1
|
Bazarkin A, Morozov A, Androsov A, Fajkovic H, Rivas JG, Singla N, Koroleva S, Teoh JYC, Zvyagin AV, Shariat SF, Somani B, Enikeev D. Assessment of Prostate and Bladder Cancer Genomic Biomarkers Using Artificial Intelligence: a Systematic Review. Curr Urol Rep 2024; 25:19-35. [PMID: 38099997 DOI: 10.1007/s11934-023-01193-2] [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] [Accepted: 12/01/2023] [Indexed: 01/14/2024]
Abstract
PURPOSE OF REVIEW The aim of the systematic review is to assess AI's capabilities in the genetics of prostate cancer (PCa) and bladder cancer (BCa) to evaluate target groups for such analysis as well as to assess its prospects in daily practice. RECENT FINDINGS In total, our analysis included 27 articles: 10 articles have reported on PCa and 17 on BCa, respectively. The AI algorithms added clinical value and demonstrated promising results in several fields, including cancer detection, assessment of cancer development risk, risk stratification in terms of survival and relapse, and prediction of response to a specific therapy. Besides clinical applications, genetic analysis aided by the AI shed light on the basic urologic cancer biology. We believe, our results of the AI application to the analysis of PCa, BCa data sets will help to identify new targets for urological cancer therapy. The integration of AI in genomic research for screening and clinical applications will evolve with time to help personalizing chemotherapy, prediction of survival and relapse, aid treatment strategies such as reducing frequency of diagnostic cystoscopies, and clinical decision support, e.g., by predicting immunotherapy response. These factors will ultimately lead to personalized and precision medicine thereby improving patient outcomes.
Collapse
Affiliation(s)
- Andrey Bazarkin
- Institute for Urology and Reproductive Health, Sechenov University, Moscow, Russia
| | - Andrey Morozov
- Institute for Urology and Reproductive Health, Sechenov University, Moscow, Russia
| | - Alexander Androsov
- Department of Pediatric Surgery, Division of Pediatric Urology and Andrology, Sechenov University, Moscow, Russia
| | - Harun Fajkovic
- Department of Urology and Comprehensive Cancer Center, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
- Karl Landsteiner Institute of Urology and Andrology, Vienna, Austria
| | - Juan Gomez Rivas
- Department of Urology, Clinico San Carlos University Hospital, Madrid, Spain
| | - Nirmish Singla
- School of Medicine, Brady Urological Institute, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Svetlana Koroleva
- Clinical Institute for Children Health Named After N.F. Filatov, Sechenov University, Moscow, Russia
| | - Jeremy Yuen-Chun Teoh
- Department of Surgery, S.H. Ho Urology Centre, The Chinese University of Hong Kong, Hong Kong, China
| | - Andrei V Zvyagin
- Institute of Molecular Theranostics, Sechenov University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997, Moscow, Russia
| | - Shahrokh François Shariat
- Department of Urology and Comprehensive Cancer Center, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
- Karl Landsteiner Institute of Urology and Andrology, Vienna, Austria
- Department of Urology, Weill Cornell Medical College, New York, NY, USA
- Department of Urology, University of Texas Southwestern, Dallas, TX, USA
- Department of Urology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
- Division of Urology, Department of Special Surgery, Jordan University Hospital, The University of Jordan, Amman, Jordan
| | - Bhaskar Somani
- Department of Urology, University Hospital Southampton, Southampton, United Kingdom
| | - Dmitry Enikeev
- Institute for Urology and Reproductive Health, Sechenov University, Moscow, Russia.
- Department of Urology and Comprehensive Cancer Center, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria.
- Karl Landsteiner Institute of Urology and Andrology, Vienna, Austria.
- Division of Urology, Rabin Medical Center, Petah Tikva, Israel.
| |
Collapse
|
2
|
Ahmed M, Mäkinen VP, Lumsden A, Boyle T, Mulugeta A, Lee SH, Olver I, Hyppönen E. Metabolic profile predicts incident cancer: A large-scale population study in the UK Biobank. Metabolism 2023; 138:155342. [PMID: 36377121 DOI: 10.1016/j.metabol.2022.155342] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/24/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND AND AIMS Analyses to predict the risk of cancer typically focus on single biomarkers, which do not capture their complex interrelations. We hypothesized that the use of metabolic profiles may provide new insights into cancer prediction. METHODS We used information from 290,888 UK Biobank participants aged 37 to 73 years at baseline. Metabolic subgroups were defined based on clustering of biochemical data using an artificial neural network approach and examined for their association with incident cancers identified through linkage to cancer registry. In addition, we evaluated associations between 38 individual biomarkers and cancer risk. RESULTS In total, 21,973 individuals developed cancer during the follow-up (median 3.87 years, interquartile range [IQR] = 2.03-5.58). Compared to the metabolically favorable subgroup (IV), subgroup III (defined as "high BMI, C-reactive protein & cystatin C") was associated with a higher risk of obesity-related cancers (hazard ratio [HR] = 1.26, 95 % CI = 1.21 to 1.32) and hematologic-malignancies (e.g., lymphoid leukemia: HR = 1.83, 95%CI = 1.44 to 2.33). Subgroup II ("high triglycerides & liver enzymes") was strongly associated with liver cancer risk (HR = 5.70, 95%CI = 3.57 to 9.11). Analysis of individual biomarkers showed a positive association between testosterone and greater risks of hormone-sensitive cancers (HR per SD higher = 1.32, 95%CI = 1.23 to 1.44), and liver cancer (HR = 2.49, 95%CI =1.47 to 4.24). Many liver tests were individually associated with a greater risk of liver cancer with the strongest association observed for gamma-glutamyl transferase (HR = 2.40, 95%CI = 2.19 to 2.65). CONCLUSIONS Metabolic profile in middle-to-older age can predict cancer incidence, in particular risk of obesity-related cancer, hematologic malignancies, and liver cancer. Elevated values from liver tests are strong predictors for later risk of liver cancer.
Collapse
Affiliation(s)
- Muktar Ahmed
- Australian Centre for Precision Health, University of South Australia, Adelaide, SA, Australia; Department of Epidemiology, Faculty of Public Health, Jimma University Institute of Health, Jimma, Ethiopia; UniSA Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia; South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Ville-Petteri Mäkinen
- Australian Centre for Precision Health, University of South Australia, Adelaide, SA, Australia; Computational Systems Biology Program, Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Amanda Lumsden
- Australian Centre for Precision Health, University of South Australia, Adelaide, SA, Australia; UniSA Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Terry Boyle
- Australian Centre for Precision Health, University of South Australia, Adelaide, SA, Australia; South Australian Health and Medical Research Institute, Adelaide, SA, Australia; UniSA Allied Health & Human Performance, University of South Australia, Adelaide, SA, Australia
| | - Anwar Mulugeta
- Australian Centre for Precision Health, University of South Australia, Adelaide, SA, Australia; UniSA Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia; South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Sang Hong Lee
- Australian Centre for Precision Health, University of South Australia, Adelaide, SA, Australia; South Australian Health and Medical Research Institute, Adelaide, SA, Australia; UniSA Allied Health & Human Performance, University of South Australia, Adelaide, SA, Australia
| | - Ian Olver
- School of Psychology, Faculty of Health and Medical Sciences, University of Adelaide, Australia
| | - Elina Hyppönen
- Australian Centre for Precision Health, University of South Australia, Adelaide, SA, Australia; UniSA Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia; South Australian Health and Medical Research Institute, Adelaide, SA, Australia.
| |
Collapse
|
3
|
Khatami A, Salavatiha Z, Razizadeh MH. Bladder cancer and human papillomavirus association: a systematic review and meta-analysis. Infect Agent Cancer 2022; 17:3. [PMID: 35062986 PMCID: PMC8780707 DOI: 10.1186/s13027-022-00415-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 01/10/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The possible association of human papillomavirus (HPV) and bladder cancer has been controversial. Older findings suggest a significant association between the virus and bladder cancer. The aim of this study was to evaluate the data from the last ten years to estimate the prevalence of the virus in bladder cancer patients and to assess the association between the virus and cancer. METHOD A search of major databases was conducted to retrieve published English language studies between January 2011 and March 2021. In the present study overall prevalence of the virus in bladder cancer patients was estimated along with the prevalence of subgroups. Also, the possible associations between the prevalence of the virus and bladder cancer and the possible impact of variables in the geographical area and the type of sample were measured by comprehensive meta-analysis software (V2.2, BIOSTAT). RESULTS Unlike previous studies, despite the relatively high prevalence of the virus [pooled prevalence: 14.3% (95% CI 8.9-22.2%)] no significant association was found between HPV and bladder cancer (OR 2.077, 95% CI 0.940-4.587). No significant association was found between geographical area (except Asia) and type of sample with bladder cancer. CONCLUSIONS Given the significant prevalence, despite the insignificance of the association between virus and cancer, it seems that more studies with case-control design are needed to elucidate this association.
Collapse
Affiliation(s)
- Alireza Khatami
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Zahra Salavatiha
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | | |
Collapse
|
4
|
Wang H, Wang X, Xu L, Cao H, Zhang J. Nonnegative matrix factorization-based bioinformatics analysis reveals that TPX2 and SELENBP1 are two predictors of the inner sub-consensuses of lung adenocarcinoma. Cancer Med 2021; 10:9058-9077. [PMID: 34734491 PMCID: PMC8683537 DOI: 10.1002/cam4.4386] [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: 02/09/2021] [Revised: 09/21/2021] [Accepted: 10/14/2021] [Indexed: 12/24/2022] Open
Abstract
Background Lung adenocarcinoma (LUAD) is a heterogeneous disease. However the inner sub‐groups of LUAD have not been fully studied. Markers predicted the sub‐groups and prognosis of LUAD are badly needed. Aims To identify biomarkers associated with the sub‐groups and prognosis of LUAD. Materials and Methods Using nonnegative matrix factorization (NMF) clustering, LUAD patients from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) datasets and LUAD cell lines from Genomics of Drug Sensitivity in Cancer (GDSC) dataset were divided into different sub‐consensuses based on the gene expression profiling. The overall survival of LUAD patients in each sub‐consensus was determined by Kaplan‐Meier survival analysis. The common genes which were differentially expressed in each sub‐consensus of LUAD patients and LUAD cell lines were identified using TBtools. The predictive accuracy of TPX2 and SELENBP1 for theinner sub‐consensuses of LUAD was determined by Receiver operator characteristic (ROC) analysis. The Kaplan‐Meier survival analysis was also used to test the prognostic significance of TPX2 and SELENBP1 in LUAD patients. Results Using nonnegative matrix factorization clustering, LUAD patients in The Cancer Genome Atlas (TCGA), GSE30219, GSE42127, GSE50081, GSE68465, and GSE72094 datasets were divided into three sub‐consensuses. Sub‐consensus3 LUAD patients were with low overall survival and were with high TP53 mutations. Similarly, LUAD cell lines were also divided into three sub‐consensuses by NMF method, and sub‐consensus2 cell lines were resistant to EGFR inhibitors. Identification of the common genes which were differentially expressed in different sub‐consensuses of LUAD patients and LUAD cell lines revealed that TPX2 was highly expressed in sub‐consensus3 LUAD patients and sub‐consensus2 LUAD cell lines. On the contrary, SELENBP1 was highly expressed in sub‐consensus1 LUAD patients and sub‐consensus1 LUAD cell lines. The expression levels of TPX2 and SELENBP1 could distinguish sub‐consensus3 LUAD patients or sub‐consensus2 LUAD cell lines from other sub‐consensuses of LUAD patients or cell lines. Moreover, compared with normal lung tissues, TPX2 was highly expressed, while, SELENBP1 was lowly expressed in LUAD tissues. Furthermore, the higher expression levels of TPX2 were associated with the lower relapse‐free survival and the lower overall survival of LUAD patients. While, the higher expression levels of SELENBP1 were associated with the higher relapse‐free survival and higher overall survival. At last, we showed that TP53 mutant LUAD patients were with higher TPX2 and lower SELENBP1 expressions. Discussion Both iCluster and NMF method are proved to be robust LUAD classification systems. However, the LUAD patients in different iclusters had no significant clinical overall survival, while, sub‐consensus3 LUAD patients from NMF classification were with lower overall survival than other sub‐consensuses. Conclusions By integrated analysis of 1765 LUAD patients and 64 LUAD cell lines, we showed that NMF was a robust inner sub‐consensuses classification method of LUAD. TPX2 and SELENBP1 were differentially expressed in different LUAD sub‐ consensuses, and predicted the inner sub‐consensuses of LUAD with high accuracy. TPX2 was an unfavorable prognostic biomarker of LUAD which was up‐regulated in LUAD tissues and associated with the low overall survival of LUAD. SELENBP1 was a favorable prognostic biomarker of LUAD which was down‐regulated in LUAD tissues and associated with the prolonged overall survival of LUAD.
Collapse
Affiliation(s)
- Haiwei Wang
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.,Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate, National Health and Family Planning Commission, Fuzhou, Fujian, China
| | - Xinrui Wang
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.,Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate, National Health and Family Planning Commission, Fuzhou, Fujian, China
| | - Liangpu Xu
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.,Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate, National Health and Family Planning Commission, Fuzhou, Fujian, China
| | - Hua Cao
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.,Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate, National Health and Family Planning Commission, Fuzhou, Fujian, China
| | - Ji Zhang
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital Affiliated to School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
5
|
Usefulness of droplet digital PCR and Sanger sequencing for detection of FGFR3 mutation in bladder cancer. Urol Oncol 2019; 37:907-915. [DOI: 10.1016/j.urolonc.2019.06.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/10/2019] [Accepted: 06/11/2019] [Indexed: 01/03/2023]
|
6
|
Guyot A, Duchesne M, Robert S, Lia AS, Derouault P, Scaon E, Lemnos L, Salle H, Durand K, Labrousse F. Analysis of CDKN2A gene alterations in recurrent and non-recurrent meningioma. J Neurooncol 2019; 145:449-459. [PMID: 31729637 DOI: 10.1007/s11060-019-03333-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 11/03/2019] [Indexed: 12/11/2022]
Abstract
PURPOSE Assessment of the risk of recurrence is essential to determine the therapeutic strategy of meningioma treatment. Many relapsing or aggressive meningiomas show elevated mitotic and/or Ki67 indices, reflecting cell cycle deregulation. As CDKN2A is a key tumor suppressor gene involved in cell cycle control, we investigated whether CDKN2A alterations may be involved in tumor recurrence. METHODS We carried out a comparative analysis of 17 recurrent and 13 non-recurrent meningiomas. CDKN2A single nucleotide variations (SNVs), deletions, methylation status of the promotor, and p16 expression were investigated. Results were correlated with the recurrent or non-recurrent status and clinicopathological data. RESULTS We identified a CDKN2A SNV (NM_000077, exon2, c.G442A, p.Ala148Thr) in five meningiomas that was significantly associated with recurrence (p = 0.03). This mutation, confirmed by Sanger sequencing and referenced in the COSMIC database in various cancers, has not been reported in meningioma. The presence of one of the three following CDKN2A alterations-p.(Ala148Thr) mutation, whole homozygous or heterozygous gene loss, or promotor methylation > 8%-was observed in 13 of the 17 relapsing meningiomas and was strongly associated with recurrence (p < 0.0001) and a Ki67 labeling index > 7% (p = 0.004). CONCLUSION We report an undescribed p.(Ala148Thr) CDKN2A mutation in meningioma that was only present in relapsing tumors. In our series, CDKN2A gene alterations were only found in recurrent meningiomas. However, our results need to be evaluated on a larger series to ensure that these CDKN2A alterations can be used as biomarkers of recurrence in meningioma.
Collapse
Affiliation(s)
- Anne Guyot
- Department of Pathology, Limoges University Hospital, 2 Avenue Martin-Luther-King, 87042, Limoges, France
| | - Mathilde Duchesne
- Department of Pathology, Limoges University Hospital, 2 Avenue Martin-Luther-King, 87042, Limoges, France
| | - Sandrine Robert
- EA 3842, CAPTuR « Contrôle de L'Activation Cellulaire, Progression Tumorale Et Résistance Thérapeutique », Faculty of Medicine, Limoges University, 2 Rue du Docteur Marcland, 87025, Limoges, France
| | - Anne-Sophie Lia
- EA 6309, MMNP « Maintenance Myélinique Et Neuropathies Périphériques », Faculty of Medicine, Limoges University, 2 Rue du Docteur Marcland, 87025, Limoges, France
| | - Paco Derouault
- EA 6309, MMNP « Maintenance Myélinique Et Neuropathies Périphériques », Faculty of Medicine, Limoges University, 2 Rue du Docteur Marcland, 87025, Limoges, France
| | - Erwan Scaon
- Bioinformatics Unit, BISCEM Platform, CBRS, University of Limoges, 2 Rue du Docteur-Marcland, 87025, Limoges, France
| | - Leslie Lemnos
- Department of Neurosurgery, Limoges University Hospital, 2 Avenue Martin-Luther-King, 87042, Limoges, France
| | - Henri Salle
- Department of Neurosurgery, Limoges University Hospital, 2 Avenue Martin-Luther-King, 87042, Limoges, France
| | - Karine Durand
- Department of Pathology, Limoges University Hospital, 2 Avenue Martin-Luther-King, 87042, Limoges, France.,EA 3842, CAPTuR « Contrôle de L'Activation Cellulaire, Progression Tumorale Et Résistance Thérapeutique », Faculty of Medicine, Limoges University, 2 Rue du Docteur Marcland, 87025, Limoges, France
| | - François Labrousse
- Department of Pathology, Limoges University Hospital, 2 Avenue Martin-Luther-King, 87042, Limoges, France. .,EA 3842, CAPTuR « Contrôle de L'Activation Cellulaire, Progression Tumorale Et Résistance Thérapeutique », Faculty of Medicine, Limoges University, 2 Rue du Docteur Marcland, 87025, Limoges, France.
| |
Collapse
|
7
|
A survey of neural network-based cancer prediction models from microarray data. Artif Intell Med 2019; 97:204-214. [PMID: 30797633 DOI: 10.1016/j.artmed.2019.01.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 10/22/2018] [Accepted: 01/27/2019] [Indexed: 12/17/2022]
Abstract
Neural networks are powerful tools used widely for building cancer prediction models from microarray data. We review the most recently proposed models to highlight the roles of neural networks in predicting cancer from gene expression data. We identified articles published between 2013-2018 in scientific databases using keywords such as cancer classification, cancer analysis, cancer prediction, cancer clustering and microarray data. Analyzing the studies reveals that neural network methods have been either used for filtering (data engineering) the gene expressions in a prior step to prediction; predicting the existence of cancer, cancer type or the survivability risk; or for clustering unlabeled samples. This paper also discusses some practical issues that can be considered when building a neural network-based cancer prediction model. Results indicate that the functionality of the neural network determines its general architecture. However, the decision on the number of hidden layers, neurons, hypermeters and learning algorithm is made using trail-and-error techniques.
Collapse
|
8
|
Moody L, Mantha S, Chen H, Pan YX. Computational methods to identify bimodal gene expression and facilitate personalized treatment in cancer patients. J Biomed Inform 2019; 100S:100001. [PMID: 34384574 DOI: 10.1016/j.yjbinx.2018.100001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 11/03/2018] [Accepted: 12/06/2018] [Indexed: 10/27/2022]
Abstract
Standard methods for detecting cancer-associated genes rely on comparison of sample means between cancer patients and healthy controls. While such methods have successfully identified several oncogenes and tumor suppressor genes, they neglect to account for heterogeneity within the cancer population. Genetic mutations, translocations, and amplifications are often inconsistent across tumors, and instead they often affect smaller subsets of patients. This concept gives rise to the idea of bimodally expressed genes, or genes that display two modes of expression within one population. Analysis of bimodal gene expression has been explored via a variety of techniques including test statistics and clustering. In this review, we summarize the methodologies used to quantify bimodal gene expression and address the utility of these genes in patient stratification and specialized therapeutics in breast and lung cancer. Finally we discuss the limitations and future directions for bimodal genes in the era of high-throughput sequencing and personalized medicine.
Collapse
Affiliation(s)
- Laura Moody
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.
| | - Suparna Mantha
- Carle Physician Group, Carle Cancer Center, Carle Foundation Hospital, Urbana, IL 61802, United States.
| | - Hong Chen
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.
| | - Yuan-Xiang Pan
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.
| |
Collapse
|
9
|
Gandía-Aguiló V, Cibrián R, Soria E, Serrano AJ, Aguiló L, Paredes V, Gandía JL. Use of self-organizing maps for analyzing the behavior of canines displaced towards midline under interceptive treatment. Med Oral Patol Oral Cir Bucal 2017; 22:e233-e241. [PMID: 28160587 PMCID: PMC5359714 DOI: 10.4317/medoral.21509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 10/01/2016] [Indexed: 11/16/2022] Open
Abstract
Background Displaced maxillary permanent canine is one of the more frequent findings in canine eruption process and it’s easy to be outlined and early diagnosed by means of x-ray images. Late diagnosis frequently needs surgery to rescue the impacted permanent canine.
In many cases, interceptive treatment to redirect canine eruption is needed. However, some patients treated by interceptive means end up requiring fenestration to orthodontically guide the canine to its normal occlusal position.
It would be interesting, therefore, to discover the dental characteristics of patients who will need additional surgical treatment to interceptive treatment. Material and Methods To study the dental characteristics associated with canine impaction, conventional statistics have traditionally been used. This approach, although serving to illustrate many features of this problem, has not provided a satisfactory response or not provided an overall idea of the characteristics of these types of patients, each one of them with their own particular set of variables.
Faced with this situation, and in order to analyze the problem of impaction despite interceptive treatment, we have used an alternative method for representing the variables that have an influence on this syndrome. This method is known as Self-Organizing Maps (SOM), a method used for analyzing problems with multiple variables. Results We analyzed 78 patients with a PMC angulation higher than 100º. All of them were subject to interceptive treatment and in 21 cases it was necessary to undertake the above-mentioned fenestration to achieve the final eruption of the canine. Conclusions In this study, we describe the process of debugging variables and selecting the appropriate number of cells in SOM so as to adequately visualize the problem posed and the dental characteristics of patients with regard to a greater or lesser probability of the need for fenestration. Key words:Interceptive orthodontic treatment, altered eruption, impacted canines, neuronal networks, self-organizing maps.
Collapse
Affiliation(s)
- V Gandía-Aguiló
- Avenida Maria Cristina n 12- 2 , CP: 46001, Valencia, Spain,
| | | | | | | | | | | | | |
Collapse
|
10
|
Higdon R, Earl RK, Stanberry L, Hudac CM, Montague E, Stewart E, Janko I, Choiniere J, Broomall W, Kolker N, Bernier RA, Kolker E. The promise of multi-omics and clinical data integration to identify and target personalized healthcare approaches in autism spectrum disorders. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 19:197-208. [PMID: 25831060 DOI: 10.1089/omi.2015.0020] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Complex diseases are caused by a combination of genetic and environmental factors, creating a difficult challenge for diagnosis and defining subtypes. This review article describes how distinct disease subtypes can be identified through integration and analysis of clinical and multi-omics data. A broad shift toward molecular subtyping of disease using genetic and omics data has yielded successful results in cancer and other complex diseases. To determine molecular subtypes, patients are first classified by applying clustering methods to different types of omics data, then these results are integrated with clinical data to characterize distinct disease subtypes. An example of this molecular-data-first approach is in research on Autism Spectrum Disorder (ASD), a spectrum of social communication disorders marked by tremendous etiological and phenotypic heterogeneity. In the case of ASD, omics data such as exome sequences and gene and protein expression data are combined with clinical data such as psychometric testing and imaging to enable subtype identification. Novel ASD subtypes have been proposed, such as CHD8, using this molecular subtyping approach. Broader use of molecular subtyping in complex disease research is impeded by data heterogeneity, diversity of standards, and ineffective analysis tools. The future of molecular subtyping for ASD and other complex diseases calls for an integrated resource to identify disease mechanisms, classify new patients, and inform effective treatment options. This in turn will empower and accelerate precision medicine and personalized healthcare.
Collapse
Affiliation(s)
- Roger Higdon
- 1 Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute , Seattle, Washington
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|