Showing posts with label pharmcat. Show all posts
Showing posts with label pharmcat. Show all posts

Monday, March 18, 2024

PharmCAT Tutorial Videos Now Available on YouTube

Pharmacogenomics Clinical Annotation Tool (PharmCAT) tutorial videos are now available on the PharmGKB YouTube channel. The tutorial videos provide clear, step-by-step instructions for running PharmCAT from command lines. By providing genotype-based drug prescribing recommendations, we hope to engage the wider genomics community and create a standard for the use in precision medicine.

The first two videos cover (1) the introduction to PharmCAT, modules, and reports and (2) a hands-on example that walks you through the setup and commands for running PharmCAT.

Future videos will cover how to supply external pharmacogenomic calls to PharmCAT, how to use ‘Research’ modes, how to use the PharmCAT functionalities for biobank-scale analyses, and more.
 
More information about PharmCAT can be found at https://pharmcat.org/. To follow PharmCAT, subscribe to the PharmGKB YouTube channel for new videos or the PharmCAT mailing list for the latest PharmCAT updates.

If you have questions regarding PharmCAT, please contact us at pharmcat@pharmgkb.org.

Thursday, February 29, 2024

ClinPGx 2024 Registration and Abstract Submission Open

 

REGISTRATION OPEN

In collaboration with CPIC, PharmGKB, PharmCAT and PharmVar, the Penn Institute for Biomedical Informatics will be hosting the ClinPGx 2024: Knowledge, Implementation, Education meeting on June 20th and 21st, 2024 in Philadelphia, PA. This meeting will provide educational content to cover all aspects of PGx implementation, including knowledgebases, implementation strategy, informatics, use of AI in precision medicine, clinical laboratory insights, and more.

Participants are invited to submit abstracts for the poster sessions. You must be registered for the meeting before your abstract will be accepted.

Please note breakfast & lunch will be provided all conference days.


Registration and detailed agenda


REMINDERS / DEADLINES:

March 22, 2024: Deadline for Abstract Submission. Abstract submission form link here.

April 30, 2024: Deadline for $350 Registration Fee (Starting May 1st, registration fee will be $450)

May 20, 2024: Deadline for Hotel Reservations. Click HERE for hotels offering special rates.

June 1, 2024: Deadline to register for the event.




Thursday, October 20, 2022

PharmCAT Version 2.0 Released

Version 2.0 of the Pharmacogenomics Clinical Annotation Tool (PharmCAT) has been released October 20, 2022. PharmCAT is a software tool that takes the genetic data (VCF file) of an individual as input, interprets the pharmacogene alleles, diplotypes, and phenotypes, and generates a report with genotype-based drug prescribing recommendations. 

In version 2.0, we have made substantial improvements and changes to the tool based in part on user feedback. Below we outline these features and provide links to read more about each one. We have also slightly reorganized and expanded the documentation found on the PharmCAT website to better support users. 

We hope you will take a look and send any comments, questions or feedback to pharmcat@pharmgkb.org. 

Major PharmCAT v2.0 features:
  • PharmCAT now includes available DPWG prescribing guidance (as annotated in the PharmGKB DB) in addition to CPIC recommendations. Read more about the genes and drugs included from DPWG and how they are sourced 
  • PharmCAT report has been redesigned for multiple recommendation sources 
  • Added functionality for research use only 
    • CYP2D6 diplotype calling based on SNPs and INDELs from a VCF file (does not include structural variants/CNVs). Warning: Because structural variation and haplotype can’t be determined from VCF, this functionality shouldn’t be used for clinical purposes. 
    • Partial and combination calls for novel combinations of PGx positions included in the PharmCAT allele definitions. This functionality helps users determine if a sample potentially contains a novel allele. 
  • Added support for the DPYD genotype based on the lowest activity score as described in CPIC’s fluoropyrimidine guideline (PMID: 29152729) for samples with more than two DPYD variants.
  • Extended support of external genotype/phenotype input (see input and output examples and outside call format). This functionality allows users to include genetic test results from other sources in PharmCAT’s report. 
  • Reworked PharmCAT command line tool/arguments. These changes are not backwards compatible with previous PharmCAT versions. 
  • VCF Preprocessor updates 
    • Harmonized the VCF preprocessor command line arguments and flags with PharmCAT
    • Unified the output file name patterns of the VCF preprocessor with what PharmCAT uses
    • Added a few amenities, e.g., bcftools and bgzip version check, switch to .bgz file suffix for clarity 
 The latest PharmCAT version and extensive documentation is available on PharmCAT.org

Wednesday, December 1, 2021

Please help secure funding for PGx!!

The ability to predict ahead of time which drugs will be effective for a unique patient and determine which medications may cause patients serious issues, will save lives, improve health care outcomes, and decrease health care costs. Several genes in the human genome play a role in how people respond to medications, including how effective they will be, how quickly medication will be metabolized, and whether a person is likely to experience side effects from a particular drug. A person’s response to a medication, therefore, is impacted by the genetic variants in their those genes.

 

Pharmacogenomic testing evaluates an individual’s genetic makeup to help identify which medication and which dose is right for each patient and hopefully, prevent an adverse drug reaction. Adverse drug events (ADEs) are the most frequently cited significant cause of injury and death among hospitalized patients and can be the result of a drug-drug or drug-gene interaction. Pharmacogenomic testing can save lives by preventing ADEs. According to one estimation, there are more than 2,216,000 serious ADEs recorded in hospitalized patients every year, causing over 106,000 deaths annually, which makes ADEs the fourth leading cause of death ahead of pulmonary disease, diabetes, AIDS, pneumonia, accidents, and automobile deaths.

 

In addition, information about drug-gene interactions is not well integrated in patient care and tools that assist with patient care, like electronic alerting systems and electronic health records. Improving pharmacogenomic education and improved record keeping would drive down health care costs. In fact, one four-month long study predicted cost-savings of $1,132 per patient using pharmacogenomic testing and an accompanying alert system as a clinical decision support tool.

 

Congressional Representatives Eric Swalwell and Tom Emmer are introducing the Right Drug Dose Now Act, a bill to improve pharmacogenomics research and patient outcomes. The bill updates the National Action Plan for Adverse Drug Event Prevention; creates a public awareness campaign for adverse drug events and pharmacogenomic testing and a separate health care professional education campaign; creates a program to improve the reporting of adverse drug events through electronic health records; and provides additional funding for NIH to improve research and reporting of adverse drug events through the Genomic Community Resources program.


Please note as part of this bill is the intent is to support with dedicated funding to PGx resources such as PharmGKB, CPIC and PharmVar.


Please reach out to Sarah Shapiro (sarah.shapiro@mail.house.gov) in Representative Swalwell’s office if you or your organization would like to support the Right Drug Dose Now Act. 


Congress needs to hear from us as community. Please help. 


Thank you in advance.  Stay Safe. Be well.


Teri

Monday, September 27, 2021

PharmCAT Version 1.0 Released

Version 1.0 of the Pharmacogenomics Clinical Annotation Tool (PharmCAT) has been released today (September 27, 2021). PharmCAT is a software tool that takes genetic data for an individual as VCF file input, interprets the pharmacogene alleles, diplotypes and phenotypes, and generates reports with CPIC's genotype-based drug prescribing recommendations which can be used to inform treatment decisions. This is the first official release of PharmCAT and it contains multiple updates to the previously published beta version.

Expanded coverage


Version 1.0 extends the coverage of alleles in existing PharmCAT genes and adds more genes, drugs and guidelines from CPIC. Content is sourced from the CPIC database. The PharmCAT site includes a list of genes and drugs (along with prescribing recommendations) included in the report.


New input and output options


v1.0 of PharmCAT enables the input of diplotypes determined by tools or genetic testing reports outside of PharmCAT to be used to predict gene phenotypes and retrieve respective CPIC recommendations. Previously, only “outside” calls for CYP2D6 diplotypes were allowed, but now diplotypes for any gene supported by PharmCAT can be supplied. For example, if you have a CYP2C9 diplotype call in hand, you can input that to PharmCAT so the CYP2C9 phenotype and CPIC recommendations are included in the final report.


The section of PharmCAT that takes diplotype calls and predicts phenotypes (e.g. metabolizer phenotypes) has been encapsulated into its own module. The "phenotyper" module allows for the input of phenotypes determined outside of PharmCAT, such as from genetic testing reports, to be used to retrieve CPIC recommendations. For example, if you have already determined a CYP2C9 phenotype, you can input that to PharmCAT so the CYP2C9 CPIC recommendations for that phenotype will be included in the final report.


The separation of the “phenotyper” code into its own module also means that if you are only interested in predicting pharmacogene diplotypes and/or phenotypes from a VCF file, you can get that information without proceeding to the final human-readable report.


More PharmCAT validation testing


v1.0 has dramatically expanded in silico testing for internal validation of PharmCAT allele matching. We have created a testing system that generates VCF files to match against expected results and report any mismatches. This system successfully tests the NamedAlleleMatcher beyond the published validation in our paper published in January 2020.


VCF preprocessor


We now provide a VCF preprocessor tool to prepare VCF files for the named allele matcher. PharmCAT requires the input VCF to follow the official VCF format specifications (version 4.1 or later) and expects a parsimonious variant representation format to avoid ambiguity. However, user-supplied VCF files may not always follow the official VCF format specifications and can represent genetic variants in different representation formats as a result of varied VCF preparation bioinformatics pipelines. Variant representation formats different from PharmCAT's requirements can cause unexpected technical hurdles and will require additional data preparation. To resolve this issue, PharmCAT provides a VCF preprocessor tool to normalize and prepare VCFs to a format readily digestible by PharmCAT. The VCF preprocessor will automatically download the Human Reference Genome Sequence fasta and index files from the NIH FTP site to normalize genetic variants in VCF. Preprocessed VCF data will include only necessary PGx allele defining positions, which will improve PharmCAT's runtime. Users will also receive a report VCF of missing PGx positions in the original VCF file.


Future releases


Development of PharmCAT continues! You can expect more releases very soon as we gather feedback from this release and issue more updates to underlying data coming from CPIC and PharmVar.


New features will also include multi-sample VCF support, GVCF support, and FHIR-formatted reports. Keep an eye on the releases page for updates.


Wednesday, September 23, 2020

PharmCAT grant awarded

The co-PIs of the Pharmacogenomics Clinical Annotation Tool (PharmCAT). Dr. Marylyn Ritchie of the University of Pennsylvania and Dr. Teri Klein of Stanford University were awarded a three year grant from the National Institutes of Health National Human Genome Research Institute (NIH NHGRI) to continue and expand the project.  PharmCAT was originally created in 2016 and is a tool that: (1) extracts variants found in CPIC guideline genes from a sequencing or genotyping Variant Call Format (VCF) file, (2) assigns star alleles, diplotypes and drug phenotypes based on slightly modified PharmVar core alleles in CPIC/PharmGKB definition tables and CPIC allele function and phenotype tables, and (3) provides an HTML/PDF report including CPIC genotype-based drug prescribing recommendations.

We published the initial assessment of PharmCAT in Clinical Pharmacology and Therapeutics in 2019 (PMID: 31306493) and the beta version is currently available for testing.  Due to limited resources, PharmCAT has only been tested on a small sample of genotype data and with information from CPIC guidelines as of 2018.  The new funding will enable PharmCAT to (1) update to current CPIC guidelines and release version 1.0, (2) create a module for VCF pre-processing and quality control, (3) export an electronic health record (EHR) compatible report using Fast Healthcare Interoperability Resources (FHIR) specifications, and (4) provide the ability to run multiple VCF files at one time (batch processing).  We will announce the PharmCAT v.1.0 release on the PharmGKB blog.  Check the PharmCAT website to see updates as they happen.

This work is supported by the NIH NHGRI U24HG010862.

PharmCAT workflow below. Yellow boxes are input files for PharmCAT. Blue boxes are PharmCAT modules.  Green boxes are PharmCAT module output and input into the next module. Grey boxes are alternate input into PharmCAT.



Monday, July 29, 2019

PharmCAT article published in Clinical Pharmacology & Therapeutics

The article describing the Pharmacogenomics Clinical Annotation Tool (PharmCATand a pilot validation using GeT-RM samples was recently published in Clinical Pharmacology & Therapeutics
PharmCAT (1) extracts variants specified in guidelines from a genetic dataset derived from sequencing or genotyping technologies; (2) infers haplotypes and diplotypes; and (3) generates a report containing genotype/diplotype-based annotations and guideline recommendations. 
In this initial version, the tool only considers variants contained in the allele definition files, which are based on CPIC guidelines and provides CPIC recommendations in the output. PharmCAT assumes the sample VCF file has already undergone extensive quality control. Requirements for the VCF files are accessible in GitHub.
PharmCAT was highly concordant with the GeT-RM data and discordant results are discussed in detail in the article and supplemental material [add link to journal or to PharmCAT.org, if we post it there].

Seeking community input and testing. With this initial beta release of PharmCAT, the pharmacogenomics community is asked to support the continuing evaluation of this freely available tool by running VCF samples, documenting issues and successfully identifying variants. GitHub can be used to communicate feedback. 

PharmCAT is available under the Mozilla Public License (MPL 2.0) for the scientific and clinical community to review, test, and improve. 

Friday, December 1, 2017

PharmCAT commentary in Clinical Pharmacology & Therapeutics

A commentary about the Pharmacogenomics Clinical Annotation Tool (PharmCAT) was recently published in Clinical Pharmacology & Therapeutics.  PharmCAT is developed in a collaboration between the former PGRN Statistical Analysis Resource (P-STAR) and the Pharmacogenomics Knowledgebase (PharmGKB) with input from other groups (click here for a list of participants). PharmCAT will extract PGx variants, beginning with variants in genes with CPIC guideline recommendations, from VCF files, infer diplotypes/genotypes, and generate an interpretation report containing the relevant CPIC recommendations.

In the article, Teri Klein and Marylyn Ritchie highlight challenges in the field and describe the rationale for PharmCAT. The tool's workflow is depicted graphically and the different components are briefly introduced.

For more information about PharmCAT read the complete commentary at Clinical Pharmacology & Therapeutics.

Wednesday, May 3, 2017

NHGRI’s Genomic Medicine X: Pharmacogenomics Meeting

On May 2 and 3, 2017, the National Human Genome Research Institute (NHGRI) held its 10th Genomic Medicine meeting, focusing on pharmacogenomics.

PharmGKBPharmCAT and CPIC were presented, as well as a review of the deposition of PharmGKB and CPIC data to ClinVar.  We thank Mary Relling from St Jude Children's Research Hospital,  Marylyn Ritchie from Geisinger and Heidi Rehm from Parnters for highlighting these activities at the meeting.

Friday, April 15, 2016

Pharmacogenomics Clinical Annotation Tool (PharmCAT)

An active area of genomic medicine implementation at many health care organizations and academic medical centers includes development of decision support and return of results around pharmacogenomics.  The Clinical Pharmacogenetics Implementation Consortium (CPIC) has established guidelines surrounding gene-drug pairs that can and should lead to treatment modifications based on genetic variants.  One of the challenges in implementing pharmacogenomics is the representation of the information in the CPIC guidelines (including star-alleles) and extracting these variants and haplotypes from genetic datasets.  In a collaboration between the PGRN Statistical Analysis Resource (P-STAR), the Pharmacogenomics Knowledgebase (PharmGKB), the Clinical Genome Resource (ClinGen), and CPIC, we are developing a software tool to extract all CPIC guideline gene variants from a genetic dataset (represented as a vcf), interpret the variant alleles, and generate a report.  The CPIC pipeline report can then be used to make future treatment decisions. 

We assembled a focus group of thought leaders in pharmacogenomics to brainstorm and design the software pipeline.  We hosted a one-week Hackathon at the PharmGKB at Stanford University to bring together computer programmers with scientific curators to implement version one of this tool.  We will host a meeting to summarize and evaluate next steps in mid-May including the development of a manuscript and dissemination plan for the tool.  This software pipeline will be made available in a Creative Commons license and disseminated in GitHub later this spring for all in the scientific community to test, explore, improve and to give us feedback.  Be a part of this project!  As many of our institutions are building implementation workflows for pharmacogenomics, our ability to automate some of the extraction of genes/variants of interest would be enormously helpful.

We welcome scientific input from our colleagues.  If you would like to become involved in this effort, we ask that you contact pharmcat@pharmgkb.org.  Thank you!