Literature DB >> 33530326

Towards a Precision Medicine Approach Based on Machine Learning for Tailoring Medical Treatment in Alkaptonuria.

Ottavia Spiga1, Vittoria Cicaloni2, Anna Visibelli1, Alessandro Davoli3, Maria Ausilia Paparo3, Maurizio Orlandini1, Barbara Vecchi3, Annalisa Santucci1.   

Abstract

ApreciseKUre is a multi-purpose digital platform facilitating data collection, integration and analysis for patients affected by Alkaptonuria (AKU), an ultra-rare autosomal recessive genetic disease. It includes genetic, biochemical, histopathological, clinical, therapeutic resources and quality of life scores that can be shared among registered researchers and clinicians in order to create a Precision Medicine Ecosystem (PME). The combination of machine learning application to analyse and re-interpret data available in the ApreciseKUre shows the potential direct benefits to achieve patient stratification and the consequent tailoring of care and treatments to a specific subgroup of patients. In this study, we have developed a tool able to investigate the most suitable treatment for AKU patients in accordance with their Quality of Life scores, which indicates changes in health status before/after the assumption of a specific class of drugs. This fact highlights the necessity of development of patient databases for rare diseases, like ApreciseKUre. We believe this is not limited to the study of AKU, but it represents a proof of principle study that could be applied to other rare diseases, allowing data management, analysis, and interpretation.

Entities:  

Keywords:  QoL scores; alkaptonuria; data analysis; machine learning; precision medicine; rare disease

Mesh:

Year:  2021        PMID: 33530326      PMCID: PMC7865235          DOI: 10.3390/ijms22031187

Source DB:  PubMed          Journal:  Int J Mol Sci        ISSN: 1422-0067            Impact factor:   5.923


  22 in total

1.  Homogentisate 1,2-dioxygenase (HGD) gene variants, their analysis and genotype-phenotype correlations in the largest cohort of patients with AKU.

Authors:  David B Ascher; Ottavia Spiga; Martina Sekelska; Douglas E V Pires; Andrea Bernini; Monica Tiezzi; Jana Kralovicova; Ivana Borovska; Andrea Soltysova; Birgitta Olsson; Silvia Galderisi; Vittoria Cicaloni; Lakshminarayan Ranganath; Annalisa Santucci; Andrea Zatkova
Journal:  Eur J Hum Genet       Date:  2019-02-08       Impact factor: 4.246

2.  Histological and Ultrastructural Characterization of Alkaptonuric Tissues.

Authors:  Lia Millucci; Giulia Bernardini; Adriano Spreafico; Maurizio Orlandini; Daniela Braconi; Marcella Laschi; Michela Geminiani; Pietro Lupetti; Giovanna Giorgetti; Cecilia Viti; Bruno Frediani; Barbara Marzocchi; Annalisa Santucci
Journal:  Calcif Tissue Int       Date:  2017-03-07       Impact factor: 4.333

3.  A new integrated and interactive tool applicable to inborn errors of metabolism: Application to alkaptonuria.

Authors:  Ottavia Spiga; Vittoria Cicaloni; Andrea Zatkova; Lia Millucci; Giulia Bernardini; Andrea Bernini; Barbara Marzocchi; Monica Bianchini; Andrea Zugarini; Alberto Rossi; Matteo Zazzeri; Alfonso Trezza; Bruno Frediani; Lakshminarayan Ranganath; Daniela Braconi; Annalisa Santucci
Journal:  Comput Biol Med       Date:  2018-10-05       Impact factor: 4.589

4.  Twelve novel HGD gene variants identified in 99 alkaptonuria patients: focus on 'black bone disease' in Italy.

Authors:  Martina Nemethova; Jan Radvanszky; Ludevit Kadasi; David B Ascher; Douglas E V Pires; Tom L Blundell; Berardino Porfirio; Alessandro Mannoni; Annalisa Santucci; Lia Milucci; Silvia Sestini; Gianfranco Biolcati; Fiammetta Sorge; Caterina Aurizi; Robert Aquaron; Mohammed Alsbou; Charles Marques Lourenço; Kanakasabapathi Ramadevi; Lakshminarayan R Ranganath; James A Gallagher; Christa van Kan; Anthony K Hall; Birgitta Olsson; Nicolas Sireau; Hana Ayoob; Oliver G Timmis; Kim-Hanh Le Quan Sang; Federica Genovese; Richard Imrich; Jozef Rovensky; Rangan Srinivasaraghavan; Shruthi K Bharadwaj; Ronen Spiegel; Andrea Zatkova
Journal:  Eur J Hum Genet       Date:  2015-03-25       Impact factor: 4.246

5.  Interactive alkaptonuria database: investigating clinical data to improve patient care in a rare disease.

Authors:  Vittoria Cicaloni; Ottavia Spiga; Giovanna Maria Dimitri; Rebecca Maiocchi; Lia Millucci; Daniela Giustarini; Giulia Bernardini; Andrea Bernini; Barbara Marzocchi; Daniela Braconi; Annalisa Santucci
Journal:  FASEB J       Date:  2019-08-28       Impact factor: 5.834

Review 6.  Ten quick tips for machine learning in computational biology.

Authors:  Davide Chicco
Journal:  BioData Min       Date:  2017-12-08       Impact factor: 2.522

7.  ApreciseKUre: an approach of Precision Medicine in a Rare Disease.

Authors:  Ottavia Spiga; Vittoria Cicaloni; Andrea Bernini; Andrea Zatkova; Annalisa Santucci
Journal:  BMC Med Inform Decis Mak       Date:  2017-04-14       Impact factor: 2.796

8.  Machine learning application for development of a data-driven predictive model able to investigate quality of life scores in a rare disease.

Authors:  Ottavia Spiga; Vittoria Cicaloni; Cosimo Fiorini; Alfonso Trezza; Anna Visibelli; Lia Millucci; Giulia Bernardini; Andrea Bernini; Barbara Marzocchi; Daniela Braconi; Filippo Prischi; Annalisa Santucci
Journal:  Orphanet J Rare Dis       Date:  2020-02-12       Impact factor: 4.123

9.  Alkaptonuria is a novel human secondary amyloidogenic disease.

Authors:  Lia Millucci; Adriano Spreafico; Laura Tinti; Daniela Braconi; Lorenzo Ghezzi; Eugenio Paccagnini; Giulia Bernardini; Loredana Amato; Marcella Laschi; Enrico Selvi; Mauro Galeazzi; Alessandro Mannoni; Maurizio Benucci; Pietro Lupetti; Federico Chellini; Maurizio Orlandini; Annalisa Santucci
Journal:  Biochim Biophys Acta       Date:  2012-07-28

10.  The advantages of the Matthews correlation coefficient (MCC) over F1 score and accuracy in binary classification evaluation.

Authors:  Davide Chicco; Giuseppe Jurman
Journal:  BMC Genomics       Date:  2020-01-02       Impact factor: 3.969

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