Andreas Halman
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View article: Protocol for Bayesian combined multi-genotype and concentration informed tacrolimus dosing in paediatric solid organ transplantation (BRUNO-PIC)
Protocol for Bayesian combined multi-genotype and concentration informed tacrolimus dosing in paediatric solid organ transplantation (BRUNO-PIC) Open
Introduction Tacrolimus is an immunosuppressant used extensively in solid organ transplantation. Whilst highly effective in preventing organ rejection, it has a narrow range of safe and effective concentrations and wide pharmacokinetic var…
View article: Frequency and Implications of High‐Risk Pharmacogenomic Phenotypes Identified in a Diverse Australian Pediatric Oncology Cohort
Frequency and Implications of High‐Risk Pharmacogenomic Phenotypes Identified in a Diverse Australian Pediatric Oncology Cohort Open
Pharmacogenomics remains underutilized in pediatric oncology, despite the existence of evidence‐based guidelines. Implementation of pharmacogenomics‐informed prescribing could improve medication safety and efficacy in pediatric oncology pa…
View article: Phenoconversion of <i>CYP3A4</i>, <i>CYP2C19</i> and <i>CYP2D6</i> in Pediatrics, Adolescents and Young Adults With Lymphoma: Rationale and Design of the <scp>PEGASUS</scp> Study
Phenoconversion of <i>CYP3A4</i>, <i>CYP2C19</i> and <i>CYP2D6</i> in Pediatrics, Adolescents and Young Adults With Lymphoma: Rationale and Design of the <span>PEGASUS</span> Study Open
Phenoconversion is the discrepancy between genotype‐predicted phenotype and clinical phenotype, due to nongenetic factors. In oncology patients, the impact of phenoconversion on drug selection, efficacy, toxicity, and treatment outcomes is…
View article: Long-Term Mental Health and Wellbeing Outcomes Associated with Naturalistic Ayahuasca Consumption
Long-Term Mental Health and Wellbeing Outcomes Associated with Naturalistic Ayahuasca Consumption Open
The durability of ayahuasca's effects on mental health and the influence of clinical diagnoses on therapeutic response is unclear. Adults with no prior exposure to ayahuasca (n = 66) participating in neo-shamanic ayahuasca ceremonies compl…
View article: <scp>BCyrius</scp>: An Upgraded Version of Cyrius for Accurate <scp>CYP2D6</scp> Genotyping From Short‐Read Sequencing Data
<span>BCyrius</span>: An Upgraded Version of Cyrius for Accurate <span>CYP2D6</span> Genotyping From Short‐Read Sequencing Data Open
Pharmacogenomics is a field of personalized medicine that aims to tailor drug dosing based on the genetics of an individual. The polymorphic and complex CYP2D6 gene is important to analyze because of its role in the metabolism of approxima…
View article: <i>CYP2D6</i> genotype and associated 5‐<scp>HT<sub>3</sub></scp> receptor antagonist outcomes: A systematic review and meta‐analysis
<i>CYP2D6</i> genotype and associated 5‐<span>HT<sub>3</sub></span> receptor antagonist outcomes: A systematic review and meta‐analysis Open
5‐hydroxytryptamine‐3 (5‐HT 3 ) receptor antagonists including ondansetron, tropisetron, dolasetron, palonosetron, granisetron, and ramosetron are commonly used to prevent and treat nausea and vomiting. Most of these medications are at lea…
View article: Analysis of Tandem Repeats in Short‐Read Sequencing Data: From Genotyping Known Pathogenic Repeats to Discovering Novel Expansions
Analysis of Tandem Repeats in Short‐Read Sequencing Data: From Genotyping Known Pathogenic Repeats to Discovering Novel Expansions Open
Short tandem repeats (STRs) and variable‐number tandem repeats (VNTRs) are repetitive genomic sequences seen widely throughout the genome. These repeat expansions are currently known to cause ∼60 diseases, with expansions in new loci linke…
View article: Harnessing Pharmacogenomics in Clinical Research on Psychedelic‐Assisted Therapy
Harnessing Pharmacogenomics in Clinical Research on Psychedelic‐Assisted Therapy Open
Psychedelics have recently re‐emerged as potential treatments for various psychiatric conditions that impose major public health costs and for which current treatment options have limited efficacy. At the same time, personalized medicine i…
View article: Artificial intelligence and psychedelic medicine
Artificial intelligence and psychedelic medicine Open
Artificial intelligence (AI) and psychedelic medicines are among the most high‐profile evolving disruptive innovations within mental healthcare in recent years. Although AI and psychedelics may not have historically shared any common groun…
View article: Benchmarking pharmacogenomics genotyping tools: Performance analysis on short‐read sequencing samples and depth‐dependent evaluation
Benchmarking pharmacogenomics genotyping tools: Performance analysis on short‐read sequencing samples and depth‐dependent evaluation Open
Pharmacogenomics (PGx) investigates the influence of genetics on drug responses, enabling tailored treatments for personalized healthcare. This study assessed the accuracy of genotyping six genes using whole genome sequencing with four dif…
View article: Protocol for a prospective feasibility study investigating phenoconversion of<i>CYP3A4</i>,<i>CYP2C19</i>and<i>CYP2D6</i>genotypes in paediatric and adolescent and young adult patients with an acute diagnosis of Hodgkin or Non-Hodgkin Lymphoma [PEGASUS]
Protocol for a prospective feasibility study investigating phenoconversion of<i>CYP3A4</i>,<i>CYP2C19</i>and<i>CYP2D6</i>genotypes in paediatric and adolescent and young adult patients with an acute diagnosis of Hodgkin or Non-Hodgkin Lymphoma [PEGASUS] Open
Introduction Phenoconversion is the discrepancy between the predicted phenotype based on genotyping (genotype-based phenotype) and the actual phenotype influenced by non-genetic factors (clinical phenotype). Despite its potential impact on…
View article: Pharmacogenomic studies of fertility outcomes in pediatric cancer survivors – A systematic review
Pharmacogenomic studies of fertility outcomes in pediatric cancer survivors – A systematic review Open
For the same age, sex, and dosage, there can be significant variation in fertility outcomes in childhood cancer survivors. Genetics may explain this variation. This study aims to: (i) review the genetic contributions to infertility, (ii) s…
View article: Minimising Adverse Drug Reactions and Verifying Economic Legitimacy-Pharmacogenomics Implementation in Children (MARVEL- PIC): protocol for a national randomised controlled trial of pharmacogenomics implementation
Minimising Adverse Drug Reactions and Verifying Economic Legitimacy-Pharmacogenomics Implementation in Children (MARVEL- PIC): protocol for a national randomised controlled trial of pharmacogenomics implementation Open
Introduction DNA-informed prescribing (termed pharmacogenomics, PGx) is the epitome of personalised medicine. Despite international guidelines existing, its implementation in paediatric oncology remains sparse. Methods and analysis Minimis…
View article: Drug–drug interactions involving classic psychedelics: A systematic review
Drug–drug interactions involving classic psychedelics: A systematic review Open
Classic psychedelics, including lysergic acid diethylamide (LSD), psilocybin, mescaline, N,N-dimethyltryptamine (DMT) and 5-methoxy-N,N-dimethyltryptamine (5-MeO-DMT), are potent psychoactive substances that have been studied for their phy…
View article: Ayahuasca: A review of historical, pharmacological, and therapeutic aspects
Ayahuasca: A review of historical, pharmacological, and therapeutic aspects Open
Ayahuasca is a psychedelic plant brew originating from the Amazon rainforest. It is formed from two basic components, the Banisteriopsis caapi vine and a plant containing the potent psychedelic dimethyltryptamine (DMT), usually Psychotria …
View article: Catchii: Empowering literature review screening in healthcare
Catchii: Empowering literature review screening in healthcare Open
A systematic review is a type of literature review that aims to collect and analyse all available evidence from the literature on a particular topic. The process of screening and identifying eligible articles from the vast amounts of liter…
View article: Drug-drug interactions between classic psychedelics and psychoactive drugs: a systematic review
Drug-drug interactions between classic psychedelics and psychoactive drugs: a systematic review Open
Classic psychedelics, lysergic acid diethylamide, psilocybin, mescaline and N,N-dimethyltryptamine, are potent psychoactive substances that have been studied for their physiological and psychological effects. However, our understanding of …
View article: Ayahuasca – a review of historical, pharmacological, and therapeutic aspects
Ayahuasca – a review of historical, pharmacological, and therapeutic aspects Open
Ayahuasca is a psychedelic plant brew originating from the Amazon Rainforest. It is formed from two basic components, the Banisteriopsis caapi vine, and a plant containing the potent psychedelic dimethyltryptamine (DMT), usually Psychotria…
View article: Catchii: empowering literature review screening in healthcare
Catchii: empowering literature review screening in healthcare Open
A systematic review is a type of literature review that aims to collect and analyse all available evidence from the literature on a particular topic. The process of screening and identifying eligible articles from the vast amounts of liter…
View article: Records used to compare duplicate detection of three systematic review screener tools
Records used to compare duplicate detection of three systematic review screener tools Open
This upload contains records obtained from PubMed, Scopus and Web of Science that were used to compare the sensitivity of the duplicate detection systems of three systematic review screening tools, as well as a custom-made dataset to evalu…
View article: Records used to compare duplicate detection of three systematic review screener tools
Records used to compare duplicate detection of three systematic review screener tools Open
This upload contains records obtained from PubMed, Scopus and Web of Science that were used to compare the sensitivity of the duplicate detection systems of three systematic review screening tools, as well as a custom-made dataset to evalu…
View article: Toblerone: detecting exon deletion events in cancer using RNA-seq
Toblerone: detecting exon deletion events in cancer using RNA-seq Open
Cancer is driven by mutations of the genome that can result in the activation of oncogenes or repression of tumour suppressor genes. In acute lymphoblastic leukemia (ALL) focal deletions in IKAROS family zinc finger 1 (IKZF1) result in the…
View article: Toblerone: detecting exon deletion events in cancer using RNA-seq
Toblerone: detecting exon deletion events in cancer using RNA-seq Open
Cancer is driven by mutations of the genome that can result in the activation of oncogenes or repression of tumour suppressor genes. In acute lymphoblastic leukemia (ALL) focal deletions in IKAROS family zinc finger 1 (IKZF1) result in the…
View article: REViewer: haplotype-resolved visualization of read alignments in and around tandem repeats
REViewer: haplotype-resolved visualization of read alignments in and around tandem repeats Open
Background Expansions of short tandem repeats are the cause of many neurogenetic disorders including familial amyotrophic lateral sclerosis, Huntington disease, and many others. Multiple methods have been recently developed that can identi…
View article: STRipy: A graphical application for enhanced genotyping of pathogenic short tandem repeats in sequencing data
STRipy: A graphical application for enhanced genotyping of pathogenic short tandem repeats in sequencing data Open
Expansions of short tandem repeats (STRs) have been implicated as the causal variant in over 50 diseases known to date. There are several tools which can genotype STRs from high-throughput sequencing (HTS) data. However, running these tool…
View article: Additional file 2 of REViewer: haplotype-resolved visualization of read alignments in and around tandem repeats
Additional file 2 of REViewer: haplotype-resolved visualization of read alignments in and around tandem repeats Open
Additional file 2: Table S1. A description of 133 repeats used for the concordance study. Each row describes the basic sample/repeat information (columns Sample, Sex, Locus), repeat size estimated by PCR and EH (columns PCR_short, PCR_long…