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Li G, Wang Y, Wang Y, Wang B, Liang Y, Wang P, He Y, Hu X, Liu G, Lei Z, Zhang B, Shi Y, Gao X, Zhang X, Ci W. PCaseek: ultraspecific urinary tumor DNA detection using deep learning for prostate cancer diagnosis and Gleason grading. Cell Discov 2024; 10:90. [PMID: 39223118 PMCID: PMC11369186 DOI: 10.1038/s41421-024-00710-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 07/11/2024] [Indexed: 09/04/2024] Open
Affiliation(s)
- Gaojie Li
- China National Center for Bioinformation, Beijing, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ye Wang
- Department of Urology, Chinese PLA General Hospital, Beijing, China
| | - Ying Wang
- China National Center for Bioinformation, Beijing, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Baojun Wang
- Department of Urology, Chinese PLA General Hospital, Beijing, China
| | - Yuan Liang
- China National Center for Bioinformation, Beijing, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Ping Wang
- China National Center for Bioinformation, Beijing, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yudan He
- China National Center for Bioinformation, Beijing, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoshan Hu
- Department of Urology, Chinese PLA General Hospital, Beijing, China
| | - Guojun Liu
- Department of Urology, Chinese PLA General Hospital, Beijing, China
| | - Zhentao Lei
- Department of Urology, Aerospace Center Hospital, Beijing, China
| | - Bao Zhang
- Department of Urology, Aerospace Center Hospital, Beijing, China
| | - Yue Shi
- China National Center for Bioinformation, Beijing, China.
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
| | - Xu Gao
- Department of Urology, Changhai Hospital, Naval Military Medical University, Shanghai, China.
| | - Xu Zhang
- Department of Urology, Chinese PLA General Hospital, Beijing, China.
| | - Weimin Ci
- China National Center for Bioinformation, Beijing, China.
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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Fang Y, Nie L, Wang S, Liu S, Li H, Yu R. A universal fluorescence biosensor based on rolling circle amplification and locking probe for DNA detection. Mikrochim Acta 2024; 191:437. [PMID: 38951284 DOI: 10.1007/s00604-024-06501-2] [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: 04/03/2024] [Accepted: 06/11/2024] [Indexed: 07/03/2024]
Abstract
A stable DNA signal amplification sensor was developed on account of rolling circle amplification (RCA). This sensor includes target DNA-controlled rolling circle amplification technology and locking probe DNA replacement technology, which can be used to detect DNA fragments with genetic information, thus constructing a biosensor for universal detection of DNA. This study takes the homologous DNA of human immunodeficiency virus (HIV) and let-7a as examples to describe this biosensor. The padlock probe is first cyclized by T4 DNA ligase in response to the target's reaction with it. Then, rolling cycle amplification is initiated by Phi29 DNA polymerase, resulting in the formation of a lengthy chain with several triggers. These triggers can open the locked probe LP1 with the fluorescence signal turned off, so that it can continue to react with H2 to form a stable H1-H2 double strand. This regulates the distance between B-DNA modified by the quenching group and H1 modified by fluorescent group, and the fluorescence signal is recovered.
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Affiliation(s)
- Ying Fang
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, P.R. China
| | - Lanxin Nie
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, P.R. China
| | - Suqin Wang
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, P.R. China
| | - Shiwen Liu
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, P.R. China.
- Jiangxi Provincial Center for Disease Control and Prevention, Nanchang, 330029, P. R. China.
| | - Hongbo Li
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, P.R. China.
| | - Ruqin Yu
- State Key Laboratory for Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, P.R. China
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3
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Sequeira JP, Salta S, Freitas R, López-López R, Díaz-Lagares Á, Henrique R, Jerónimo C. Biomarkers for Pre-Treatment Risk Stratification of Prostate Cancer Patients: A Systematic Review. Cancers (Basel) 2024; 16:1363. [PMID: 38611041 PMCID: PMC11011064 DOI: 10.3390/cancers16071363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/24/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND Prostate cancer (PCa) is one of the most frequently occurring malignancies. Although most cases are not life-threatening, approximately 20% endure an unfavorable outcome. PSA-based screening reduced mortality but at the cost of an increased overdiagnosis/overtreatment of low-risk (lrPCa) and favorable intermediate-risk (firPCa) PCa. PCa risk-groups are usually identified based on serum Prostate-Specific Antigen (PSA), the Gleason score, and clinical T stage, which have consistent although variable specificity or subjectivity. Thus, more effective and specific tools for risk assessment are needed, ideally making use of minimally invasive methods such as liquid biopsies. In this systematic review we assessed the clinical potential and analytical performance of liquid biopsy-based biomarkers for pre-treatment risk stratification of PCa patients. METHODS Studies that assessed PCa pre-treatment risk were retrieved from PubMed, Scopus, and MedLine. PCa risk biomarkers were analyzed, and the studies' quality was assessed using the QUADAS-2 tool. RESULTS The final analysis comprised 24 full-text articles, in which case-control studies predominated, mostly reporting urine-based biomarkers (54.2%) and biomarker quantification by qPCR (41.7%). Categorization into risk groups was heterogeneous, predominantly making use of the Gleason score. CONCLUSION This systematic review unveils the substantial clinical promise of using circulating biomarkers in assessing the risk for prostate cancer patients. However, the standardization of groups, categories, and biomarker validation are mandatory before this technique can be implemented. Circulating biomarkers might represent a viable alternative to currently available tools, obviating the need for tissue biopsies, and allowing for faster and more cost-effective testing, with superior analytical performance, specificity, and reproducibility.
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Affiliation(s)
- José Pedro Sequeira
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/CI-IPOP @RISE (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (J.P.S.); (S.S.); (R.F.); (R.H.)
- Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, Spain; (R.L.-L.); (Á.D.-L.)
- Doctoral Program in Biomedical Sciences, ICBAS-School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Sofia Salta
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/CI-IPOP @RISE (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (J.P.S.); (S.S.); (R.F.); (R.H.)
- Doctoral Program in Pathology and Molecular Genetics, ICBAS-School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Rui Freitas
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/CI-IPOP @RISE (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (J.P.S.); (S.S.); (R.F.); (R.H.)
- Department of Urology & Urology Clinic, Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Rafael López-López
- Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, Spain; (R.L.-L.); (Á.D.-L.)
- Roche-Chus Joint Unit, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), 15706 Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), ISCIII, 28029 Madrid, Spain
| | - Ángel Díaz-Lagares
- Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, Spain; (R.L.-L.); (Á.D.-L.)
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), ISCIII, 28029 Madrid, Spain
- Department of Clinical Analysis, University Hospital Complex of Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain
| | - Rui Henrique
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/CI-IPOP @RISE (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (J.P.S.); (S.S.); (R.F.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, ICBAS-School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/CI-IPOP @RISE (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (J.P.S.); (S.S.); (R.F.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, ICBAS-School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
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Liquid Biopsy in Diagnosis and Prognosis of Non-Metastatic Prostate Cancer. Biomedicines 2022; 10:biomedicines10123115. [PMID: 36551871 PMCID: PMC9776104 DOI: 10.3390/biomedicines10123115] [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: 11/01/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 12/10/2022] Open
Abstract
Currently, sensitive and specific methods for the detection and prognosis of early stage PCa are lacking. To establish the diagnosis and further identify an appropriate treatment strategy, prostate specific antigen (PSA) blood test followed by tissue biopsy have to be performed. The combination of tests is justified by the lack of a highly sensitive, specific, and safe single test. Tissue biopsy is specific but invasive and may have severe side effects, and therefore is inappropriate for screening of the disease. At the same time, the PSA blood test, which is conventionally used for PCa screening, has low specificity and may be elevated in the case of noncancerous prostate tumors and inflammatory conditions, including benign prostatic hyperplasia and prostatitis. Thus, diverse techniques of liquid biopsy have been investigated to supplement or replace the existing tests of prostate cancer early diagnosis and prognostics. Here, we provide a review on the advances in diagnosis and prognostics of non-metastatic prostate cancer by means of various biomarkers extracted via liquid biopsy, including circulating tumor cells, exosomal miRNAs, and circulating DNAs.
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He W, Xiao Y, Yan S, Zhu Y, Ren S. Cell-free DNA in the management of prostate cancer: Current status and future prospective. Asian J Urol 2022. [PMID: 37538150 PMCID: PMC10394290 DOI: 10.1016/j.ajur.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Objective With the escalating prevalence of prostate cancer (PCa) in China, there is an urgent demand for novel diagnostic and therapeutic approaches. Extensive investigations have been conducted on the clinical implementation of circulating free DNA (cfDNA) in PCa. This review aims to provide a comprehensive overview of the present state of cfDNA as a biomarker for PCa and to examine its merits and obstacles for future clinical utilization. Methods Relevant peer-reviewed manuscripts on cfDNA as a PCa marker were evaluated by PubMed search (2010-2022) to evaluate the roles of cfDNA in PCa diagnosis, prognosis, and prediction, respectively. Results cfDNA is primarily released from cells undergoing necrosis and apoptosis, allowing for non-invasive insight into the genomic, transcriptomic, and epigenomic alterations within various PCa disease states. Next-generation sequencing, among other detection methods, enables the assessment of cfDNA abundance, mutation status, fragment characteristics, and epigenetic modifications. Multidimensional analysis based on cfDNA can facilitate early detection of PCa, risk stratification, and treatment monitoring. However, standardization of cfDNA detection methods is still required to expedite its clinical application. Conclusion cfDNA provides a non-invasive, rapid, and repeatable means of acquiring multidimensional information from PCa patients, which can aid in guiding clinical decisions and enhancing patient management. Overcoming the application barriers of cfDNA necessitates increased data sharing and international collaboration.
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DeLouize AM, Eick G, Karam SD, Snodgrass JJ. Current and future applications of biomarkers in samples collected through minimally invasive methods for cancer medicine and population-based research. Am J Hum Biol 2022; 34:e23665. [PMID: 34374148 PMCID: PMC9894104 DOI: 10.1002/ajhb.23665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 02/04/2023] Open
Abstract
Despite advances in cancer medicine and research, invasive and potentially risky procedures such as biopsies, venous blood tests, imaging, colonoscopy, and pap smear tests are still primarily used for screening, staging, and assessing response to therapy. The development and interdisciplinary use of biomarkers from urine, feces, saliva, scent, and capillary blood collected with minimally invasive methods represents a potential opportunity for integration with biomarker analysis for cancers, both in clinical practice (e.g., in screening, treatment, and disease monitoring, and improved quality of life for patients) and population-based research (e.g., in epidemiology/public health, studies of social and environmental determinants, and evolutionary medicine). In this article, we review the scientific rationale, benefits, challenges, and potential opportunities for measuring cancer-related biomarkers in samples collected through minimally invasive methods.
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Affiliation(s)
| | - Geeta Eick
- Department of Anthropology, University of Oregon, Eugene, Oregon, USA
| | - Sana D. Karam
- Department of Radiation Oncology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - J. Josh Snodgrass
- Department of Anthropology, University of Oregon, Eugene, Oregon, USA
- Center for Global Health, University of Oregon, Eugene, Oregon, USA
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7
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Biosensors as diagnostic tools in clinical applications. Biochim Biophys Acta Rev Cancer 2022; 1877:188726. [DOI: 10.1016/j.bbcan.2022.188726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/18/2022] [Accepted: 03/25/2022] [Indexed: 11/19/2022]
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8
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van Dongen JE, Spoelstra LR, Berendsen JTW, Loessberg-Zahl JT, Eijkel JCT, Segerink LI. A Multiplexable Plasmonic Hairpin-DNA Sensor Based On Target-specific Tether Dynamics. ACS Sens 2021; 6:4297-4303. [PMID: 34851614 PMCID: PMC8715532 DOI: 10.1021/acssensors.1c02097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The need for measurements
of multiple biomarkers simultaneously
at subnanomolar concentrations asks for the development of new sensors
with high sensitivity, specificity, precision, and accuracy. Currently,
multiplexed sensing in single molecule sensors increases the complexity
of the system in terms of reagents and sample read-out. In this letter,
we propose a novel approach to multiplex hairpin-based single-DNA
molecule sensors, which overcomes the limitations of the present approaches
for multiplexing. By target-dependent ssDNA hairpin design, we can
create DNA tethers that have distinct tether dynamics upon target
binding. Our numerical model shows that by changing the stem length
of the ssDNA hairpin, significantly different dynamic tether behavior
will be observed. By exploiting the distance-dependent coupling of
AuNPs to gold films, we can probe this dynamic behavior along the z-axis using a simple laser equipped microscope.
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Affiliation(s)
- Jeanne Elisabeth van Dongen
- BIOS Lab on a Chip Group, MESA+ & TechMed Institutes, Max Planck Center for Complex Fluid Dynamics, University of Twente, P.O. Box 217 7500 AE Enschede, The Netherlands
| | - Laurens Rudi Spoelstra
- BIOS Lab on a Chip Group, MESA+ & TechMed Institutes, Max Planck Center for Complex Fluid Dynamics, University of Twente, P.O. Box 217 7500 AE Enschede, The Netherlands
| | - Johanna Theodora Wilhelmina Berendsen
- BIOS Lab on a Chip Group, MESA+ & TechMed Institutes, Max Planck Center for Complex Fluid Dynamics, University of Twente, P.O. Box 217 7500 AE Enschede, The Netherlands
| | - Joshua Taylor Loessberg-Zahl
- BIOS Lab on a Chip Group, MESA+ & TechMed Institutes, Max Planck Center for Complex Fluid Dynamics, University of Twente, P.O. Box 217 7500 AE Enschede, The Netherlands
| | - Jan Cornelis Titus Eijkel
- BIOS Lab on a Chip Group, MESA+ & TechMed Institutes, Max Planck Center for Complex Fluid Dynamics, University of Twente, P.O. Box 217 7500 AE Enschede, The Netherlands
| | - Loes Irene Segerink
- BIOS Lab on a Chip Group, MESA+ & TechMed Institutes, Max Planck Center for Complex Fluid Dynamics, University of Twente, P.O. Box 217 7500 AE Enschede, The Netherlands
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Clinical Relevance of Circulating Tumor Cells in Prostate Cancer Management. Biomedicines 2021; 9:biomedicines9091179. [PMID: 34572366 PMCID: PMC8471111 DOI: 10.3390/biomedicines9091179] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/29/2021] [Accepted: 09/04/2021] [Indexed: 02/08/2023] Open
Abstract
Given the low specificity of the routinely used biomarker prostate-specific antigen, circulating tumor cell (CTC) enumeration seems to be particularly useful in the monitoring of prostate cancer. In this review, we focused on a few aspects of CTC enumeration in prostate malignancies: prognostic value in metastatic and non-metastatic tumors, role in the monitoring of treatment outcomes, use as a surrogate marker for survival, and other applications, mostly for research purposes. CTC enumeration, without a doubt, offers an attractive perspective in the management of prostate cancer. However, the vast majority of available data about the role of CTC in this malignancy originate from randomized studies of anticancer agents and do not necessarily translate into real-world clinical practice. Further, most studies on the application of CTC in prostate cancer patients were limited to advanced stages of this malignancy. Meanwhile, the role of CTC in the early stages of prostate cancer, in which some patients may present with occult disseminated disease, is still relatively poorly understood, and should thus be studied extensively. Other obstacles in the widespread application of CTC enumeration in routine clinical practice include considerable discrepancies in the number of cells determined with various commercially available systems.
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Kim CJ, Dong L, Amend SR, Cho YK, Pienta KJ. The role of liquid biopsies in prostate cancer management. LAB ON A CHIP 2021; 21:3263-3288. [PMID: 34346466 DOI: 10.1039/d1lc00485a] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Liquid biopsy has emerged as a complement to invasive tissue biopsy to guide cancer diagnosis and treatment. The common liquid biopsy biomarkers are circulating tumor cells (CTCs), extracellular vesicles (EVs), and circulating tumor DNA (ctDNA). Each biomarker provides specific information based on its intrinsic characteristics. Prostate cancer is the second most common cancer in males worldwide. In men with low-grade localized prostate cancer, the disease can often be managed by active surveillance. For men who require treatment, the 5-year survival rate of localized prostate cancer is the highest among all cancer types, but the metastatic disease remains incurable. Metastatic prostate cancer invariably progresses to involve multiple bone sites and develops into a castration-resistant disease that leads to cancer death. The need to appropriately diagnose and guide the serial treatment of men with prostate cancer has led to the implementation of many studies to apply liquid biopsies to prostate cancer management. This review describes recent advancements in isolation and detection technology and the strength and weaknesses of the three circulating biomarkers. The clinical studies based on liquid biopsy results are summarized to depict the future perspective in the role of liquid biopsy on prostate cancer management.
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Affiliation(s)
- Chi-Ju Kim
- The Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
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Kim H, Park S, Jeong IG, Song SH, Jeong Y, Kim CS, Lee KH. Noninvasive Precision Screening of Prostate Cancer by Urinary Multimarker Sensor and Artificial Intelligence Analysis. ACS NANO 2021; 15:4054-4065. [PMID: 33296173 DOI: 10.1021/acsnano.0c06946] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Screening for prostate cancer relies on the serum prostate-specific antigen test, which provides a high rate of false positives (80%). This results in a large number of unnecessary biopsies and subsequent overtreatment. Considering the frequency of the test, there is a critical unmet need of precision screening for prostate cancer. Here, we introduced a urinary multimarker biosensor with a capacity to learn to achieve this goal. The correlation of clinical state with the sensing signals from urinary multimarkers was analyzed by two common machine learning algorithms. As the number of biomarkers was increased, both algorithms provided a monotonic increase in screening performance. Under the best combination of biomarkers, the machine learning algorithms screened prostate cancer patients with more than 99% accuracy using 76 urine specimens. Urinary multimarker biosensor leveraged by machine learning analysis can be an important strategy of precision screening for cancers using a drop of bodily fluid.
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Affiliation(s)
- Hojun Kim
- Biomaterials Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Sungwook Park
- Biomaterials Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - In Gab Jeong
- Department of Urology, Asan Medical Center (AMC), University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Sang Hoon Song
- Department of Urology, Asan Medical Center (AMC), University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Youngdo Jeong
- Biomaterials Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Choung-Soo Kim
- Department of Urology, Asan Medical Center (AMC), University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Kwan Hyi Lee
- Biomaterials Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
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12
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Chen C, Chen C, Sadeghi M. Evaluation of cell-free DNA accuracy as diagnostic biomarker for prostate cancer: A systematic review and meta-analysis. Biotechnol Appl Biochem 2021; 69:749-766. [PMID: 33749048 DOI: 10.1002/bab.2149] [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: 12/29/2020] [Accepted: 03/15/2021] [Indexed: 12/09/2022]
Abstract
PURPOSE This updated meta-analysis aimed to assess the diagnostic performance of circulating cell-free DNA (cf-DNA) for prostate cancer (PCa). METHODS A systematic search was conducted in PubMed, Scopus, Web of Science, and Embase databases to retrieve related studies. Several diagnostic estimates, including sensitivity (SE), specificity (SP), likelihood ratios (LRs), and diagnostic odds ratio (DOR) were also used to perform the meta-synthesis. Additionally, the area under hierarchical summary receiver operating characteristic curves (AU-HSROC) was used as a global measure of test accuracy. RESULTS Twenty-nine unique articles were enrolled in the meta-analysis. Pooled SE and SP for overall accuracy of cf-DNA in PCa were obtained as 0.54 (95% CI: 0.47-0.61) and 0.92 (95% CI: 0.88-0.95), respectively. Positive LR (PLR) was 6.8 (95% CI: 4.9-9.5, I2 : 92.98%) and negative LR (NLR) was 0.5 (95% CI: 0.43-0.58). Pooled DOR was 13.56 (95% CI: 9.49-19.37) and the AU-HSROC was 0.83 (95% CI: 0.79-0.86). CONCLUSION The present study suggested that cf-DNA assays have comparable SE as well as remarkably higher SP (qualitative assays) than common biomarkers in the detection of PCa like prostate-specific antigen (PSA). In addition, cf-DNA assays have better performance in PCa confirmation and almost similar performance to PSA in excluding PCa patients.
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Affiliation(s)
- Caixia Chen
- Department of Laboratory Medicine, Henan Provincial People's Hospital, Zhengzhou, China
| | - Chunfeng Chen
- Department of the Third Affiliated Hospital, Henan University of Traditional Chinese Medicine, Zhengzhou, China
| | - Morteza Sadeghi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
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van den Helder R, Wever BMM, van Trommel NE, van Splunter AP, Mom CH, Kasius JC, Bleeker MCG, Steenbergen RDM. Non-invasive detection of endometrial cancer by DNA methylation analysis in urine. Clin Epigenetics 2020; 12:165. [PMID: 33143739 PMCID: PMC7640380 DOI: 10.1186/s13148-020-00958-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 10/23/2020] [Indexed: 12/24/2022] Open
Abstract
Background The incidence of endometrial cancer is rising, and current diagnostics often require invasive biopsy procedures. Urine may offer an alternative sample type, which is easily accessible and allows repetitive self-sampling at home. Here, we set out to investigate the feasibility of endometrial cancer detection in urine using DNA methylation analysis. Results Urine samples of endometrial cancer patients (n = 42) and healthy controls (n = 46) were separated into three fractions (full void urine, urine sediment, and urine supernatant) and tested for three DNA methylation markers (GHSR, SST, ZIC1). Strong to very strong correlations (r = 0.77–0.92) were found amongst the different urine fractions. All DNA methylation markers showed increased methylation levels in patients as compared to controls, in all urine fractions. The highest diagnostic potential for endometrial cancer detection in urine was found in full void urine, with area under the receiver operating characteristic curve values ranging from 0.86 to 0.95. Conclusions This feasibility study demonstrates, for the first time, that DNA methylation analysis in urine could provide a non-invasive alternative for the detection of endometrial cancer. Further investigation is warranted to validate its clinical usefulness. Potential applications of this diagnostic approach include the screening of asymptomatic women, triaging women with postmenopausal bleeding symptoms, and monitoring women with increased endometrial cancer risk.
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Affiliation(s)
- Rianne van den Helder
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands.,Antoni van Leeuwenhoek/Netherlands Cancer Institute, Center of Gynecologic Oncology Amsterdam, Department of Gynecologic Oncology, Amsterdam, The Netherlands
| | - Birgit M M Wever
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Nienke E van Trommel
- Antoni van Leeuwenhoek/Netherlands Cancer Institute, Center of Gynecologic Oncology Amsterdam, Department of Gynecologic Oncology, Amsterdam, The Netherlands
| | - Annina P van Splunter
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Constantijne H Mom
- Amsterdam UMC, University of Amsterdam, Center of Gynecologic Oncology Amsterdam, Department of Gynecologic Oncology, Cancer Center Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Jenneke C Kasius
- Amsterdam UMC, University of Amsterdam, Center of Gynecologic Oncology Amsterdam, Department of Gynecologic Oncology, Cancer Center Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Maaike C G Bleeker
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Renske D M Steenbergen
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands.
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14
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Carson JJK, Di Lena MA, Berman DM, Siemens DR, Mueller CR. Development and initial clinical correlation of a DNA methylation-based blood test for prostate cancer. Prostate 2020; 80:1038-1042. [PMID: 32506642 DOI: 10.1002/pros.24025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 05/19/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND One of the principle limitations for more precise management of advanced prostate cancer is the lack of accurate biomarkers allowing estimation of tumor burden, ongoing assessment of progression, and response to treatment. Although prostate-specific antigen (PSA) performs modestly, nonsecreting cancers including those with early castrate-resistance warrant investigation of other predictive biomarkers. The objectives of these studies were to develop and perform initial validation of a circulating tumor DNA (ctDNA) methylation assay. METHODS Methylation DETection of Circulating Tumor DNA (mDETECT) is a highly multiplexed targeted sequencing DNA methylation-based ctDNA blood test that captures the vast majority of prostate cancer phenotypes due to a careful development process that ensures that each probe region is methylated in at least 50% of all methylation-based subtypes and is not methylated in normal tissues. Next-generation sequencing of targeted polymerase chain reaction (PCR) products whose amplification is biased towards methylated DNA ensures the specificity of the assay by identifying multiple tumor-specific methylated CpG residues in each read. RESULTS The final test is comprised of 46 PCR probes to 40 regions. It is relatively resistant to contaminating normal DNA and as a result functions in both serum and plasma samples. The assay was initially validated in a variety of prostate cancer cell lines to ensure specificity. Using a small number of longitudinal samples from prostate cancer patients initiating androgen deprivation therapy, the ability of mDETECT to track tumor burden was assessed compared with PSA. The mDETECT test signal generally paralleled that of PSA increasing and decreasing commensurate with tumor evolution in these patients. In two cases it appeared to anticipate clinical progression by a number of months compared to PSA and in a PSA nonproducing case, it was able to track tumor progression. CONCLUSIONS mDETECT offers a promising tool for the assessment of prostate cancer burden based on the sensitive detection of prostate-specific ctDNA and requires further validation.
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Affiliation(s)
- Jacob J K Carson
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Michael A Di Lena
- Department of Urology, Queen's University, Kingston, Ontario, Canada
| | - David M Berman
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
- Division of Cancer Biology and Genetics, Queen's Cancer Research Institute, Queen's University, Kingston, Ontario, Canada
| | - D Robert Siemens
- Department of Urology, Queen's University, Kingston, Ontario, Canada
| | - Christopher R Mueller
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
- Division of Cancer Biology and Genetics, Queen's Cancer Research Institute, Queen's University, Kingston, Ontario, Canada
- Department of Biological and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
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15
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Heidrich I, Ačkar L, Mossahebi Mohammadi P, Pantel K. Liquid biopsies: Potential and challenges. Int J Cancer 2020; 148:528-545. [PMID: 32683679 DOI: 10.1002/ijc.33217] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 07/09/2020] [Accepted: 07/10/2020] [Indexed: 12/24/2022]
Abstract
The analysis of tumor cells or tumor cell products obtained from blood or other body fluids ("liquid biopsy" [LB]) provides a broad range of opportunities in the field of oncology. Clinical application areas include early detection of cancer or tumor recurrence, individual risk assessment and therapy monitoring. LB allows to portray the entire disease as tumor cells or tumor cell products are released from all metastatic or primary tumor sites, providing comprehensive and real-time information on tumor cell evolution, therapeutic targets and mechanisms of resistance to therapy. Here, we focus on the most prominent LB markers, circulating tumor cells (CTCs) and circulating tumor-derived DNA (ctDNA), in the blood of patients with breast, prostate, lung and colorectal cancer, as the four most frequent tumor types in Europe. After a brief introduction of key technologies used to detect CTCs and ctDNA, we discuss recent clinical studies on these biomarkers for early detection and prognostication of cancer as well as prediction and monitoring of cancer therapies. We also point out current methodological and biological limitations that still hamper the implementation of LB into clinical practice.
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Affiliation(s)
- Isabel Heidrich
- Department of Tumor Biology, Center of Experimental Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lucija Ačkar
- Department of Tumor Biology, Center of Experimental Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Parinaz Mossahebi Mohammadi
- Department of Tumor Biology, Center of Experimental Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Klaus Pantel
- Department of Tumor Biology, Center of Experimental Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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16
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Wu J, Cang S, Liu C, Ochiai W, Chiao JW. Development of human prostate cancer stem cells involves epigenomic alteration and PI3K/AKT pathway activation. Exp Hematol Oncol 2020; 9:12. [PMID: 32537260 PMCID: PMC7288500 DOI: 10.1186/s40164-020-00168-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 06/04/2020] [Indexed: 12/11/2022] Open
Abstract
Background Human prostate cancer spheres endowed with stem cell properties have been obtained from androgen-dependent cell line LNCaP after exposure to an epigenomic modulator phenethyl isothiocynate (PEITC). Sphere cells can self-renew and grow with androgen, and also without androgen. Little is known about the signaling pathway and mechanism in the development of the stem cells in the spheres. Methods Expression of phosphoinositol-3 kinase (PI3K) pathway members and histone acetylation were quantified in the tumor spheres and LNCaP cells by western immunoblotting. Results The level of phosphorylated AKT was significantly increased in the sphere stem cells than the LNCaP cells at an average of 7.4 folds (range 5.8–10.7 folds), whereas the P27 level was elevated 5.4 folds (range 4.8–6.3 folds) (P < 0.05). The acetylation level on histone H3 lysine 9 was decreased. Conclusions PEITC appears to regulate the epigenome through histone acetylation and activate the PI3K/AKT pathway in the LNCaP cells. This mechanism may be responsible in part for the development of the prostate cancer stem cells.
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Affiliation(s)
- Jingjing Wu
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province China
| | - Shundong Cang
- Department of Oncology, The Henan Province Hospital of Zhengzhou University, Zhengzhou, Henan Province China
| | | | - Whitman Ochiai
- Department of Medicine, New York Medical College, Valhalla, NY 10595 USA
| | - Jen Wei Chiao
- Department of Medicine, New York Medical College, Valhalla, NY 10595 USA
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17
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Ge S, Sun C, Hu Q, Guo Y, Xia G, Mi Y, Zhu L. Differential expression profiles of circRNAs in human prostate cancer based on chip and bioinformatic analysis. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2020; 13:1045-1052. [PMID: 32509077 PMCID: PMC7270690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 03/26/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Increasing evidence suggests that circRNAs are involved in the pathogenesis of multiple kinds of cancer. Nevertheless, the differential expression of circRNAs in prostate cancer (PCA) is rarely reported. MATERIAL/METHOD In our present analyses, circRNAs expression profiles were identified in PCA, based on 5 pairs of PCA and matched non-PCA tissues using circRNA chips. RESULTS A number of 749 differential circRNAs were expressed between PCA tumor and paracancerous tissues (Fold Change, FC ≥ 2.0 and P < 0.05): 261 were upregulated, whereas 487 were downregulated in PCA tissues. Gene ontology and KEGG pathway analyses indicated that many of the circRNAs are related to carcinogenesis. Circ_0033074 and circ_0016064 both showed changes of maximum magnitude among differentially expressed circRNAs. CONCLUSIONS Our study detected a relative comprehensive differential map of circRNAs in PCA, which may become novel biomarkers for diagnosis, treatment and follow-up in the future.
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Affiliation(s)
- Shengyang Ge
- Department of Urology, Huashan Hospital, Fudan UniversityShanghai, P. R. China
| | - Chuanyu Sun
- Department of Urology, Huashan Hospital, Fudan UniversityShanghai, P. R. China
| | - Qingfeng Hu
- Department of Urology, Huashan Hospital, Fudan UniversityShanghai, P. R. China
| | - Yijun Guo
- Department of Urology, Shanghai Jing’an District Central Hospital (Jing’an Branch of Huashan Hospital Affiliated to Fudan University)Shanghai, P. R. China
| | - Guowei Xia
- Department of Urology, Huashan Hospital, Fudan UniversityShanghai, P. R. China
| | - Yuanyuan Mi
- Department of Urology, Affiliated Hospital of Jiangnan UniversityWuxi, P. R. China
| | - Lijie Zhu
- Department of Urology, Affiliated Hospital of Jiangnan UniversityWuxi, P. R. China
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18
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Ramić J, Kulovac B, Lojo-Kadrić N, Hadžić M, Eminagić Đ, Pojskić N, Bajrović K, Pojskić L. Cut-off value for KLK3 gene expression from urine sediment to rationalize diagnosis of prostate cancer. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2019.1707118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Affiliation(s)
- Jasmin Ramić
- Laboratory for Human Genetics, Institute for Genetic Engineering and Biotechnology, University of Sarajevo, Sarajevo, BiH
| | - Benjamin Kulovac
- Clinic of Urology, University Clinical Centre Sarajevo, University of Sarajevo, Sarajevo, BiH
| | - Naida Lojo-Kadrić
- Laboratory for Human Genetics, Institute for Genetic Engineering and Biotechnology, University of Sarajevo, Sarajevo, BiH
| | - Maida Hadžić
- Laboratory for Human Genetics, Institute for Genetic Engineering and Biotechnology, University of Sarajevo, Sarajevo, BiH
| | - Đenana Eminagić
- Clinic of Urology, University Clinical Centre Sarajevo, University of Sarajevo, Sarajevo, BiH
| | - Naris Pojskić
- Laboratory for Human Genetics, Institute for Genetic Engineering and Biotechnology, University of Sarajevo, Sarajevo, BiH
| | - Kasim Bajrović
- Laboratory for Human Genetics, Institute for Genetic Engineering and Biotechnology, University of Sarajevo, Sarajevo, BiH
| | - Lejla Pojskić
- Laboratory for Human Genetics, Institute for Genetic Engineering and Biotechnology, University of Sarajevo, Sarajevo, BiH
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