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Xie K, Ge X, Alvi HAK, Liu K, Song J, Yu Q. OTSUCNV: an adaptive segmentation and OTSU-based anomaly classification method for CNV detection using NGS data. BMC Genomics 2024; 25:126. [PMID: 38291375 PMCID: PMC10826217 DOI: 10.1186/s12864-024-10018-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 01/15/2024] [Indexed: 02/01/2024] Open
Abstract
Copy-number variations (CNVs), which refer to deletions and duplications of chromosomal segments, represent a significant source of variation among individuals, contributing to human evolution and being implicated in various diseases ranging from mental illness and developmental disorders to cancer. Despite the development of several methods for detecting copy number variations based on next-generation sequencing (NGS) data, achieving robust detection performance for CNVs with arbitrary coverage and amplitude remains challenging due to the inherent complexity of sequencing samples. In this paper, we propose an alternative method called OTSUCNV for CNV detection on whole genome sequencing (WGS) data. This method utilizes a newly designed adaptive sequence segmentation algorithm and an OTSU-based CNV prediction algorithm, which does not rely on any distribution assumptions or involve complex outlier factor calculations. As a result, the effective detection of CNVs is achieved with lower computational complexity. The experimental results indicate that the proposed method demonstrates outstanding performance, and hence it may be used as an effective tool for CNV detection.
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Affiliation(s)
- Kun Xie
- School of Computer Science and Technology, Xidian University, Xi'an, 710071, China
| | - Xiaojun Ge
- School of Computer Science and Technology, Xidian University, Xi'an, 710071, China
| | - Haque A K Alvi
- School of Computer Science and Technology, Xidian University, Xi'an, 710071, China
| | - Kang Liu
- School of Computer Science and Technology, Xidian University, Xi'an, 710071, China
| | - Jianfeng Song
- School of Computer Science and Technology, Xidian University, Xi'an, 710071, China.
| | - Qiang Yu
- School of Computer Science and Technology, Xidian University, Xi'an, 710071, China.
- Hangzhou Institute of Technology, Xidian University, Hangzhou, 311200, China.
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2
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Zhang Y, Liu W, Duan J. On the core segmentation algorithms of copy number variation detection tools. Brief Bioinform 2024; 25:bbae022. [PMID: 38340093 PMCID: PMC10858679 DOI: 10.1093/bib/bbae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/26/2023] [Indexed: 02/12/2024] Open
Abstract
Shotgun sequencing is a high-throughput method used to detect copy number variants (CNVs). Although there are numerous CNV detection tools based on shotgun sequencing, their quality varies significantly, leading to performance discrepancies. Therefore, we conducted a comprehensive analysis of next-generation sequencing-based CNV detection tools over the past decade. Our findings revealed that the majority of mainstream tools employ similar detection rationale: calculates the so-called read depth signal from aligned sequencing reads and then segments the signal by utilizing either circular binary segmentation (CBS) or hidden Markov model (HMM). Hence, we compared the performance of those two core segmentation algorithms in CNV detection, considering varying sequencing depths, segment lengths and complex types of CNVs. To ensure a fair comparison, we designed a parametrical model using mainstream statistical distributions, which allows for pre-excluding bias correction such as guanine-cytosine (GC) content during the preprocessing step. The results indicate the following key points: (1) Under ideal conditions, CBS demonstrates high precision, while HMM exhibits a high recall rate. (2) For practical conditions, HMM is advantageous at lower sequencing depths, while CBS is more competitive in detecting small variant segments compared to HMM. (3) In case involving complex CNVs resembling real sequencing, HMM demonstrates more robustness compared with CBS. (4) When facing large-scale sequencing data, HMM costs less time compared with the CBS, while their memory usage is approximately equal. This can provide an important guidance and reference for researchers to develop new tools for CNV detection.
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Affiliation(s)
- Yibo Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education and Department of Biomedical Engineering, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Wenyu Liu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education and Department of Biomedical Engineering, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Junbo Duan
- Key Laboratory of Biomedical Information Engineering of Ministry of Education and Department of Biomedical Engineering, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
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3
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Cabello-Aguilar S, Vendrell JA, Solassol J. A Bioinformatics Toolkit for Next-Generation Sequencing in Clinical Oncology. Curr Issues Mol Biol 2023; 45:9737-9752. [PMID: 38132454 PMCID: PMC10741970 DOI: 10.3390/cimb45120608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 11/28/2023] [Accepted: 12/02/2023] [Indexed: 12/23/2023] Open
Abstract
Next-generation sequencing (NGS) has taken on major importance in clinical oncology practice. With the advent of targeted therapies capable of effectively targeting specific genomic alterations in cancer patients, the development of bioinformatics processes has become crucial. Thus, bioinformatics pipelines play an essential role not only in the detection and in identification of molecular alterations obtained from NGS data but also in the analysis and interpretation of variants, making it possible to transform raw sequencing data into meaningful and clinically useful information. In this review, we aim to examine the multiple steps of a bioinformatics pipeline as used in current clinical practice, and we also provide an updated list of the necessary bioinformatics tools. This resource is intended to assist researchers and clinicians in their genetic data analyses, improving the precision and efficiency of these processes in clinical research and patient care.
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Affiliation(s)
- Simon Cabello-Aguilar
- Montpellier BioInformatics for Clinical Diagnosis (MOBIDIC), Molecular Medicine and Genomics Platform (PMMG), CHU Montpellier, 34295 Montpellier, France
- Laboratoire de Biologie des Tumeurs Solides, Département de Pathologie et Oncobiologie, CHU Montpellier, Université de Montpellier, 34295 Montpellier, France; (J.A.V.); (J.S.)
| | - Julie A. Vendrell
- Laboratoire de Biologie des Tumeurs Solides, Département de Pathologie et Oncobiologie, CHU Montpellier, Université de Montpellier, 34295 Montpellier, France; (J.A.V.); (J.S.)
| | - Jérôme Solassol
- Laboratoire de Biologie des Tumeurs Solides, Département de Pathologie et Oncobiologie, CHU Montpellier, Université de Montpellier, 34295 Montpellier, France; (J.A.V.); (J.S.)
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4
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Li C, Fan S, Zhao H, Liu X. CNV-FB: A Feature bagging strategy-based approach to detect copy number variants from NGS data. J Bioinform Comput Biol 2023; 21:2350026. [PMID: 38212874 DOI: 10.1142/s0219720023500269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Copy number variation (CNV), as a type of genomic structural variation, accounts for a large proportion of structural variation and is related to the pathogenesis and susceptibility to some human diseases, playing an important role in the development and change of human diseases. The development of next-generation sequencing technology (NGS) provides strong support for the design of CNV detection algorithms. Although a large number of methods have been developed to detect CNVs using NGS data, it is still considered a difficult problem to detect CNVs with low purity and coverage. In this paper, a new calculation method CNV-FB is proposed to detect CNVs from NGS data. The core idea of CNV-FB is to randomly sample the read depth values of the genome fragment, and then each sample is individually detected for outliers, and finally combined into a final outlier score. The CNV-FB method was applied to simulation data and real data experiments and compared with the other five methods of the same type. The results show that the CNV-FB method has a better detection effect than other methods. Therefore, the CNV-FB method may be an effective algorithm for detecting genomic mutations.
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Affiliation(s)
- Chengyou Li
- School of Computer Science, Liaocheng University, Liaocheng 252000, P. R. China
| | - Shiqiang Fan
- School of Computer Science, Liaocheng University, Liaocheng 252000, P. R. China
| | - Haiyong Zhao
- School of Computer Science, Liaocheng University, Liaocheng 252000, P. R. China
| | - Xiaotong Liu
- School of Agronomy and Agricultural Engineering, Liaocheng University, Liaocheng 252000, P. R. China
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5
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Adaptive Savitzky–Golay Filters for Analysis of Copy Number Variation Peaks from Whole-Exome Sequencing Data. INFORMATION 2023. [DOI: 10.3390/info14020128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
Copy number variation (CNV) is a form of structural variation in the human genome that provides medical insight into complex human diseases; while whole-genome sequencing is becoming more affordable, whole-exome sequencing (WES) remains an important tool in clinical diagnostics. Because of its discontinuous nature and unique characteristics of sparse target-enrichment-based WES data, the analysis and detection of CNV peaks remain difficult tasks. The Savitzky–Golay (SG) smoothing is well known as a fast and efficient smoothing method. However, no study has documented the use of this technique for CNV peak detection. It is well known that the effectiveness of the classical SG filter depends on the proper selection of the window length and polynomial degree, which should correspond with the scale of the peak because, in the case of peaks with a high rate of change, the effectiveness of the filter could be restricted. Based on the Savitzky–Golay algorithm, this paper introduces a novel adaptive method to smooth irregular peak distributions. The proposed method ensures high-precision noise reduction by dynamically modifying the results of the prior smoothing to automatically adjust parameters. Our method offers an additional feature extraction technique based on density and Euclidean distance. In comparison to classical Savitzky–Golay filtering and other peer filtering methods, the performance evaluation demonstrates that adaptive Savitzky–Golay filtering performs better. According to experimental results, our method effectively detects CNV peaks across all genomic segments for both short and long tags, with minimal peak height fidelity values (i.e., low estimation bias). As a result, we clearly demonstrate how well the adaptive Savitzky–Golay filtering method works and how its use in the detection of CNV peaks can complement the existing techniques used in CNV peak analysis.
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Liu G, Yang H, Yuan X. A shortest path-based approach for copy number variation detection from next-generation sequencing data. Front Genet 2023; 13:1084974. [PMID: 36733945 PMCID: PMC9887524 DOI: 10.3389/fgene.2022.1084974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/27/2022] [Indexed: 01/18/2023] Open
Abstract
Copy number variation (CNV) is one of the main structural variations in the human genome and accounts for a considerable proportion of variations. As CNVs can directly or indirectly cause cancer, mental illness, and genetic disease in humans, their effective detection in humans is of great interest in the fields of oncogene discovery, clinical decision-making, bioinformatics, and drug discovery. The advent of next-generation sequencing data makes CNV detection possible, and a large number of CNV detection tools are based on next-generation sequencing data. Due to the complexity (e.g., bias, noise, alignment errors) of next-generation sequencing data and CNV structures, the accuracy of existing methods in detecting CNVs remains low. In this work, we design a new CNV detection approach, called shortest path-based Copy number variation (SPCNV), to improve the detection accuracy of CNVs. SPCNV calculates the k nearest neighbors of each read depth and defines the shortest path, shortest path relation, and shortest path cost sets based on which further calculates the mean shortest path cost of each read depth and its k nearest neighbors. We utilize the ratio between the mean shortest path cost for each read depth and the mean of the mean shortest path cost of its k nearest neighbors to construct a relative shortest path score formula that is able to determine a score for each read depth. Based on the score profile, a boxplot is then applied to predict CNVs. The performance of the proposed method is verified by simulation data experiments and compared against several popular methods of the same type. Experimental results show that the proposed method achieves the best balance between recall and precision in each set of simulated samples. To further verify the performance of the proposed method in real application scenarios, we then select real sample data from the 1,000 Genomes Project to conduct experiments. The proposed method achieves the best F1-scores in almost all samples. Therefore, the proposed method can be used as a more reliable tool for the routine detection of CNVs.
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Affiliation(s)
- Guojun Liu
- School of Statistics, Xi’an University of Finance and Economics, Xi’an, China,*Correspondence: Guojun Liu, ; Xiguo Yuan,
| | - Hongzhi Yang
- Medical Imaging Center, Xidian Group Hospital, Xi’an, China
| | - Xiguo Yuan
- Hangzhou Institute of Technology, Xidian University, Hangzhou, China,*Correspondence: Guojun Liu, ; Xiguo Yuan,
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7
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Zhang T, Dong J, Jiang H, Zhao Z, Zhou M, Yuan T. CNV-PCC: An efficient method for detecting copy number variations from next-generation sequencing data. Front Bioeng Biotechnol 2022; 10:1000638. [DOI: 10.3389/fbioe.2022.1000638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 11/18/2022] [Indexed: 12/03/2022] Open
Abstract
Copy number variations (CNVs) significantly influence the diversity of the human genome and the occurrence of many complex diseases. The next-generation sequencing (NGS) technology provides rich data for detecting CNVs, and the read depth (RD)-based approach is widely used. However, low CN (copy number of 3–4) duplication events are challenging to identify with existing methods, especially when the size of CNVs is small. In addition, the RD-based approach can only obtain rough breakpoints. We propose a new method, CNV-PCC (detection of CNVs based on Principal Component Classifier), to identify CNVs in whole genome sequencing data. CNV-PPC first uses the split read signal to search for potential breakpoints. A two-stage segmentation strategy is then implemented to enhance the identification capabilities of low CN duplications and small CNVs. Next, the outlier scores are calculated for each segment by PCC (Principal Component Classifier). Finally, the OTSU algorithm calculates the threshold to determine the CNVs regions. The analysis of simulated data results indicates that CNV-PCC outperforms the other methods for sensitivity and F1-score and improves breakpoint accuracy. Furthermore, CNV-PCC shows high consistency on real sequencing samples with other methods. This study demonstrates that CNV-PCC is an effective method for detecting CNVs, even for low CN duplications and small CNVs.
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WAVECNV: A New Approach for Detecting Copy Number Variation by Wavelet Clustering. MATHEMATICS 2022. [DOI: 10.3390/math10122151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Copy number variation (CNV) detection based on second-generation sequencing technology is the basis of much gene research, but the read depth is affected by mapping errors, repeated reads, and GC bias. The existing methods have low sensitivity to variation regions with a short length and small variation range. Therefore, it is necessary to improve the sensitivity of algorithms to short-variation fragments. This study proposes a new CNV-detection method named WAVECNV to solve this issue. The algorithm uses wavelet clustering to process the read depth and determine the normal cluster and abnormal cluster according to the size of the cluster. Then, according to the distance between genome bins and normal clusters, the outlier of each genome bin is evaluated. Finally, a statistical model is established, and the p-value test is used for calling CNVs. Through this method, the information of the short variation region is retained. WAVECNV was tested and compared with peer methods in terms of simulated data and real cancer-sequencing data. The results show that the sensitivity of WAVECNV is better than the existing methods. It also has high precision in data with low purity and coverage. In real data experiments, WAVECNV can detect more cancer genes than existing methods. Therefore, this method can be regarded as a conventional method in the field of genomic mutation analysis of cancer samples.
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9
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Wang X, Junqing L, Huang T. CNVABNN: An AdaBoost algorithm and neural networks-based detection of copy number variations from NGS data. Comput Biol Chem 2022; 99:107720. [DOI: 10.1016/j.compbiolchem.2022.107720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 11/03/2022]
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svBreak: A New Approach for the Detection of Structural Variant Breakpoints Based on Convolutional Neural Network. BIOMED RESEARCH INTERNATIONAL 2022; 2022:7196040. [PMID: 35345526 PMCID: PMC8957449 DOI: 10.1155/2022/7196040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 01/04/2022] [Accepted: 01/27/2022] [Indexed: 12/01/2022]
Abstract
Structural variation (SV) is an important type of genome variation and confers susceptibility to human cancer diseases. Systematic analysis of SVs has become a crucial step for the exploration of mechanisms and precision diagnosis of cancers. The central point is how to accurately detect SV breakpoints by using next-generation sequencing (NGS) data. Due to the cooccurrence of multiple types of SVs in the human genome and the intrinsic complexity of SVs, the discrimination of SV breakpoint types is a challenging task. In this paper, we propose a convolutional neural network- (CNN-) based approach, called svBreak, for the detection and discrimination of common types of SV breakpoints. The principle of svBreak is that it extracts a set of SV-related features for each genome site from the sequencing reads aligned to the reference genome and establishes a data matrix where each row represents one site and each column represents one feature and then adopts a CNN model to analyze such data matrix for the prediction of SV breakpoints. The performance of the proposed approach is tested via simulation studies and application to a real sequencing sample. The experimental results demonstrate the merits of the proposed approach when compared with existing methods. Thus, svBreak can be expected to be a supplementary approach in the field of SV analysis in human tumor genomes.
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Agaoglu NB, Unal B, Akgun Dogan O, Zolfagharian P, Shairfli P, Karakurt A, Can Senay B, Kizilboga T, Yildiz J, Dinler Doganay G, Doganay L. Determining the Accuracy of Next Generation Sequencing Based Copy Number Variation Analysis in Hereditary Breast and Ovarian Cancer. Expert Rev Mol Diagn 2022; 22:239-246. [PMID: 35240897 DOI: 10.1080/14737159.2022.2048373] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Copy number variations (CNVs) are commonly associated with malignancies, including hereditary breast and ovarian cancers. Next generation sequencing (NGS) provides solutions for CNV detection in a single run. This study aimed to compare the accuracy of CNV detection by NGS analysing tool against Multiplex Ligation Dependent Probe Amplification (MLPA). RESEARCH DESIGN AND METHODS In total, 1276 cases were studied by targeted NGS panels and 691 cases (61 calls in 58 NGS-CNV positive and 633 NGS-CNV negative cases) were validated by MLPA. RESULTS Twenty-eight (46%) NGS-CNV positive calls were consistent, whereas 33 (54%) calls showed discordance with MLPA. Two cases were detected as SNV by the NGS and CNV by the MLPA analysis. In total, 2% of the cases showed an MLPA confirmed CNV region in BRCA1/2. The results of this study showed that despite the high false positive call rate of the NGS-CNV algorithm, there were no false negative calls. The cases that were determined to be negative by the NGS and positive by the MLPA were actually carrying SNVs that were located on the MLPA probe binding sites. CONCLUSION The diagnostic performance of NGS-CNV analysis is promising; however, the need for confirmation by different methods remains.
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Affiliation(s)
- Nihat Bugra Agaoglu
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey.,Department of Medical Genetics, Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Busra Unal
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Ozlem Akgun Dogan
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey.,Department of Pediatric Genetics, Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Payam Zolfagharian
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Pari Shairfli
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Aylin Karakurt
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Burak Can Senay
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Tugba Kizilboga
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey.,Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey
| | - Jale Yildiz
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey.,Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey
| | - Gizem Dinler Doganay
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey
| | - Levent Doganay
- Genomic Laboratory (GLAB), Umraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
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Obtaining spatially resolved tumor purity maps using deep multiple instance learning in a pan-cancer study. PATTERNS (NEW YORK, N.Y.) 2022; 3:100399. [PMID: 35199060 PMCID: PMC8848022 DOI: 10.1016/j.patter.2021.100399] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/07/2021] [Accepted: 11/03/2021] [Indexed: 02/07/2023]
Abstract
Tumor purity is the percentage of cancer cells within a tissue section. Pathologists estimate tumor purity to select samples for genomic analysis by manually reading hematoxylin-eosin (H&E)-stained slides, which is tedious, time consuming, and prone to inter-observer variability. Besides, pathologists' estimates do not correlate well with genomic tumor purity values, which are inferred from genomic data and accepted as accurate for downstream analysis. We developed a deep multiple instance learning model predicting tumor purity from H&E-stained digital histopathology slides. Our model successfully predicted tumor purity in eight The Cancer Genome Atlas (TCGA) cohorts and a local Singapore cohort. The predictions were highly consistent with genomic tumor purity values. Thus, our model can be utilized to select samples for genomic analysis, which will help reduce pathologists' workload and decrease inter-observer variability. Furthermore, our model provided tumor purity maps showing the spatial variation within sections. They can help better understand the tumor microenvironment. MIL model successfully predicts a sample's tumor purity from histopathology slides MIL model learns to spatially resolve tumor purity from sample-level labels Tumor purity varies spatially within a sample Pathologists’ region selection is vital for correct percentage tumor nuclei estimation
Given some big data and coarse-level labels, extracting fine-level information is a demanding yet rewarding challenge in data science. This study develops a machine learning model utilizing big data and exploiting coarse-level labels to reveal fine-level details within the data. Although it can be applied to different data science tasks with enormous data and coarse labels, we applied it to a computational histopathology task with gigapixel histopathology slides and sample-level labels. Specifically, the model revealed spatial resolution of tumor purity within histopathology slides using only sample-level genomic tumor purity values during training. This can also be extended to other omics features, providing precious information about cancer biology and promising personalized, precision medicine. Such studies are of great clinical importance in discovering imaging biomarkers and better understanding the tumor microenvironment.
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Lee WP, Zhu Q, Yang X, Liu S, Cerveira E, Ryan M, Mil-Homens A, Bellfy L, Ye K, Lee C, Zhang C. JAX-CNV: A Whole-genome Sequencing-based Algorithm for Copy Number Detection at Clinical Grade Level. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:1197-1206. [PMID: 35085778 DOI: 10.1016/j.gpb.2021.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 04/30/2021] [Accepted: 09/06/2021] [Indexed: 10/19/2022]
Abstract
We aimed to develop a whole-genome sequencing (WGS)-based copy number variant (CNV) calling algorithm with the potential of replacing chromosomal microarray assay (CMA) for clinical diagnosis. JAX-CNV is thus developed for CNV detection from WGS data. The performance of this CNV calling algorithm was evaluated in a blinded manner on 31 samples and compared to the 112 CNVs reported by clinically validated CMAs for these 31 samples. The result showed that JAX-CNV recalled 100% of these CNVs. Besides, JAX-CNV identified an average of 30 CNVs per individual that was an approximately seven-fold increase compared to calls of clinically validated CMAs. Experimental validation of 24 randomly selected CNVs showed one false positive, i.e., a false discovery rate (FDR) of 4.17%. A robustness test on lower-coverage data revealed a 100% sensitivity for CNVs larger than 300 kb (the current threshold for College of American Pathologists) down to 10× coverage. For CNVs larger than 50 kb, sensitivities were 100% for coverages deeper than 20×, 97% for 15×, and 95% for 10×. We developed a WGS-based CNV pipeline, including this newly developed CNV caller JAX-CNV, and found it capable of detecting CMA-reported CNVs at a sensitivity of 100% with about a FDR of 4%. We propose that JAX-CNV could be further examined in a multi-institutional study to justify the transition of first-tier genetic testing from CMAs to WGS. JAX-CNV is available at https://github.com/TheJacksonLaboratory/JAX-CNV.
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Affiliation(s)
- Wan-Ping Lee
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China; The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; School of Cyber Science and Engineering, Xi'an Jiaotong University, Xi'an 710049, China; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Qihui Zhu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Xiaofei Yang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; School of Computer Science and Technology, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China; MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Silvia Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Eliza Cerveira
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Mallory Ryan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Adam Mil-Homens
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Lauren Bellfy
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Kai Ye
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China; MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Charles Lee
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China; The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Life Sciences, Ewha Womans University, Seoul 03760, South Korea
| | - Chengsheng Zhang
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China; The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
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14
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Xie K, Liu K, Alvi HAK, Chen Y, Wang S, Yuan X. KNNCNV: A K-Nearest Neighbor Based Method for Detection of Copy Number Variations Using NGS Data. Front Cell Dev Biol 2022; 9:796249. [PMID: 35004691 PMCID: PMC8728060 DOI: 10.3389/fcell.2021.796249] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 11/23/2021] [Indexed: 11/19/2022] Open
Abstract
Copy number variation (CNV) is a well-known type of genomic mutation that is associated with the development of human cancer diseases. Detection of CNVs from the human genome is a crucial step for the pipeline of starting from mutation analysis to cancer disease diagnosis and treatment. Next-generation sequencing (NGS) data provides an unprecedented opportunity for CNVs detection at the base-level resolution, and currently, many methods have been developed for CNVs detection using NGS data. However, due to the intrinsic complexity of CNVs structures and NGS data itself, accurate detection of CNVs still faces many challenges. In this paper, we present an alternative method, called KNNCNV (K-Nearest Neighbor based CNV detection), for the detection of CNVs using NGS data. Compared to current methods, KNNCNV has several distinctive features: 1) it assigns an outlier score to each genome segment based solely on its first k nearest-neighbor distances, which is not only easy to extend to other data types but also improves the power of discovering CNVs, especially the local CNVs that are likely to be masked by their surrounding regions; 2) it employs the variational Bayesian Gaussian mixture model (VBGMM) to transform these scores into a series of binary labels without a user-defined threshold. To evaluate the performance of KNNCNV, we conduct both simulation and real sequencing data experiments and make comparisons with peer methods. The experimental results show that KNNCNV could derive better performance than others in terms of F1-score.
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Affiliation(s)
- Kun Xie
- School of Computer Science and Technology, Xidian University, Xi'an, China.,Hangzhou Institute of Technology, Xidian University, Hangzhou, China
| | - Kang Liu
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Haque A K Alvi
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Yuehui Chen
- Shandong Provincial Key Laboratory of Network Based Intelligent Computing, University of Jinan, Jinan, China
| | - Shuzhen Wang
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Xiguo Yuan
- School of Computer Science and Technology, Xidian University, Xi'an, China.,Hangzhou Institute of Technology, Xidian University, Hangzhou, China
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15
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Liu Y, Xie G, Li A, He Z, Hei X. Prediction of Cancer-Related piRNAs Based on Network-Based Stratification Analysis. INT J PATTERN RECOGN 2021. [DOI: 10.1142/s0218001422590029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
PIWI-interacting RNA (PiRNA) was discovered in 2006 and is expected to become a new biomarker for diagnosis and prognosis of various diseases. The purpose of this study is to explore functions of piRNAs and identify cancer subtypes on the basis of the pattern of transcriptome and somatic mutation data. A total of 285 510 SNPs in piRNAs and genes, which might affect piRNA biogenesis or piRNA targets binding were identified. Significant co-expression networks of piRNAs were then constructed separately for 12 major types of cancer. Finally, mutational matrices were mapped to piRNA network, propagated, and clustered for identification of cancer-related piRNAs and cancer subtypes. Findings showed that subtypes of three types of cancer (COAD, STAD and UCEC), which are significantly associated with survival were identified. Analysis of differentially expressed piRNAs in UCEC subtypes showed that piRNA function is closely related to cancer hallmarks “Enabling Replicative Immortality” and contributes to initiation of cancer.
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Affiliation(s)
- Yajun Liu
- Shaanxi Key Laboratory for Network Computing and Security Technology, School of Computer Science and Engineering, Xi’an University of Technology, Xi’an 710048, Shaanxi, P. R. China
| | - Guo Xie
- Shaanxi Key Laboratory of Complex System Control and Intelligent Information Processing, School of Information Technology and Equipment Engineering, Xi’an University of Technology, P. R. China
| | - Aimin Li
- Shaanxi Key Laboratory for Network Computing and Security Technology, School of Computer Science and Engineering, Xi’an University of Technology, Xi’an 710048, Shaanxi, P. R. China
| | - Zongzhen He
- Xi’an University of Finance and Economics, Xi’an 710100, Shaanxi, P. R. China
| | - Xinhong Hei
- Shaanxi Key Laboratory for Network Computing and Security Technology, School of Computer Science and Engineering, Xi’an University of Technology, Xi’an 710048, Shaanxi, P. R. China
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16
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Yuan X, Ma C, Zhao H, Yang L, Wang S, Xi J. STIC: Predicting Single Nucleotide Variants and Tumor Purity in Cancer Genome. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:2692-2701. [PMID: 32086221 DOI: 10.1109/tcbb.2020.2975181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Single nucleotide variant (SNV) plays an important role in cellular proliferation and tumorigenesis in various types of human cancer. Next-generation sequencing (NGS) has provided high-throughput data at an unprecedented resolution to predict SNVs. Currently, there exist many computational methods for either germline or somatic SNV discovery from NGS data, but very few of them are versatile enough to adapt to any situations. In the absence of matched normal samples, the prediction of somatic SNVs from single-tumor samples becomes considerably challenging, especially when the tumor purity is unknown. Here, we propose a new approach, STIC, to predict somatic SNVs and estimate tumor purity from NGS data without matched normal samples. The main features of STIC include: (1) extracting a set of SNV-relevant features on each site and training the BP neural network algorithm on the features to predict SNVs; (2) creating an iterative process to distinguish somatic SNVs from germline ones by disturbing allele frequency; and (3) establishing a reasonable relationship between tumor purity and allele frequencies of somatic SNVs to accurately estimate the purity. We quantitatively evaluate the performance of STIC on both simulation and real sequencing datasets, the results of which indicate that STIC outperforms competing methods.
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17
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Huang T, Li J, Jia B, Sang H. CNV-MEANN: A Neural Network and Mind Evolutionary Algorithm-Based Detection of Copy Number Variations From Next-Generation Sequencing Data. Front Genet 2021; 12:700874. [PMID: 34484298 PMCID: PMC8415314 DOI: 10.3389/fgene.2021.700874] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/19/2021] [Indexed: 11/20/2022] Open
Abstract
Copy number variation (CNV), is defined as repetitions or deletions of genomic segments of 1 Kb to 5 Mb, and is a major trigger for human disease. The high-throughput and low-cost characteristics of next-generation sequencing technology provide the possibility of the detection of CNVs in the whole genome, and also greatly improve the clinical practicability of next-generation sequencing (NGS) testing. However, current methods for the detection of CNVs are easily affected by sequencing and mapping errors, and uneven distribution of reads. In this paper, we propose an improved approach, CNV-MEANN, for the detection of CNVs, involving changing the structure of the neural network used in the MFCNV method. This method has three differences relative to the MFCNV method: (1) it utilizes a new feature, mapping quality, to replace two features in MFCNV, (2) it considers the influence of the loss categories of CNV on disease prediction, and refines the output structure, and (3) it uses a mind evolutionary algorithm to optimize the backpropagation (neural network) neural network model, and calculates individual scores for each genome bin to predict CNVs. Using both simulated and real datasets, we tested the performance of CNV-MEANN and compared its performance with those of seven widely used CNV detection methods. Experimental results demonstrated that the CNV-MEANN approach outperformed other methods with respect to sensitivity, precision, and F1-score. The proposed method was able to detect many CNVs that other approaches could not, and it reduced the boundary bias. CNV-MEANN is expected to be an effective method for the analysis of changes in CNVs in the genome.
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Affiliation(s)
- Tihao Huang
- School of Computer Science and Technology, Liaocheng University, Liaocheng, China
| | - Junqing Li
- School of Computer Science and Technology, Liaocheng University, Liaocheng, China
| | - Baoxian Jia
- School of Computer Science and Technology, Liaocheng University, Liaocheng, China
| | - Hongyan Sang
- School of Computer Science and Technology, Liaocheng University, Liaocheng, China
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18
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Filer DL, Kuo F, Brandt AT, Tilley CR, Mieczkowski PA, Berg JS, Robasky K, Li Y, Bizon C, Tilson JL, Powell BC, Bost DM, Jeffries CD, Wilhelmsen KC. Pre-capture multiplexing provides additional power to detect copy number variation in exome sequencing. BMC Bioinformatics 2021; 22:374. [PMID: 34284719 PMCID: PMC8293537 DOI: 10.1186/s12859-021-04246-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/18/2021] [Indexed: 11/10/2022] Open
Abstract
Background As exome sequencing (ES) integrates into clinical practice, we should make every effort to utilize all information generated. Copy-number variation can lead to Mendelian disorders, but small copy-number variants (CNVs) often get overlooked or obscured by under-powered data collection. Many groups have developed methodology for detecting CNVs from ES, but existing methods often perform poorly for small CNVs and rely on large numbers of samples not always available to clinical laboratories. Furthermore, methods often rely on Bayesian approaches requiring user-defined priors in the setting of insufficient prior knowledge. This report first demonstrates the benefit of multiplexed exome capture (pooling samples prior to capture), then presents a novel detection algorithm, mcCNV (“multiplexed capture CNV”), built around multiplexed capture. Results We demonstrate: (1) multiplexed capture reduces inter-sample variance; (2) our mcCNV method, a novel depth-based algorithm for detecting CNVs from multiplexed capture ES data, improves the detection of small CNVs. We contrast our novel approach, agnostic to prior information, with the the commonly-used ExomeDepth. In a simulation study mcCNV demonstrated a favorable false discovery rate (FDR). When compared to calls made from matched genome sequencing, we find the mcCNV algorithm performs comparably to ExomeDepth. Conclusion Implementing multiplexed capture increases power to detect single-exon CNVs. The novel mcCNV algorithm may provide a more favorable FDR than ExomeDepth. The greatest benefits of our approach derive from (1) not requiring a database of reference samples and (2) not requiring prior information about the prevalance or size of variants. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04246-w.
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Affiliation(s)
- Dayne L Filer
- Department of Genetics, UNC School of Medicine, Chapel Hill, USA. .,Renaissance Computing Institute, Chapel Hill, USA.
| | - Fengshen Kuo
- Renaissance Computing Institute, Chapel Hill, USA
| | - Alicia T Brandt
- Department of Genetics, UNC School of Medicine, Chapel Hill, USA
| | | | | | - Jonathan S Berg
- Department of Genetics, UNC School of Medicine, Chapel Hill, USA
| | - Kimberly Robasky
- Department of Genetics, UNC School of Medicine, Chapel Hill, USA.,Renaissance Computing Institute, Chapel Hill, USA.,UNC School of Information and Library Science, Chapel Hill, USA
| | - Yun Li
- Department of Genetics, UNC School of Medicine, Chapel Hill, USA.,Department of Biostatistics, UNC Gillings School of Global Public Health, Chapel Hill, USA
| | - Chris Bizon
- Renaissance Computing Institute, Chapel Hill, USA
| | | | - Bradford C Powell
- Department of Genetics, UNC School of Medicine, Chapel Hill, USA.,Renaissance Computing Institute, Chapel Hill, USA
| | - Darius M Bost
- Department of Genetics, UNC School of Medicine, Chapel Hill, USA.,Renaissance Computing Institute, Chapel Hill, USA
| | | | - Kirk C Wilhelmsen
- Department of Genetics, UNC School of Medicine, Chapel Hill, USA.,Renaissance Computing Institute, Chapel Hill, USA.,Department of Neurology, UNC School of Medicine, Chapel Hill, USA
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19
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Zhao HY, Li Q, Tian Y, Chen YH, Alvi HAK, Yuan XG. CIRCNV: Detection of CNVs Based on a Circular Profile of Read Depth from Sequencing Data. BIOLOGY 2021; 10:biology10070584. [PMID: 34202028 PMCID: PMC8301091 DOI: 10.3390/biology10070584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/10/2021] [Accepted: 06/21/2021] [Indexed: 12/29/2022]
Abstract
Simple Summary In this study, we propose a copy number variation (CNV) detection method called CIRCNV, which is based on a circular profile of the read depth from sequencing data. The proposed method is an extended version of our previously developed method CNV-LOF. The main difference of CIRCNV from CNV-LOF lies in its two new features: (1) it transfers the read depth profile from a line shape to a circular shape via a polar coordinate transformation to generate a meaningful two-dimensional dataset for CNV analysis and promote fairness between the ends and middle part of the genome, and (2) it performs two rounds of CNV declaration via estimating tumor purity and recovering the truth circular RD profile. We test and evaluate the performance of CIRCNV via conducting simulation studies and real sequencing tumor sample applications. The experimental results show that CIRCNV outperforms peer methods with respect to sensitivity, precision, and the F1-score. The experiments prove that the proposed method is a reliable and effective tool in the field of variation analysis of tumor genomes. Abstract Copy number variation (CNV) is a common type of structural variation in the human genome. Accurate detection of CNVs from tumor genomes can provide crucial information for the study of tumor genesis and cancer precision diagnosis. However, the contamination of normal genomes in tumor genomes and the crude profiles of the read depth make such a task difficult. In this paper, we propose an alternative approach, called CIRCNV, for the detection of CNVs from sequencing data. CIRCNV is an extension of our previously developed method CNV-LOF, which uses local outlier factors to predict CNVs. Comparatively, CIRCNV can be performed on individual tumor samples and has the following two new features: (1) it transfers the read depth profile from a line shape to a circular shape via a polar coordinate transformation, in order to improve the efficiency of the read depth (RD) profile for the detection of CNVs; and (2) it performs a second round of CNV declaration based on the truth circular RD profile, which is recovered by estimating tumor purity. We test and validate the performance of CIRCNV based on simulation and real sequencing data and perform comparisons with several peer methods. The results demonstrate that CIRCNV can obtain superior performance in terms of sensitivity and precision. We expect that our proposed method will be a supplement to existing methods and become a routine tool in the field of variation analysis of tumor genomes.
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Affiliation(s)
- Hai-Yong Zhao
- School of Computer Science and Technology, Liaocheng University, Liaocheng 252000, China;
| | - Qi Li
- School of Computer Science and Technology, Xidian University, Xi’an 710071, China; (Q.L.); (Y.T.); (H.A.K.A.)
| | - Ye Tian
- School of Computer Science and Technology, Xidian University, Xi’an 710071, China; (Q.L.); (Y.T.); (H.A.K.A.)
| | - Yue-Hui Chen
- Shandong Provincial Key Laboratory of Network Based Intelligent Computing, University of Jinan, Ji’nan 250022, China;
| | - Haque A. K. Alvi
- School of Computer Science and Technology, Xidian University, Xi’an 710071, China; (Q.L.); (Y.T.); (H.A.K.A.)
| | - Xi-Guo Yuan
- School of Computer Science and Technology, Xidian University, Xi’an 710071, China; (Q.L.); (Y.T.); (H.A.K.A.)
- Correspondence:
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20
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Guo Y, Wang S, Yuan X. HBOS-CNV: A New Approach to Detect Copy Number Variations From Next-Generation Sequencing Data. Front Genet 2021; 12:642473. [PMID: 34163521 PMCID: PMC8215577 DOI: 10.3389/fgene.2021.642473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 05/05/2021] [Indexed: 11/13/2022] Open
Abstract
Copy number variation (CNV) is a genomic mutation that plays an important role in tumor evolution and tumor genesis. Accurate detection of CNVs from next-generation sequencing (NGS) data is still a challenging task due to artifacts such as uneven mapped reads and unbalanced amplitudes of gains and losses. This study proposes a new approach called HBOS-CNV to detect CNVs from NGS data. The central point of HBOS-CNV is that it uses a new statistic, the histogram-based outlier score (HBOS), to evaluate the fluctuation of genome bins to determine those of changed copy numbers. In comparison with existing statistics in the evaluation of CNVs, HBOS is a non-linearly transformed value from the observed read depth (RD) value of each genome bin, having the potential ability to relieve the effects resulted from the above artifacts. In the calculation of HBOS values, a dynamic width histogram is utilized to depict the density of bins on the genome being analyzed, which can reduce the effects of noises partially contributed by mapping and sequencing errors. The evaluation of genome bins using such a new statistic can lead to less extremely significant CNVs having a high probability of detection. We evaluated this method using a large number of simulation datasets and compared it with four existing methods (CNVnator, CNV-IFTV, CNV-LOF, and iCopyDav). The results demonstrated that our proposed method outperforms the others in terms of sensitivity, precision, and F1-measure. Furthermore, we applied the proposed method to a set of real sequencing samples from the 1000 Genomes Project and determined a number of CNVs with biological meanings. Thus, the proposed method can be regarded as a routine approach in the field of genome mutation analysis for cancer samples.
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Affiliation(s)
- Yang Guo
- The School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Shuzhen Wang
- The School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Xiguo Yuan
- The School of Computer Science and Technology, Xidian University, Xi'an, China
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21
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He Z, Zhang J, Yuan X, Zhang Y. Integrating Somatic Mutations for Breast Cancer Survival Prediction Using Machine Learning Methods. Front Genet 2021; 11:632901. [PMID: 33537063 PMCID: PMC7848170 DOI: 10.3389/fgene.2020.632901] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 12/30/2020] [Indexed: 12/13/2022] Open
Abstract
Breast cancer is the most common malignancy in women, and because it has a high mortality rate, it is urgent to develop computational methods to increase the accuracy of breast cancer survival predictive models. Although multi-omics data such as gene expression have been extensively used in recent studies, the accurate prognosis of breast cancer remains a challenge. Somatic mutations are another important and promising data source for studying cancer development, and its effect on the prognosis of breast cancer remains to be further explored. Meanwhile, these omics datasets are high-dimensional and redundant. Therefore, we adopted multiple kernel learning (MKL) to efficiently integrate somatic mutation to currently molecular data including gene expression, copy number variation (CNV), methylation, and protein expression data for the prediction of breast cancer survival. Before integration, the maximum relevance minimum redundancy (mRMR) feature selection method was utilized to select features that present high relevance to survival and low redundancy among themselves for each type of data. The experimental results demonstrated that the proposed method achieved the most optimal performance and there was a remarkable improvement in the prediction performance when somatic mutations were included, indicating that somatic mutations are critical for improving breast cancer survival predictions. Moreover, mRMR was superior to other feature selection methods used in previous studies. Furthermore, MKL outperformed the other traditional classifiers in multi-omics data integration. Our analysis indicated that through employing promising omics data such as somatic mutations and harnessing the power of proper feature selection methods and effective integration frameworks, the breast cancer survival predictive accuracy can be further increased, thereby providing a more optimal clinical diagnosis and more effective treatment for breast cancer patients.
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Affiliation(s)
- Zongzhen He
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Junying Zhang
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Xiguo Yuan
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Yuanyuan Zhang
- School of Information and Control Engineering, Qingdao University of Technology, Qingdao, China
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22
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Abstract
Gains and losses of large segments of genomic DNA, known as copy number variants (CNVs) gained considerable interest in clinical diagnostics lately, as particular forms may lead to inherited genetic diseases. In recent decades, researchers developed a wide variety of cytogenetic and molecular methods with different detection capabilities to detect clinically relevant CNVs. In this review, we summarize methodological progress from conventional approaches to current state of the art techniques capable of detecting CNVs from a few bases up to several megabases. Although the recent rapid progress of sequencing methods has enabled precise detection of CNVs, determining their functional effect on cellular and whole-body physiology remains a challenge. Here, we provide a comprehensive list of databases and bioinformatics tools that may serve as useful assets for researchers, laboratory diagnosticians, and clinical geneticists facing the challenge of CNV detection and interpretation.
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23
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Xie K, Tian Y, Yuan X. A Density Peak-Based Method to Detect Copy Number Variations From Next-Generation Sequencing Data. Front Genet 2021; 11:632311. [PMID: 33519925 PMCID: PMC7838601 DOI: 10.3389/fgene.2020.632311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 12/21/2020] [Indexed: 11/29/2022] Open
Abstract
Copy number variation (CNV) is a common type of structural variations in human genome and confers biological meanings to human complex diseases. Detection of CNVs is an important step for a systematic analysis of CNVs in medical research of complex diseases. The recent development of next-generation sequencing (NGS) platforms provides unprecedented opportunities for the detection of CNVs at a base-level resolution. However, due to the intrinsic characteristics behind NGS data, accurate detection of CNVs is still a challenging task. In this article, we propose a new density peak-based method, called dpCNV, for the detection of CNVs from NGS data. The algorithm of dpCNV is designed based on density peak clustering algorithm. It extracts two features, i.e., local density and minimum distance, from sequencing read depth (RD) profile and generates a two-dimensional data. Based on the generated data, a two-dimensional null distribution is constructed to test the significance of each genome bin and then the significant genome bins are declared as CNVs. We test the performance of the dpCNV method on a number of simulated datasets and make comparison with several existing methods. The experimental results demonstrate that our proposed method outperforms others in terms of sensitivity and F1-score. We further apply it to a set of real sequencing samples and the results demonstrate the validity of dpCNV. Therefore, we expect that dpCNV can be used as a supplementary to existing methods and may become a routine tool in the field of genome mutation analysis.
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Affiliation(s)
- Kun Xie
- The School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Ye Tian
- The School of Computer Science and Technology, Xidian University, Xi'an, China.,Xi'an Key Laboratory of Computational Bioinformatics, The School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Xiguo Yuan
- The School of Computer Science and Technology, Xidian University, Xi'an, China.,Xi'an Key Laboratory of Computational Bioinformatics, The School of Computer Science and Technology, Xidian University, Xi'an, China
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24
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Liu G, Zhang J, Yuan X, Wei C. RKDOSCNV: A Local Kernel Density-Based Approach to the Detection of Copy Number Variations by Using Next-Generation Sequencing Data. Front Genet 2020; 11:569227. [PMID: 33329705 PMCID: PMC7673372 DOI: 10.3389/fgene.2020.569227] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/04/2020] [Indexed: 12/04/2022] Open
Abstract
Copy number variations (CNVs) are significant causes of many human cancers and genetic diseases. The detection of CNVs has become a common method by which to analyze human diseases using next-generation sequencing (NGS) data. However, effective detection of insignificant CNVs is still a challenging task. In this study, we propose a new detection method, RKDOSCNV, to meet the need. RKDOSCNV uses kernel density estimation method to evaluate the local kernel density distribution of each read depth segment (RDS) based on an expanded nearest neighbor (k-nearest neighbors, reverse nearest neighbors, and shared nearest neighbors of each RDS) data set, and assigns a relative kernel density outlier score (RKDOS) for each RDS. According to the RKDOS profile, RKDOSCNV predicts the candidate CNVs by choosing a reasonable threshold, which it uses split read approach to correct the boundaries of candidate CNVs. The performance of RKDOSCNV is assessed by comparing it with several current popular methods via experiments with simulated and real data at different tumor purity levels. The experimental results verify that the performance of RKDOSCNV is superior to that of several other methods. In summary, RKDOSCNV is a simple and effective method for the detection of CNVs from whole genome sequencing (WGS) data, especially for samples with low tumor purity.
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Affiliation(s)
- Guojun Liu
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Junying Zhang
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Xiguo Yuan
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Chao Wei
- School of Computer Science and Technology, Xidian University, Xi'an, China
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25
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Dong J, Qi M, Wang S, Yuan X. DINTD: Detection and Inference of Tandem Duplications From Short Sequencing Reads. Front Genet 2020; 11:924. [PMID: 32849857 PMCID: PMC7433346 DOI: 10.3389/fgene.2020.00924] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/24/2020] [Indexed: 11/21/2022] Open
Abstract
Tandem duplication (TD) is an important type of structural variation (SV) in the human genome and has biological significance for human cancer evolution and tumor genesis. Accurate and reliable detection of TDs plays an important role in advancing early detection, diagnosis, and treatment of disease. The advent of next-generation sequencing technologies has made it possible for the study of TDs. However, detection is still challenging due to the uneven distribution of reads and the uncertain amplitude of TD regions. In this paper, we present a new method, DINTD (Detection and INference of Tandem Duplications), to detect and infer TDs using short sequencing reads. The major principle of the proposed method is that it first extracts read depth and mapping quality signals, then uses the DBSCAN (Density-Based Spatial Clustering of Applications with Noise) algorithm to find the possible TD regions. The total variation penalized least squares model is fitted with read depth and mapping quality signals to denoise signals. A 2D binary search tree is used to search the neighbor points effectively. To further identify the exact breakpoints of the TD regions, split-read signals are integrated into DINTD. The experimental results of DINTD on simulated data sets showed that DINTD can outperform other methods for sensitivity, precision, F1-score, and boundary bias. DINTD is further validated on real samples, and the experiment results indicate that it is consistent with other methods. This study indicates that DINTD can be used as an effective tool for detecting TDs.
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Affiliation(s)
- Jinxin Dong
- School of Computer Science and Technology, Xidian University, Xi'an, China.,School of Computer Science and Technology, Liaocheng University, Liaocheng, China
| | - Minyong Qi
- School of Computer Science and Technology, Xidian University, Xi'an, China.,School of Computer Science and Technology, Liaocheng University, Liaocheng, China
| | - Shaoqiang Wang
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Xiguo Yuan
- School of Computer Science and Technology, Xidian University, Xi'an, China
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26
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Zhao H, Huang T, Li J, Liu G, Yuan X. MFCNV: A New Method to Detect Copy Number Variations From Next-Generation Sequencing Data. Front Genet 2020; 11:434. [PMID: 32499814 PMCID: PMC7243272 DOI: 10.3389/fgene.2020.00434] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 04/08/2020] [Indexed: 11/13/2022] Open
Abstract
Copy number variation (CNV) is a very important phenomenon in tumor genomes and plays a significant role in tumor genesis. Accurate detection of CNVs has become a routine and necessary procedure for a deep investigation of tumor cells and diagnosis of tumor patients. Next-generation sequencing (NGS) technique has provided a wealth of data for the detection of CNVs at base-pair resolution. However, such task is usually influenced by a number of factors, including GC-content bias, sequencing errors, and correlations among adjacent positions within CNVs. Although many existing methods have dealt with some of these artifacts by designing their own strategies, there is still a lack of comprehensive consideration of all the factors. In this paper, we propose a new method, MFCNV, for an accurate detection of CNVs from NGS data. Compared with existing methods, the characteristics of the proposed method include the following: (1) it makes a full consideration of the intrinsic correlations among adjacent positions in the genome to be analyzed, (2) it calculates read depth, GC-content bias, base quality, and correlation value for each genome bin and combines them as multiple features for the evaluation of genome bins, and (3) it addresses the joint effect among the factors via training a neural network algorithm for the prediction of CNVs. We test the performance of the MFCNV method by using simulation and real sequencing data and make comparisons with several peer methods. The results demonstrate that our method is superior to other methods in terms of sensitivity, precision, and F1-score and can detect many CNVs that other methods have not discovered. MFCNV is expected to be a complementary tool in the analysis of mutations in tumor genomes and can be extended to be applied to the analysis of single-cell sequencing data.
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Affiliation(s)
- Haiyong Zhao
- School of Computer Science and Technology, Liaocheng University, Liaocheng, China.,The School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Tihao Huang
- School of Computer Science and Technology, Liaocheng University, Liaocheng, China
| | - Junqing Li
- School of Computer Science and Technology, Liaocheng University, Liaocheng, China
| | - Guojun Liu
- The School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Xiguo Yuan
- The School of Computer Science and Technology, Xidian University, Xi'an, China
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Yuan X, Li Z, Zhao H, Bai J, Zhang J. Accurate Inference of Tumor Purity and Absolute Copy Numbers From High-Throughput Sequencing Data. Front Genet 2020; 11:458. [PMID: 32425990 PMCID: PMC7205152 DOI: 10.3389/fgene.2020.00458] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 04/14/2020] [Indexed: 02/06/2023] Open
Abstract
Inference of absolute copy numbers in tumor genomes is one of the key points in the study of tumor genesis. However, the mixture of tumor and normal cells poses a big challenge to this task. Accurate estimation of tumor purity (i.e., the fraction of tumor cells) is a necessary step to solve this problem. In this paper, we propose a new approach, AITAC, to accurately infer tumor purity and absolute copy numbers in a tumor sample by using high-throughput sequencing (HTS) data. In contrast to many existing algorithms for estimating tumor purity, which usually rely on pre-detected mutation genotypes (heterogeneity and homogeneity), AITAC just requires read depths (RDs) observed at the regions with copy number losses. AITAC creates a non-linear model to correlate tumor purity, observed and expected RDs. It adopts an exhaustive search strategy to scan tumor purity in a wide range, and chooses the tumor purity that minimizes the deviation between observed RDs and expected ones as the optimal solution. We apply the proposed approach to both simulation and real sequencing data sets and demonstrate its performance by comparing with two classical approaches. AITAC is freely available at https://github.com/BDanalysis/aitac and can be expected to become a useful approach for researchers to analyze copy numbers in cancer genome.
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Affiliation(s)
- Xiguo Yuan
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Zhe Li
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Haiyong Zhao
- School of Computer Science and Technology, Liaocheng University, Liaocheng, China
| | - Jun Bai
- Department of Medical Oncology, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Junying Zhang
- School of Computer Science and Technology, Xidian University, Xi'an, China
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