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Improving genomics-based predictions for precision medicine through active elicitation of expert knowledge

Iiris Sundin, Tomi Peltola, Luana Micallef, Homayun Afrabandpey, Marta Soare, Muntasir Mamun Majumder, Pedram Daee, Chen He, Baris Serim, Aki Havulinna, Caroline Heckman, Giulio Jacucci (+2 others)
2018 Bioinformatics  
Predicting the efficacy of a drug for a given individual, using high-dimensional genomic measurements, is at the core of precision medicine.  ...  Incorporating expert knowledge offers a promising alternative to improve a prediction model, but collecting such knowledge is laborious to the expert if the number of candidate features is very large.  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/bty257 pmid:29949984 pmcid:PMC6022689 fatcat:auc3lajuprbl5mjxkih2p6m4vq

Regression with n→1 by Expert Knowledge Elicitation

Marta Soare, Muhammad Ammad-Ud-Din, Samuel Kaski
2016 2016 15th IEEE International Conference on Machine Learning and Applications (ICMLA)  
This setup occurs in personalized medicine, for instance, when predicting treatment outcomes for an individual patient based on noisy high-dimensional genomics data.  ...  Experiments on simulated experts, both on synthetic and genomics data, demonstrate that the proposed strategy can drastically improve prediction accuracy.  ...  Then, by simulating a knowledgeable user, we show the potential prediction improvement when using a genomics dataset, relevant for the personalized medicine settings.  ... 
doi:10.1109/icmla.2016.0131 dblp:conf/icmla/SoareAK16 fatcat:lni32fh5d5e77owlju3r5qxg6q

The Future of Precision Medicine: Potential Impacts for Health Technology Assessment

James Love-Koh, Alison Peel, Juan Carlos Rejon-Parilla, Kate Ennis, Rosemary Lovett, Andrea Manca, Anastasia Chalkidou, Hannah Wood, Matthew Taylor
2018 PharmacoEconomics (Auckland)  
Precision medicine allows healthcare interventions to be tailored to groups of patients based on their disease susceptibility, diagnostic or prognostic information, or treatment response.  ...  We analysed what developments are expected in precision medicine over the next decade and considered the implications for health technology assessment (HTA) agencies.  ...  Based Biomarkers Many current precision medicine tools use genetic and genomic information to estimate disease prognosis and predict treatment response [23] .  ... 
doi:10.1007/s40273-018-0686-6 pmid:30003435 pmcid:PMC6244622 fatcat:atfygbfpbjd2ldlebjjbxxvzoq

Knowledge elicitation via sequential probabilistic inference for high-dimensional prediction

Pedram Daee, Tomi Peltola, Marta Soare, Samuel Kaski
2017 Machine Learning  
We formulate knowledge elicitation generally as a probabilistic inference process, where expert knowledge is sequentially queried to improve predictions.  ...  Evaluations of our method in experiments with simulated and real users show improved prediction accuracy already with a small effort from the expert.  ...  Acknowledgements This work was financially supported by the Academy of Finland (Finnish Center of  ... 
doi:10.1007/s10994-017-5651-7 fatcat:bswdrak4m5hpnlouzhb4pwffny

Development of an implementation and evaluation strategy for the Australian 'Zero Childhood Cancer' (Zero) Program: a study protocol

Frances Rapport, James Smith, Tracey A O'Brien, Vanessa J Tyrrell, Emily VA Mould, Janet C Long, Hossai Gul, Jeffrey Braithwaite
2020 BMJ Open  
The aim of this study is to assess the 'Zero Childhood Cancer Personalised Medicine Program' (the Zero Program), an Australian first-ever and most comprehensive personalised medicine programme for children  ...  A repeat of the social network analysis downstream will examine network changes over time, followed by an expert panel using the expert recommendations for implementing change to assess the integration  ...  ) to plan, predict, guide and evaluate the process of implementation of precision medicine programmes. 9 owever, a recent review demonstrated that fewer than 2% of studies aiming to translate genomic  ... 
doi:10.1136/bmjopen-2019-034522 pmid:32580982 fatcat:nw37h23tuzf3diijsbroj46bxq

The "GEnomics of Musculo Skeletal Traits TranslatiOnal NEtwork": Origins, Rationale, Organization, and Prospects

Fjorda Koromani, Nerea Alonso, Ines Alves, Maria Luisa Brandi, Ines Foessl, Melissa M. Formosa, Milana Frenkel Morgenstern, David Karasik, Mikhail Kolev, Outi Makitie, Evangelia Ntzani, Barbara Obermayer Pietsch (+7 others)
2021 Frontiers in Endocrinology  
candidates responsible for monogenic presentations, through biological plausibility.  ...  and/or improve study design of future investigations in a potential therapeutic context (e.g. clinical trials) for musculoskeletal diseases.  ...  ACKNOWLEDGMENTS This publication is based upon work from COST Action GEMSTONE, supported by COST (European Cooperation in Science and Technology).  ... 
doi:10.3389/fendo.2021.709815 pmid:34484122 pmcid:PMC8415473 fatcat:e7m7lewpc5drtmtpuem53xzxry

Text and data mining for biomedical discovery

Graciela Gonzalez, Kevin Bretonnel Cohen, Casey S Greene, Udo Hahn, Maricel G Kann, Robert Leaman, Nigam Shah, Jieping Ye
2013 Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  
), as well as an integrative approach that combines data from genetic (SNP) and transcriptomic (microarray) sources for clinical prediction.  ...  detecting the catalytic sites in proteins in the biomedical literature, and a method for automatically extending a taxonomy of health-related terms to integrate consumer-friendly synonyms for medical  ...  Methods capable of connecting measurements of the genome to measurements of transcript and protein abundance for prediction of a clinically relevant phenotype are expected to play a key role in precision  ... 
pmid:23424141 pmcid:PMC6230431 fatcat:3on3xcf3wvgsfm66e4xns4ycdy

Unraveling the Ethical, Legal, and Social Implications of Neurobiobanking and Stroke Genomic Research in Africa: A Study Protocol of the African Neurobiobank for Precision Stroke Medicine ELSI Project

Rufus O. Akinyemi, Carolyn Jenkins, Michelle Nichols, Arti Singh, Kolawole Wahab, Albert Akpalu, Fred S. Sarfo, Lukman F. Owolabi, Reginald Obiako, Joshua Akinyemi, Babatunde Ojebuyi, Muyiwa Adigun (+22 others)
2020 International Journal of Qualitative Methods  
The overarching goal of the African Neurobiobank for Precision Stroke Medicine–—ELSI Project is to identify, examine, and develop novel approaches to address ELSI issues of biobanking and stroke genomic  ...  The huge potential for neurobiobanking and genomics research in Africa to advance precision medicine applicable to stroke and other neurological disorders requires addressing ELSI challenges while building  ...  After the training, the project will facilitate continued support and institutionalized mentoring of the ECRs through the Centre for Genomic and Precision Medicine at the College of Medicine, University  ... 
doi:10.1177/1609406920923194 fatcat:pfuq3cubojhyhalyus7u4uj6y4

Disaggregating asthma: Big investigation versus big data

Danielle Belgrave, John Henderson, Angela Simpson, Iain Buchan, Christopher Bishop, Adnan Custovic
2017 Journal of Allergy and Clinical Immunology  
Full terms of use are available: We are facing a major challenge in bridging the gap between identifying subtypes of asthma to understand causal mechanisms and translating this knowledge into personalized  ...  One of the dangers of ready accessibility of health care data and computational tools for data analysis is that the process of data mining can become uncoupled from the scientific process of clinical interpretation  ...  nonatopic wheezing. 42 This suggests that replication of gene-environment interactions can be improved through a more precise definition of the outcome of interest. 43 The lessons for intervention  ... 
doi:10.1016/j.jaci.2016.11.003 pmid:27871876 pmcid:PMC5292995 fatcat:v4kxb7yrajdr3f4ptezhicbjlm

TEXT AND DATA MINING FOR BIOMEDICAL DISCOVERY

GRACIELA GONZALEZ, KEVIN BRETONNEL COHEN, CASEY S. GREENE, UDO HAHN, MARICEL G. KANN, ROBERT LEAMAN, NIGAM SHAH, JIEPING YE
2012 Biocomputing 2013  
), as well as an integrative approach that combines data from genetic (SNP) and transcriptomic (microarray) sources for clinical prediction.  ...  Work presented in this session includes data mining techniques applied to the discovery of 3-way genetic interactions and to the analysis of genetic data in the context of electronic medical records (EMRs  ...  Methods capable of connecting measurements of the genome to measurements of transcript and protein abundance for prediction of a clinically relevant phenotype are expected to play a key role in precision  ... 
doi:10.1142/9789814447973_0036 fatcat:f522y2grifc6xeh7hs245doscy

Attitudes toward Genomics and Precision Medicine

James M. DuBois, Jessica Mozersky, Alison Antes, Tammy English, Meredith V. Parsons, Kari Baldwin
2021 Journal of Clinical and Translational Science  
and genome editing - activities necessary to achieve the goals of precision medicine.  ...  The AGPM will be useful for researchers who want to explore attitudes toward genomics and precision medicine.  ...  overall level of concern with six genomic and precision medicine activities.  ... 
doi:10.1017/cts.2021.774 pmid:34267947 pmcid:PMC8278159 fatcat:2dkbdybqz5bt5iqg3nn5lkzpqu

Application of Machine Learning in Translational Medicine: Current Status and Future Opportunities

Nadia Terranova, Karthik Venkatakrishnan, Lisa J. Benincosa
2021 AAPS Journal  
and Precision Medicine.  ...  Patient-centered iterative forward and reverse translation is at the heart of precision medicine discovery and development across the continuum from target validation to optimization of pharmacotherapy  ...  Use cases accommodate predictions for specific cancer types based on a variety of genomic and systemic datasets fed into a support vector machine (SVM) classifier and then target validation through inhibition  ... 
doi:10.1208/s12248-021-00593-x pmid:34008139 pmcid:PMC8130984 fatcat:4bkqmfkebjhhjnzy5modwbplda

Translating New Science Into the Drug Review Process

Rodney Rouse, Naomi Kruhlak, James Weaver, Keith Burkhart, Vikram Patel, David G. Strauss
2017 Therapeutic Innovation and Regulatory Science  
antibiotics; and precision medicine.  ...  review issues and for longer-range projects requiring the development of predictive models, tools, and biomarkers to speed the development and regulatory evaluation of safe and effective drugs.  ...  knowledge bases and predictive models.  ... 
doi:10.1177/2168479017720249 pmid:29568713 pmcid:PMC5844453 fatcat:z5qpiykjsfaatbshjer3xfgo6u

SMART Work Design: Accelerating the Diagnosis of Rare Diseases in the Western Australian Undiagnosed Diseases Program

Georgia J Hay, Florian E Klonek, Cati S Thomas, Alicia Bauskis, Gareth Baynam, Sharon K Parker
2020 Frontiers in Pediatrics  
from other fields and to take full advantage of cutting-edge precision medicine technologies and precision public health approaches.  ...  Based on the effectiveness of UDP-WA and its SMART design, we provide a framework that clinicians, healthcare managers, and policymakers can consider when they re-design work so that they can create SMART  ...  Further, improving work structures is a critical element of sustainably implementing new (precision medicine) technologies, including through an equitable lens for those that need them the most, and for  ... 
doi:10.3389/fped.2020.00582 pmid:33072663 pmcid:PMC7530738 fatcat:injc7f2bsrcbhhys2sj5zuodjm

The fuzzy world of precision medicine: deliberations of a precision medicine tumor board

Sarah A McGraw, Judy Garber, Pasi A Jänne, Neal Lindeman, Nelly Oliver, Lynette M Sholl, Eliezer M Van Allen, Nikhil Wagle, Levi A Garraway, Steven Joffe, Stacy W Gray
2017 Personalized Medicine  
Aim: To understand how a cancer precision medicine tumor board (CPM-TB) made choices about return of results.  ...  Members had concerns both about potential harms due to returning results based on weak evidence and about withholding potentially meaningful results.  ...  As the knowledge of genomics evolves, precision medicine in cancer care will become more evidencebased.  ... 
doi:10.2217/pme-2016-0074 pmid:28757884 pmcid:PMC5480788 fatcat:hfjjb5ymtfbajnzso3vuncz2xq
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