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Precision medicine genomics

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https://read.qxmd.com/read/30768178/personalized-medicine-in-cardio-oncology-the-role-of-ipsc
#1
Nazish Sayed, Mohamed Ameen, Joseph C Wu
Treatment of cancer has evolved in the last decade with the introduction of new therapies. Despite these successes, the lingering cardiotoxic side-effects from chemotherapy remain a major cause of morbidity and mortality in cancer survivors. These effects can develop acutely during treatment, or even years later. Although many risk factors can be identified prior to beginning therapy, unexpected toxicity still occurs, often with lasting consequences. Specifically, cardiotoxicity results in cardiac cell death, eventually leading to cardiomyopathy and heart failure...
February 15, 2019: Cardiovascular Research
https://read.qxmd.com/read/30763338/tailored-neoadjuvant-epirubicin-cyclophosphamide-and-nanoparticle-albumin-bound-paclitaxel-for-breast-cancer-the-phase-ii-neonab-trial-clinical-outcomes-and-molecular-determinants-of-response
#2
Caitlin Murphy, Andrea Muscat, David Ashley, Violet Mukaro, Linda West, Yang Liao, David Chisanga, Wei Shi, Ian Collins, Sally Baron-Hay, Sujata Patil, Geoffrey Lindeman, Mustafa Khasraw
BACKGROUND: This study evaluated the feasibility of achieving high response rates in stage II or III breast cancer by tailoring neoadjuvant therapy using clinical and histopathological features and the Oncotype DX Breast Recurrence Score. Genomic determinants of response and resistance were also explored. PATIENTS AND OUTCOME MEASURES: Fifty-one patients were enrolled. The primary cohort comprised 40 patients: 15 human epidermal growth factor receptor type 2 (HER2)-amplified; 15 triple-negative (TNBC); and ten hormone receptor (HR)-positive, HER2-non-amplified tumours; with recurrence scores ≥25...
2019: PloS One
https://read.qxmd.com/read/30759475/-genome-editing-with-crispr-cas9-first-steps-towards-a-new-era-in-medicine
#3
Bernhard Schermer, Thomas Benzing
The emergence of genome editing technologies can be regarded as one of the most groundbreaking revolutions in the history of science. Modern genome editing allows the introduction of precise mutations into the genome of virtually all cells and organisms without leaving any additional trace. Undoubtedly, genome editing with CRISPR/Cas9, often casually referred to as "genetic scissors", will revolutionize medical research and development. However, at the same time it creates a great need for ethical considerations as it might hold risks for both people and the environment that cannot yet be fully assessed...
February 2019: Deutsche Medizinische Wochenschrift
https://read.qxmd.com/read/30746333/male-infertility-precision-medicine-and-systems-proteomics
#4
REVIEW
Niloofar Agharezaee, Mehrdad Hashemi, Minoo Shahani, Kambiz Gilany
Precision medicine (PM) is an approach that has the power to create the best effect and safety of medicine and treatment with the least side effects for each person. PM is very helpful as sometimes due to inaccurate or late diagnosis or toxicities of the drugs irreversible side effect for patient's health are generated. This seemingly new and emerging science is also effective in preventing disease, due to differences in the genes, environment, and lifestyles of any particular person. PM can be a prominent criterion in infertility research...
October 2018: Journal of Reproduction & Infertility
https://read.qxmd.com/read/30742610/how-good-are-pathogenicity-predictors-in-detecting-benign-variants
#5
Abhishek Niroula, Mauno Vihinen
Computational tools are widely used for interpreting variants detected in sequencing projects. The choice of these tools is critical for reliable variant impact interpretation for precision medicine and should be based on systematic performance assessment. The performance of the methods varies widely in different performance assessments, for example due to the contents and sizes of test datasets. To address this issue, we obtained 63,160 common amino acid substitutions (allele frequency ≥1% and <25%) from the Exome Aggregation Consortium (ExAC) database, which contains variants from 60,706 genomes or exomes...
February 11, 2019: PLoS Computational Biology
https://read.qxmd.com/read/30722070/potential-of-multidimensional-large-scale-biodatabases-to-elucidate-coagulation-and-platelet-pathways-as-an-approach-towards-precision-medicine-in-thrombotic-disease
#6
Marina Panova-Noeva, Lisa Eggebrecht, Jürgen H Prochaska, Philipp S Wild
Cardiovascular and especially thrombotic diseases remain a major cause of morbidity and mortality worldwide. In past years, significant improvements in understanding disease processes, risk assessment, and prediction of clinical outcome in the field of thrombosis and haemostasis have been made by using large-scale biodatabases. These important research resources enable a comprehensive research approach by integrating clinical, environmental, genomic, and molecular information. Cutting edge, high throughput technologies open new data dimensions for clinical large-scale investigations...
February 5, 2019: Hämostaseologie
https://read.qxmd.com/read/30720542/the-neurointensive-nursery-concept-development-and-insights-gained
#7
Hannah C Glass, Donna M Ferriero, David H Rowitch, Thomas K Shimotake
PURPOSE OF REVIEW: With the advent of therapeutic hypothermia for treatment of hypoxic ischemic encephalopathy, and improvements in neuroimaging and bedside neuromonitoring, a new era of neonatal brain-focused care has emerged in recent years. We describe the development of the first neurointensive care nursery (NICN) as a model for comanagement of neonates with identified neurologic risk factors by a multidisciplinary team constituted of neurologists, neonatologists, specialized nurses, and others with the goal of optimizing management, preventing secondary injury and maximizing long-term outcomes...
January 31, 2019: Current Opinion in Pediatrics
https://read.qxmd.com/read/30715560/application-of-genetics-and-biotechnology-for-improving-medicinal-plants
#8
REVIEW
Mohsen Niazian
Plant tissue culture has been used for conservation, micropropagation, and in planta overproduction of some pharma molecules of medicinal plants. New biotechnology-based breeding methods such as targeted genome editing methods are able to create custom-designed medicinal plants with different secondary metabolite profiles. For a long time, humans have used medicinal plants for therapeutic purposes and in food and other industries. Classical biotechnology techniques have been exploited in breeding medicinal plants...
February 4, 2019: Planta
https://read.qxmd.com/read/30712512/the-international-conference-on-intelligent-biology-and-medicine-icibm-2018-genomics-with-bigger-data-and-wider-applications
#9
EDITORIAL
Zhijin Wu, Jingwen Yan, Kai Wang, Xiaoming Liu, Yan Guo, Degui Zhi, Jianhua Ruan, Zhongming Zhao
The sixth International Conference on Intelligent Biology and Medicine (ICIBM) took place in Los Angeles, California, USA on June 10-12, 2018. This conference featured eleven regular scientific sessions, four tutorials, one poster session, four keynote talks, and four eminent scholar talks. The scientific program covered a wide range of topics from bench to bedside, including 3D Genome Organization, reconstruction of large scale evolution of genomes and gene functions, artificial intelligence in biological and biomedical fields, and precision medicine...
February 4, 2019: BMC Genomics
https://read.qxmd.com/read/30711678/de-novo-mutations-in-patients-with-chronic-ultra-refractory-epilepsy-with-onset-after-age-five-years
#10
Mark McCormack, Ronan McGinty, Xiaolin Zhu, Lisa Slattery, Erin L Heinzen, Daniel J Costello, Norman Delanty, Gianpiero L Cavalleri
We set out to investigate whether a de-novo paradigm could explain genetic causes of chronic ultra-refractory epilepsy, with onset later than the typical age for the epileptic encephalopathies. We performed exome sequencing on nine adult patients with MRI-negative epilepsy and no preceding intellectual disability. All had an onset of seizures after five years old and had chronic ultra-refractory epilepsy defined here as having failed more than six anti-epileptic drugs and currently experiencing ≥4 disabling seizures per month...
January 31, 2019: European Journal of Medical Genetics
https://read.qxmd.com/read/30704472/comparison-of-different-functional-prediction-scores-using-a-gene-based-permutation-model-for-identifying-cancer-driver-genes
#11
Alice Djotsa Nono, Ken Chen, Xiaoming Liu
BACKGROUND: Identifying cancer driver genes (CDG) is a crucial step in cancer genomic toward the advancement of precision medicine. However, driver gene discovery is a very challenging task because we are not only dealing with huge amount of data; but we are also faced with the complexity of the disease including the heterogeneity of background somatic mutation rate in each cancer patient. It is generally accepted that CDG harbor variants conferring growth advantage in the malignant cell and they are positively selected, which are critical to cancer development; whereas, non-driver genes harbor random mutations with no functional consequence on cancer...
January 31, 2019: BMC Medical Genomics
https://read.qxmd.com/read/30704450/development-of-somatic-mutation-signatures-for-risk-stratification-and-prognosis-in-lung-and-colorectal-adenocarcinomas
#12
Mark Menor, Yong Zhu, Yu Wang, Jicai Zhang, Bin Jiang, Youping Deng
BACKGROUND: Prognostic signatures are vital to precision medicine. However, development of somatic mutation prognostic signatures for cancers remains a challenge. In this study we developed a novel method for discovering somatic mutation based prognostic signatures. RESULTS: Somatic mutation and clinical data for lung adenocarcinoma (LUAD) and colorectal adenocarcinoma (COAD) from The Cancer Genome Atlas (TCGA) were randomly divided into training (n = 328 for LUAD and 286 for COAD) and validation (n = 167 for LUAD and 141 for COAD) datasets...
January 31, 2019: BMC Medical Genomics
https://read.qxmd.com/read/30701196/cancer-prevention-and-screening-the-next-step-in-the-era-of-precision-medicine
#13
REVIEW
Holli A Loomans-Kropp, Asad Umar
A primary mode of cancer prevention and early detection in the United States is the widespread practice of screening. Although many strategies for early detection and prevention are available, adverse outcomes, such as overdiagnosis and overtreatment, are prevalent among those utilizing these approaches. Broad use of mammography and prostate cancer screening are key examples illustrating the potential harms stemming from the detection of indolent lesions and the subsequent overtreatment. Furthermore, there are several cancers for which prevention strategies do not currently exist...
2019: NPJ Precision Oncology
https://read.qxmd.com/read/30697061/precision-medicine-approaches-for-the-management-of-ewing-sarcoma-current-perspectives
#14
Victoria T Rizk, Christine M Walko, Andrew S Brohl
Advancements in molecular and genetic techniques have significantly furthered our biological understanding of Ewing sarcoma (ES). ES is typified by a driving TET-ETS fusion with an otherwise relatively quiet genome. Detection of one of several characteristic fusions, most commonly EWSR1-FLI1 , is the gold standard for diagnosis. We discuss the current role of precision medicine in the diagnosis, treatment, and monitoring of ES. Continued efforts toward molecularly guided approaches are actively being pursued in ES to better refine prognosis, identify germline markers of disease susceptibility, influence therapeutic selection, effectively monitor disease activity in real time, and identify genetic and immunotherapeutic targets for therapeutic development...
2019: Pharmacogenomics and Personalized Medicine
https://read.qxmd.com/read/30696086/machine-learning-and-integrative-analysis-of-biomedical-big-data
#15
REVIEW
Bilal Mirza, Wei Wang, Jie Wang, Howard Choi, Neo Christopher Chung, Peipei Ping
Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies...
January 28, 2019: Genes
https://read.qxmd.com/read/30694442/the-challenge-of-managing-bladder-cancer-and-upper-tract-urothelial-carcinoma-a-review-with-treatment-recommendations-from-the-spanish-oncology-genitourinary-group-sogug
#16
Albert Font, Raquel Luque, José Carlos Villa, Montse Domenech, Sergio Vázquez, Enrique Gallardo, Juan Antonio Virizuela, Carmen Beato, Rafael Morales-Barrera, Antoni Gelabert, Sonia Maciá, Javier Puente, Gustavo Rubio, Xavier Maldonado, Begoña Perez-Valderrama, Alvaro Pinto, Ovidio Fernández Calvo, Enrique Grande, Javier Garde-Noguera, Eva Fernández-Parra, José Ángel Arranz
Bladder cancer is the fourth most common cancer in men and the ninth most common in women in the Western world. The management of bladder carcinoma requires a multidisciplinary approach. Optimal treatment depends on several factors, including histology, stage, patient status, and possible comorbidities. Here we review recent findings on the treatment of muscle-invasive bladder carcinoma, advanced urothelial carcinoma, upper tract urothelial carcinoma, non-urothelial carcinoma, and urologic complications arising from the disease or treatment...
January 29, 2019: Targeted Oncology
https://read.qxmd.com/read/30689846/overview-of-the-biocreative-vi-precision-medicine-track-mining-protein-interactions-and-mutations-for-precision-medicine
#17
Rezarta Islamaj Dogan, Sun Kim, Andrew Chatr-Aryamontri, Chih-Hsuan Wei, Donald C Comeau, Rui Antunes, Sérgio Matos, Qingyu Chen, Aparna Elangovan, Nagesh C Panyam, Karin Verspoor, Hongfang Liu, Yanshan Wang, Zhuang Liu, Berna Altinel, Zehra Melce Hüsünbeyi, Arzucan Özgür, Aris Fergadis, Chen-Kai Wang, Hong-Jie Dai, Tung Tran, Ramakanth Kavuluru, Ling Luo, Albert Steppi, Jinfeng Zhang, Jinchan Qu, Zhiyong Lu
The Precision Medicine Initiative is a multicenter effort aiming at formulating personalized treatments leveraging on individual patient data (clinical, genome sequence and functional genomic data) together with the information in large knowledge bases (KBs) that integrate genome annotation, disease association studies, electronic health records and other data types. The biomedical literature provides a rich foundation for populating these KBs, reporting genetic and molecular interactions that provide the scaffold for the cellular regulatory systems and detailing the influence of genetic variants in these interactions...
January 1, 2019: Database: the Journal of Biological Databases and Curation
https://read.qxmd.com/read/30689737/hipscs-in-cardio-oncology-deciphering-the-genomics
#18
Emily A Pinheiro, K Ashley Fetterman, Paul W Burridge
The genomic predisposition to oncology-drug-induced cardiovascular toxicity has been postulated for many decades. Only recently has it become possible to experimentally validate this hypothesis via the use of patient-specific human induced pluripotent stem cells (hiPSCs) and suitably powered genome-wide association studies (GWAS). Identifying the individual single nucleotide polymorphisms (SNPs) responsible for the susceptibility to toxicity from a specific drug is a daunting task as this precludes the use of one of the most powerful tools in genomics: comparing phenotypes to close relatives, as these are highly unlikely to have been treated with the same drug...
January 24, 2019: Cardiovascular Research
https://read.qxmd.com/read/30689231/whole-genome-sequencing-of-breast-cancer
#19
REVIEW
Maria Rossing, Claus Storgaard Sørensen, Bent Ejlertsen, Finn Cilius Nielsen
Breast cancer was the first to take advantage of targeted therapy using endocrine therapy, and for up to 20% of all breast cancer patients a further significant improvement has been obtained by HER2-targeted therapy. Greater insight in precision medicine is to some extent driven by technical and computational progress, with the first wave of a true technical advancement being the application of transcriptomic analysis. Molecular subtyping further improved our understanding of breast cancer biology and has through a new tumor classification enabled allocation of personalized treatment regimens...
January 28, 2019: APMIS: Acta Pathologica, Microbiologica, et Immunologica Scandinavica
https://read.qxmd.com/read/30687632/the-sick-lobe-hypothesis-field-cancerisation-and-the-new-era-of-precision-breast-surgery
#20
REVIEW
Mona P Tan, Tibor Tot
Understanding the ductal anatomy of the breast provides insights into tumorigenesis, which in turn offers guidance on therapeutic decisions. In this regard, the sick lobe hypothesis, which states that cancer arises from genetically unstable cells through mutations acquired in utero, forms the basis of malignant transformation. These 'at risk' cells line the mammary ductal-lobular system of a single 'sick' lobe and when exposed to noxious events in the surrounding microenvironment, further genetic changes occur which completes conversion to malignancy, in certain defined patterns...
December 2018: Gland Surgery
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