scholarly journals The Cancer Genome: Paradigm or Paradox?

Cancers ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 674
Author(s):  
Shi-Ming Tu

Nowadays, many professionals are sequencing the DNA and studying the cancer genome. However, if the genetic theory of cancer is flawed, our faith in the cancer genome will falter. If gene sequencing is only a tool, we should question what we are making or creating with this tool. When we do not have the right cancer theory at our disposal, we cannot be sure that what we create from the cancer genome is meaningful or useful. In this article, we illustrate that mosaicism, CHIP, and heteroplasmy dispute our traditional perspectives about a genetic origin of cancer and challenge our current narratives about the cancer genome. We caution that when we have the wrong cancer theory, big data can provide poor evidence. Precision medicine may become rather imprecise. Targeted therapy either does not work or work for the wrong reasons. The cancer genome thus becomes a paradox rather than a paradigm.

2021 ◽  
Vol 8 ◽  
Author(s):  
Yoshihiko Raita ◽  
Carlos A. Camargo ◽  
Liming Liang ◽  
Kohei Hasegawa

Clinicians handle a growing amount of clinical, biometric, and biomarker data. In this “big data” era, there is an emerging faith that the answer to all clinical and scientific questions reside in “big data” and that data will transform medicine into precision medicine. However, data by themselves are useless. It is the algorithms encoding causal reasoning and domain (e.g., clinical and biological) knowledge that prove transformative. The recent introduction of (health) data science presents an opportunity to re-think this data-centric view. For example, while precision medicine seeks to provide the right prevention and treatment strategy to the right patients at the right time, its realization cannot be achieved by algorithms that operate exclusively in data-driven prediction modes, as do most machine learning algorithms. Better understanding of data science and its tasks is vital to interpret findings and translate new discoveries into clinical practice. In this review, we first discuss the principles and major tasks of data science by organizing it into three defining tasks: (1) association and prediction, (2) intervention, and (3) counterfactual causal inference. Second, we review commonly-used data science tools with examples in the medical literature. Lastly, we outline current challenges and future directions in the fields of medicine, elaborating on how data science can enhance clinical effectiveness and inform medical practice. As machine learning algorithms become ubiquitous tools to handle quantitatively “big data,” their integration with causal reasoning and domain knowledge is instrumental to qualitatively transform medicine, which will, in turn, improve health outcomes of patients.


2016 ◽  
Vol 9 (2) ◽  
pp. 351-357
Author(s):  
Vina Pulido ◽  
Shin Yin Lee ◽  
Naomi Yu Ko

In the era of precision medicine and targeted therapy, diagnostic inaccuracy can have tremendous ramifications. We present the case of a 61-year-old man initially diagnosed with small cell lung cancer by pathology. Prior to initiating chemotherapy, multidisciplinary discussions led to an amendment of the diagnosis to medullary thyroid cancer.


2021 ◽  
Vol 15 ◽  
Author(s):  
Ziwen Wang ◽  
Yuanying Chi ◽  
Kaiye Gao ◽  
Rui Peng

Background: Precision medicine has emerged with the development of science and technology and the rise of big data. This study first defines and presents the advantages of precision medicine and then introduces the development of three technologies: gene sequencing, cellular immunotherapy, and gene editing. The clinical applications of precision medicine in lung cancer, cervical cancer, breast cancer, and prostate cancer are thus analyzed. Lastly, the existing problems and future development directions of precision medicine are identified. The introduction of gene sequencing, bioanalytical techniques, and big data analysis tools has propelled medicine into the era of precision medicine. Key technologies in precision medicine form the foundation of its development. Therefore, this study elaborates on the development of key technologies in precision medicine, the current status of its clinical application, and the main problems that currently exist. This study also suggests solutions to the problems. Objective: To systematically explain the development and principle of three core technologies in precision medicine and to predict the main research trends of precision medicine. Results: Research in gene sequencing, cell immunotherapy, and gene editing technology has shown significant progress, and accurate medical treatment has achieved remarkable results, effectively prolonging the survival time and improving the quality of life of patients. Conclusion: Precision medicine has made significant achievements, but problems remain. Ensuring safety and efficiency in precision medicine should be the focus of future research.


2021 ◽  
Vol 11 (13) ◽  
pp. 6047
Author(s):  
Soheil Rezaee ◽  
Abolghasem Sadeghi-Niaraki ◽  
Maryam Shakeri ◽  
Soo-Mi Choi

A lack of required data resources is one of the challenges of accepting the Augmented Reality (AR) to provide the right services to the users, whereas the amount of spatial information produced by people is increasing daily. This research aims to design a personalized AR that is based on a tourist system that retrieves the big data according to the users’ demographic contexts in order to enrich the AR data source in tourism. This research is conducted in two main steps. First, the type of the tourist attraction where the users interest is predicted according to the user demographic contexts, which include age, gender, and education level, by using a machine learning method. Second, the correct data for the user are extracted from the big data by considering time, distance, popularity, and the neighborhood of the tourist places, by using the VIKOR and SWAR decision making methods. By about 6%, the results show better performance of the decision tree by predicting the type of tourist attraction, when compared to the SVM method. In addition, the results of the user study of the system show the overall satisfaction of the participants in terms of the ease-of-use, which is about 55%, and in terms of the systems usefulness, about 56%.


2021 ◽  
Vol 5 (2) ◽  
Author(s):  
Nancy Wassef ◽  
David Sarkar ◽  
Girish Viswanathan ◽  
Gareth Morgan Hughes ◽  
Thomas Sailsbury ◽  
...  

Abstract Background The prevalence of culture negative infective endocarditis (IEC) is reported as 2–7% though this figure may be as high as 70% in developing countries.1 This higher rate will, at least in part, be due to reduced diagnostic facilities though some data suggests higher rates even when appropriate cultures were taken. The frequency is significantly elevated in patients who have already been exposed to antibiotics prior to blood cultures.1,2 A rare cause of culture negative IEC is the HACEK group of organisms that are normal habitants of the oropharyngeal flora and account for 1–3% of native valve endocarditis.3Aggregatibacter aphrophilus (A. aphrophilus) is a member of the HACEK group of organisms. Case summary A 32-year-old gentleman with a previous bioprosthetic aortic valve presented with a 1-week history of diarrhoea, vomiting, malaise, and weight loss. He was awaiting redo surgery for stenosis of the bioprosthesis, which had been inserted aged 17 for aortic stenosis secondary to a bicuspid valve. The initial blood tests revealed liver and renal impairment with anaemia. A transoesophageal echocardiogram demonstrated a complex cavitating aortic root abscess, complicated by perforation into the right ventricle. He underwent emergency redo surgery requiring debridement of the aortic abscess, insertion of a mechanical aortic prosthesis (St Jude Medical, USA), annular reconstruction and graft replacement of the ascending aorta. Despite antibiotic therapy, he remained septic with negative blood and tissue cultures. Bacterial 16S rRNA gene sequencing confirmed A. aphrophilus infection, for which intravenous ceftriaxone was initiated. This was subsequently changed to ciprofloxacin due to neutropenia. The patient self-discharged from the hospital during the third week of antibiotic therapy. One week later, he was re-admitted with fever, night sweats, and dyspnoea. Transthoracic echocardiogram revealed a large recurrent aortic abscess cavity around the aortic annulus fistulating into the right heart chambers; this was confirmed by a computed tomography scan. There was dehiscence of the patch repair. Emergency redo aortic root replacement (25 mm mechanical valve conduit, ATS Medical, USA) and annular reconstruction was performed with venoarterial extracorporeal membrane oxygenation (VA-ECMO) support. VA-ECMO was weaned after 3 days. The patient completed a full course of intravenous meropenem and ciprofloxacin and made a good recovery. Discussion IEC with oropharyngeal HACEK organisms is rare and difficult to diagnose, due to negative blood culture results. The broad-range polymerase chain reaction and gene sequencing with comparison to the DNA database is useful in these circumstances. This case demonstrates the importance of the 16S rRNA gene sequencing for HACEK infection diagnosis and appropriate antibiotic treatment.


2015 ◽  
Vol 4 ◽  
pp. 10-13 ◽  
Author(s):  
Carol Isaacson Barash ◽  
Keith O. Elliston ◽  
W. Andrew Faucett ◽  
Jonathan Hirsch ◽  
Gauri Naik ◽  
...  

2020 ◽  
Vol 22 (Supplement_3) ◽  
pp. iii367-iii367
Author(s):  
Jayne VonBergen ◽  
Beth Armstrong ◽  
Morgan Schmitt

Abstract Low grade gliomas are the most common type of central nervous system tumors among children. Despite the fact that they are not typically life threatening, low grade gliomas remain a significant clinical challenge. Case Study: Patient is a 4-year-old male who presented at 20 months of age with several weeks of ataxia, emesis, and head tilt. Imaging revealed a right temporal lobe lesion; he was subsequently taken to surgery, where a gross total resection was achieved. Imaging 9 months post resection revealed recurrent disease within the right temporal region with leptomeningeal involvement. Four months later imaging revealed progression of multifocal disease and new growth within the sella. At this time the patient started standard treatment, Carboplatin and Vincristine, per CCG 9952A. Persistent slow progression was observed despite receiving standard therapy. The patient developed a grade 3 reaction to carboplatin, worsening with each subsequent dose. At this time, he was referred to our Precision Genomics Neuro Oncology program for tumor molecular characterization. Somatic tumor testing revealed an ETV6-NTRK3 fusion, at which time standard treatment was stopped, and patient began targeted therapy, Larotrectinib. Imaging was preformed 2 months post start of targeted therapy and revealed interval decrease in size of previously enhancing nodular lesions; findings consistent with treatment response. Disease burden continues to decrease with therapy. This case illustrates a clear benefit of using molecular guided therapy in low grade gliomas.


2021 ◽  
pp. 561-569
Author(s):  
Steven A. Eschrich ◽  
Jamie K. Teer ◽  
Phillip Reisman ◽  
Erin Siegel ◽  
Chandan Challa ◽  
...  

PURPOSE The use of genomics within cancer research and clinical oncology practice has become commonplace. Efforts such as The Cancer Genome Atlas have characterized the cancer genome and suggested a wealth of targets for implementing precision medicine strategies for patients with cancer. The data produced from research studies and clinical care have many potential secondary uses beyond their originally intended purpose. Effective storage, query, retrieval, and visualization of these data are essential to create an infrastructure to enable new discoveries in cancer research. METHODS Moffitt Cancer Center implemented a molecular data warehouse to complement the extensive enterprise clinical data warehouse (Health and Research Informatics). Seven different sequencing experiment types were included in the warehouse, with data from institutional research studies and clinical sequencing. RESULTS The implementation of the molecular warehouse involved the close collaboration of many teams with different expertise and a use case–focused approach. Cornerstones of project success included project planning, open communication, institutional buy-in, piloting the implementation, implementing custom solutions to address specific problems, data quality improvement, and data governance, unique aspects of which are featured here. We describe our experience in selecting, configuring, and loading molecular data into the molecular data warehouse. Specifically, we developed solutions for heterogeneous genomic sequencing cohorts (many different platforms) and integration with our existing clinical data warehouse. CONCLUSION The implementation was ultimately successful despite challenges encountered, many of which can be generalized to other research cancer centers.


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