBAP 是免费提供的 Nextflow 管道,可在 github.com/hoelzer-lab/ribap 和 zenodo.org/doi/10.5281/zenodo.10890871 上下载。
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引用次数: 0
Benchmarking computational variant effect predictors by their ability to infer human traits. 根据推断人类特征的能力对计算变异效应预测器进行标杆分析。
IF 12.3 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-07-01 DOI: 10.1186/s13059-024-03314-7
Daniel R Tabet, Da Kuang, Megan C Lancaster, Roujia Li, Karen Liu, Jochen Weile, Atina G Coté, Yingzhou Wu, Robert A Hegele, Dan M Roden, Frederick P Roth

Background: Computational variant effect predictors offer a scalable and increasingly reliable means of interpreting human genetic variation, but concerns of circularity and bias have limited previous methods for evaluating and comparing predictors. Population-level cohorts of genotyped and phenotyped participants that have not been used in predictor training can facilitate an unbiased benchmarking of available methods. Using a curated set of human gene-trait associations with a reported rare-variant burden association, we evaluate the correlations of 24 computational variant effect predictors with associated human traits in the UK Biobank and All of Us cohorts.

Results: AlphaMissense outperformed all other predictors in inferring human traits based on rare missense variants in UK Biobank and All of Us participants. The overall rankings of computational variant effect predictors in these two cohorts showed a significant positive correlation.

Conclusion: We describe a method to assess computational variant effect predictors that sidesteps the limitations of previous evaluations. This approach is generalizable to future predictors and could continue to inform predictor choice for personal and clinical genetics.

背景:计算变异效应预测器为解释人类遗传变异提供了一种可扩展且日益可靠的方法,但循环性和偏倚问题限制了以往评估和比较预测器的方法。未被用于预测器训练的基因分型和表型参与者的群体级队列有助于对现有方法进行无偏见的基准测试。我们利用一组已报告的罕见变异负担关联的人类基因-性状关联,评估了英国生物库和 "我们所有人 "队列中 24 个计算变异效应预测因子与相关人类性状的相关性:结果:在根据英国生物库和 "我们所有人 "参与者的罕见错义变异推断人类特征方面,AlphaMissense优于所有其他预测因子。在这两个队列中,计算变异效应预测因子的总体排名显示出显著的正相关性:我们描述了一种评估计算变异效应预测因子的方法,它避免了以往评估的局限性。这种方法适用于未来的预测因子,并能继续为个人和临床遗传学的预测因子选择提供信息。
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引用次数: 0
BORIS/CTCFL epigenetically reprograms clustered CTCF binding sites into alternative transcriptional start sites. BORIS/CTCFL 从表观遗传学角度将成簇的 CTCF 结合位点重新编程为替代转录起始位点。
IF 12.3 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-01-31 DOI: 10.1186/s13059-024-03175-0
Elena M Pugacheva, Dharmendra Nath Bhatt, Samuel Rivero-Hinojosa, Md Tajmul, Liron Fedida, Emma Price, Yon Ji, Dmitri Loukinov, Alexander V Strunnikov, Bing Ren, Victor V Lobanenkov

Background: Pervasive usage of alternative promoters leads to the deregulation of gene expression in carcinogenesis and may drive the emergence of new genes in spermatogenesis. However, little is known regarding the mechanisms underpinning the activation of alternative promoters.

Results: Here we describe how alternative cancer-testis-specific transcription is activated. We show that intergenic and intronic CTCF binding sites, which are transcriptionally inert in normal somatic cells, could be epigenetically reprogrammed into active de novo promoters in germ and cancer cells. BORIS/CTCFL, the testis-specific paralog of the ubiquitously expressed CTCF, triggers the epigenetic reprogramming of CTCF sites into units of active transcription. BORIS binding initiates the recruitment of the chromatin remodeling factor, SRCAP, followed by the replacement of H2A histone with H2A.Z, resulting in a more relaxed chromatin state in the nucleosomes flanking the CTCF binding sites. The relaxation of chromatin around CTCF binding sites facilitates the recruitment of multiple additional transcription factors, thereby activating transcription from a given binding site. We demonstrate that the epigenetically reprogrammed CTCF binding sites can drive the expression of cancer-testis genes, long noncoding RNAs, retro-pseudogenes, and dormant transposable elements.

Conclusions: Thus, BORIS functions as a transcription factor that epigenetically reprograms clustered CTCF binding sites into transcriptional start sites, promoting transcription from alternative promoters in both germ cells and cancer cells.

背景:替代启动子的广泛使用导致致癌过程中基因表达的失调,并可能推动精子发生过程中新基因的出现。然而,人们对替代启动子的激活机制知之甚少:结果:我们在这里描述了癌症睾丸特异性替代转录是如何被激活的。结果:我们在这里描述了癌症睾丸特异性转录是如何被激活的。我们发现,在正常体细胞中转录惰性的基因间和基因内 CTCF 结合位点,在生殖细胞和癌细胞中可被表观遗传学重编程为活跃的新启动子。BORIS/CTCFL是普遍表达的CTCF的睾丸特异性旁系亲属,它能触发CTCF位点的表观遗传重编程,使其成为活跃的转录单位。BORIS 的结合启动了染色质重塑因子 SRCAP 的招募,随后 H2A 组蛋白被 H2A.Z 代替,导致 CTCF 结合位点两侧核小体的染色质状态更加松弛。CTCF 结合位点周围染色质的松弛有利于招募多个额外的转录因子,从而激活特定结合位点的转录。我们证明,经表观遗传学重编程的 CTCF 结合位点可驱动癌试管基因、长非编码 RNA、逆转录伪基因和休眠转座元件的表达:因此,BORIS 是一种转录因子,它能将成簇的 CTCF 结合位点表观遗传重编程为转录起始位点,促进生殖细胞和癌细胞中替代启动子的转录。
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引用次数: 0
RExPRT: a machine learning tool to predict pathogenicity of tandem repeat loci. REXPRT:预测串联重复位点致病性的机器学习工具。
IF 12.3 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-01-31 DOI: 10.1186/s13059-024-03171-4
Sarah Fazal, Matt C Danzi, Isaac Xu, Shilpa Nadimpalli Kobren, Shamil Sunyaev, Chloe Reuter, Shruti Marwaha, Matthew Wheeler, Egor Dolzhenko, Francesca Lucas, Stefan Wuchty, Mustafa Tekin, Stephan Züchner, Vanessa Aguiar-Pulido

Expansions of tandem repeats (TRs) cause approximately 60 monogenic diseases. We expect that the discovery of additional pathogenic repeat expansions will narrow the diagnostic gap in many diseases. A growing number of TR expansions are being identified, and interpreting them is a challenge. We present RExPRT (Repeat EXpansion Pathogenicity pRediction Tool), a machine learning tool for distinguishing pathogenic from benign TR expansions. Our results demonstrate that an ensemble approach classifies TRs with an average precision of 93% and recall of 83%. RExPRT's high precision will be valuable in large-scale discovery studies, which require prioritization of candidate loci for follow-up studies.

串联重复序列(TRs)的扩展导致了大约 60 种单基因疾病。我们预计,更多致病性重复序列扩展的发现将缩小许多疾病的诊断差距。越来越多的串联重复序列扩展被发现,而解释这些扩展是一项挑战。我们介绍了 RExPRT(Repeat EXpansion Pathogenicity pRediction Tool,重复扩展致病性预测工具),这是一种用于区分致病性和良性 TR 扩展的机器学习工具。我们的研究结果表明,采用集合方法对 TR 进行分类的平均精确度为 93%,召回率为 83%。RExPRT 的高精确度将在大规模发现研究中发挥重要作用,因为大规模发现研究需要为后续研究确定候选位点的优先顺序。
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引用次数: 0
Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc. 利用 CNAqc 计算验证来自肿瘤大样本测序的克隆和亚克隆拷贝数改变。
IF 12.3 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-01-31 DOI: 10.1186/s13059-024-03170-5
Alice Antonello, Riccardo Bergamin, Nicola Calonaci, Jacob Househam, Salvatore Milite, Marc J Williams, Fabio Anselmi, Alberto d'Onofrio, Vasavi Sundaram, Alona Sosinsky, William C H Cross, Giulio Caravagna

Copy number alterations (CNAs) are among the most important genetic events in cancer, but their detection from sequencing data is challenging because of unknown sample purity, tumor ploidy, and general intra-tumor heterogeneity. Here, we present CNAqc, an evolution-inspired method to perform the computational validation of clonal and subclonal CNAs detected from bulk DNA sequencing. CNAqc is validated using single-cell data and simulations, is applied to over 4000 TCGA and PCAWG samples, and is incorporated into the validation process for the clinically accredited bioinformatics pipeline at Genomics England. CNAqc is designed to support automated quality control procedures for tumor somatic data validation.

拷贝数改变(CNA)是癌症中最重要的遗传事件之一,但由于样本纯度、肿瘤倍性和肿瘤内异质性未知,从测序数据中检测CNA具有挑战性。在此,我们介绍一种受进化启发的方法--CNAqc,该方法可对从批量 DNA 测序中检测到的克隆和亚克隆 CNA 进行计算验证。CNAqc 利用单细胞数据和模拟进行了验证,已应用于 4000 多个 TCGA 和 PCAWG 样本,并已纳入英格兰基因组研究所临床认可的生物信息学管道的验证流程。CNAqc 设计用于支持肿瘤体细胞数据验证的自动质量控制程序。
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引用次数: 0
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Genome Biology
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