Machine learning in onco-pharmacogenomics: a path to precision medicine with many challenges

Mondello, Alessia; Dal Bo, Michele; Toffoli, Giuseppe; Polano, Maurizio

doi:10.3389/fphar.2023.1260276

Cited by 2 publications

(1 citation statement)

References 238 publications

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“…As the available data have increased, computational analysis approaches in the context of pharmacogenetics have become more sophisticated and geared toward improving outcome reliability and accuracy. To that effect, due to its flexibility, machine learning has been used in the field of pharmacogenetics where the generated complex data structures accumulated are analyzed with the aim of predicting treatment outcomes [ 116 ]. Machine learning approaches have impacted cancer research through their potential for diagnosis and prognosis improvement.…”

Section: Predicting Gut Microbiota–xenobiotic Interactionsmentioning

confidence: 99%

Orally Administered Drugs and Their Complicated Relationship with Our Gastrointestinal Tract

Bashiardes,

Christodoulou

2024

Microorganisms

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Orally administered compounds represent the great majority of all pharmaceutical compounds produced for human use and are the most popular among patients since they are practical and easy to self-administer. Following ingestion, orally administered drugs begin a “perilous” journey down the gastrointestinal tract and their bioavailability is modulated by numerous factors. The gastrointestinal (GI) tract anatomy can modulate drug bioavailability and accounts for interpatient drug response heterogeneity. Furthermore, host genetics is a contributor to drug bioavailability modulation. Importantly, a component of the GI tract that has been gaining notoriety with regard to drug treatment interactions is the gut microbiota, which shares a two-way interaction with pharmaceutical compounds in that they can be influenced by and are able to influence administered drugs. Overall, orally administered drugs are a patient-friendly treatment option. However, during their journey down the GI tract, there are numerous host factors that can modulate drug bioavailability in a patient-specific manner.

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Section: Predicting Gut Microbiota–xenobiotic Interactionsmentioning

confidence: 99%

Orally Administered Drugs and Their Complicated Relationship with Our Gastrointestinal Tract

Bashiardes,

Christodoulou

2024

Microorganisms

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Rare Genetic Developmental Disabilities: Mabry Syndrome (MIM 239300) Index Cases and Glycophosphatidylinositol (GPI) Disorders

Thompson,

Knaus

2024

Genes

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The case report by Mabry et al. (1970) of a family with four children with elevated tissue non-specific alkaline phosphatase, seizures and profound developmental disability, became the basis for phenotyping children with the features that became known as Mabry syndrome. Aside from improvements in the services available to patients and families, however, the diagnosis and treatment of this, and many other developmental disabilities, did not change significantly until the advent of massively parallel sequencing. As more patients with features of the Mabry syndrome were identified, exome and genome sequencing were used to identify the glycophosphatidylinositol (GPI) biosynthesis disorders (GPIBDs) as a group of congenital disorders of glycosylation (CDG). Biallelic variants of the phosphatidylinositol glycan (PIG) biosynthesis, type V (PIGV) gene identified in Mabry syndrome became evidence of the first in a phenotypic series that is numbered HPMRS1-6 in the order of discovery. HPMRS1 [MIM: 239300] is the phenotype resulting from inheritance of biallelic PIGV variants. Similarly, HPMRS2 (MIM 614749), HPMRS5 (MIM 616025) and HPMRS6 (MIM 616809) result from disruption of the PIGO, PIGW and PIGY genes expressed in the endoplasmic reticulum. By contrast, HPMRS3 (MIM 614207) and HPMRS4 (MIM 615716) result from disruption of post attachment to proteins PGAP2 (HPMRS3) and PGAP3 (HPMRS4). The GPI biosynthesis disorders (GPIBDs) are currently numbered GPIBD1-21. Working with Dr. Mabry, in 2020, we were able to use improved laboratory diagnostics to complete the molecular diagnosis of patients he had originally described in 1970. We identified biallelic variants of the PGAP2 gene in the first reported HPMRS patients. We discuss the longevity of the Mabry syndrome index patients in the context of the utility of pyridoxine treatment of seizures and evidence for putative glycolipid storage in patients with HPMRS3. From the perspective of the laboratory innovations made that enabled the identification of the HPMRS phenotype in Dr. Mabry’s patients, the need for treatment innovations that will benefit patients and families affected by developmental disabilities is clear.

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Machine learning in onco-pharmacogenomics: a path to precision medicine with many challenges

Cited by 2 publications

References 238 publications

Orally Administered Drugs and Their Complicated Relationship with Our Gastrointestinal Tract

Orally Administered Drugs and Their Complicated Relationship with Our Gastrointestinal Tract

Rare Genetic Developmental Disabilities: Mabry Syndrome (MIM 239300) Index Cases and Glycophosphatidylinositol (GPI) Disorders

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