Software tools to use pharmacogenetic information for precision medicine- Group 1
by Oscar Perez
1. WfG - Watson for Genomics
1.1. An Artificial intelligence software that analyzes and categorizes genetics alterations related to disease progression in hematological patients. It provides potential therapeutic options at the rate of 3 minutes per sample.
2. Companies working on developing precision medicine software
2.1. Clinical trial matching
2.1.1. 2bPrecise
2.2. Web-based tool
2.2.1. Syapse
2.2.2. PrecisionFDA
2.3. AI-driven software
2.3.1. Fabric Genomics
2.3.2. SOPHiA
2.3.3. Human Longevity Inc
3. CGDnet - Cancer Drug Gene Network
3.1. Allows to look at biomarkers or targets which are downstream of oncogenes and is personalized for patients which is done through cancer type and molecular alterations
4. PHARMGKB - Clinical Pharmacogenetics Database
4.1. Diverse array of Pharmacogenomics information - contains annotations, primary literature and guidelines for adjusting doses based on genetic information
5. Human Protein Atlas
5.1. Consortium devloping specific antibodies against every protein encoded in the human genome. Antibodies are then used to determine the cellular location of every protein in cells of human tissue.
6. NCBI - National Center for Biotechnology Information
6.1. The SPDI data model at NCBI defines variants attributing to sequence, position, deletion and insertion of nucleotides and proteins. SPDI aggregates variants in order to clarify genetic basis of disease and biological function.
7. NCI - National Cancer Institute
7.1. The Genomic Data Commons has an information system for storing, analyzing and sharing raw genomic and clinical data from cancer patients. Data is continuously analyzed in order to be used for all NCI cancer genomics projects.
8. CPIC - Clinical Pharmacogenetics Implementation Consortium
8.1. Allows the prescription of drugs through evidence based translation of genetic laboratory test results
9. dbSNP - Single Nucleotide Polymorphism Database
9.1. Collection of all known single nucleotide polymorphisms, including small changes that involve more than one nucleotide and less than 50.
10. Uniprot - Protein Database
10.1. The UniProt knowledgebase is a large resource of protein sequences and associated detailed annotation. The database contains over 60 million sequences, of which over half a million sequences have been curated by experts who critically review experimental and predicted data for each protein.
11. PreMedKB -Precision Medicine Knowledgebase
11.1. Allows to search each of the 4 components of precision medicine : Drug, Variant, Gene and Disease. Also shows the relationships of one or more of those components
12. Difficulties applying Precision Medicine
12.1. Lack of 'open source' molecular medicine global knowledge network
12.1.1. Protecting patient information
12.1.2. Requires patient education and consent
12.2. Collection of Patient Samples
12.3. Introduction of new biomarkers
12.3.1. Multiple single biomarker tests become unfeasible
12.3.1.1. Need development of next-generation sequencing technologies such as new assays for multiple biomarkers