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ViroISDC：一种基于特征编码的乙型肝炎病毒整合位点调用方法。

ViroISDC: a method for calling integration sites of hepatitis B virus based on feature encoding.

机构信息

College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.

College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.

出版信息

BMC Bioinformatics. 2024 May 4;25(1):177. doi: 10.1186/s12859-024-05763-0.

DOI:10.1186/s12859-024-05763-0
PMID:38704528
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11070082/
Abstract

BACKGROUND

Hepatitis B virus (HBV) integrates into human chromosomes and can lead to genomic instability and hepatocarcinogenesis. Current tools for HBV integration site detection lack accuracy and stability.

RESULTS

This study proposes a deep learning-based method, named ViroISDC, for detecting integration sites. ViroISDC generates corresponding grammar rules and encodes the characteristics of the language data to predict integration sites accurately. Compared with Lumpy, Pindel, Seeksv, and SurVirus, ViroISDC exhibits better overall performance and is less sensitive to sequencing depth and integration sequence length, displaying good reliability, stability, and generality. Further downstream analysis of integrated sites detected by ViroISDC reveals the integration patterns and features of HBV. It is observed that HBV integration exhibits specific chromosomal preferences and tends to integrate into cancerous tissue. Moreover, HBV integration frequency was higher in males than females, and high-frequency integration sites were more likely to be present on hepatocarcinogenesis- and anti-cancer-related genes, validating the reliability of the ViroISDC.

CONCLUSIONS

ViroISDC pipeline exhibits superior precision, stability, and reliability across various datasets when compared to similar software. It is invaluable in exploring HBV infection in the human body, holding significant implications for the diagnosis, treatment, and prognosis assessment of HCC.

摘要

背景

乙型肝炎病毒（HBV）整合到人类染色体中，可导致基因组不稳定和肝癌发生。目前用于检测 HBV 整合位点的工具准确性和稳定性不足。

结果

本研究提出了一种基于深度学习的方法，命名为 ViroISDC，用于检测整合位点。ViroISDC 生成相应的语法规则，并对语言数据的特征进行编码，以准确预测整合位点。与 Lumpy、Pindel、Seeksv 和 SurVirus 相比，ViroISDC 表现出更好的整体性能，对测序深度和整合序列长度的敏感性较低，具有良好的可靠性、稳定性和通用性。通过 ViroISDC 检测到的整合位点的下游分析揭示了 HBV 的整合模式和特征。研究发现，HBV 整合表现出特定的染色体偏好，倾向于整合到癌组织中。此外，HBV 整合在男性中的频率高于女性，高频整合位点更可能存在于与肝癌发生和抗癌相关的基因上，验证了 ViroISDC 的可靠性。

结论

与类似软件相比，ViroISDC 管道在各种数据集上表现出优越的精度、稳定性和可靠性。它对于探索人体中的 HBV 感染具有重要意义，对 HCC 的诊断、治疗和预后评估具有重要意义。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e2bc/11070082/b37667f78522/12859_2024_5763_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e2bc/11070082/b0b0720c1507/12859_2024_5763_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e2bc/11070082/e556d8b6a5a2/12859_2024_5763_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e2bc/11070082/289ab9534113/12859_2024_5763_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e2bc/11070082/834f1a8489ac/12859_2024_5763_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e2bc/11070082/a4b8545a3a17/12859_2024_5763_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e2bc/11070082/f785ce362c93/12859_2024_5763_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e2bc/11070082/b57a60b75bd2/12859_2024_5763_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e2bc/11070082/b37667f78522/12859_2024_5763_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e2bc/11070082/b0b0720c1507/12859_2024_5763_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e2bc/11070082/e556d8b6a5a2/12859_2024_5763_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e2bc/11070082/289ab9534113/12859_2024_5763_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e2bc/11070082/834f1a8489ac/12859_2024_5763_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e2bc/11070082/a4b8545a3a17/12859_2024_5763_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e2bc/11070082/f785ce362c93/12859_2024_5763_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e2bc/11070082/b57a60b75bd2/12859_2024_5763_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e2bc/11070082/b37667f78522/12859_2024_5763_Fig8_HTML.jpg

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Bioinformatics. 2023 Aug 1;39(8). doi: 10.1093/bioinformatics/btad451.
2
GKLOMLI: a link prediction model for inferring miRNA-lncRNA interactions by using Gaussian kernel-based method on network profile and linear optimization algorithm.GKLOMLI：一种基于高斯核函数的网络特征和线性优化算法的 miRNA-lncRNA 相互作用预测模型。
BMC Bioinformatics. 2023 May 8;24(1):188. doi: 10.1186/s12859-023-05309-w.
3
Hepatitis B Virus DNA Integration Drives Carcinogenesis and Provides a New Biomarker for HBV-related HCC.
乙型肝炎病毒 DNA 整合驱动肝癌发生，并为 HBV 相关 HCC 提供了新的生物标志物。
Cell Mol Gastroenterol Hepatol. 2023;15(4):921-929. doi: 10.1016/j.jcmgh.2023.01.001. Epub 2023 Jan 20.
4
Comparative assessment of genes driving cancer and somatic evolution in non-cancer tissues: an update of the Network of Cancer Genes (NCG) resource.比较非癌组织中驱动癌症和体细胞进化的基因：癌症基因网络 (NCG) 资源的更新。
Genome Biol. 2022 Jan 26;23(1):35. doi: 10.1186/s13059-022-02607-z.
5
Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries.《全球癌症统计数据 2020：全球 185 个国家和地区 36 种癌症的发病率和死亡率估计》。
CA Cancer J Clin. 2021 May;71(3):209-249. doi: 10.3322/caac.21660. Epub 2021 Feb 4.
6
SurVirus: a repeat-aware virus integration caller.SurVirus：一种具有重复识别功能的病毒整合调用器。
Nucleic Acids Res. 2021 Apr 6;49(6):e33. doi: 10.1093/nar/gkaa1237.
7
Accurate, scalable cohort variant calls using DeepVariant and GLnexus.使用DeepVariant和GLnexus进行准确、可扩展的队列变异检测。
Bioinformatics. 2021 Apr 5;36(24):5582-5589. doi: 10.1093/bioinformatics/btaa1081.
8
Hepatitis B Virus: Advances in Prevention, Diagnosis, and Therapy.乙型肝炎病毒：预防、诊断和治疗的新进展。
Clin Microbiol Rev. 2020 Feb 26;33(2). doi: 10.1128/CMR.00046-19. Print 2020 Mar 18.
9
Milestones in the pathogenesis and management of primary liver cancer.原发性肝癌发病机制与治疗的里程碑
J Hepatol. 2020 Feb;72(2):209-214. doi: 10.1016/j.jhep.2019.11.006.
10
Environmental risk factors for liver cancer and nonalcoholic fatty liver disease.肝癌和非酒精性脂肪性肝病的环境危险因素。
Curr Epidemiol Rep. 2019 Mar;6(1):50-66. doi: 10.1007/s40471-019-0183-2. Epub 2019 Feb 6.