Sunday, December 20, 2015

ACMG Issues a Revised Position Statement Regarding DTC Genetic Testing

The American College of Medical Genetics (ACMG) recently revised its position statement regarding direct-to-consumer (DTC) genetic testing. Briefly, the ACMG recommends that:

  • Knowledgeable professionals order the genetic test, which should be undertaken by a Clinical Laboratory Improvement Amendments (CLIA) accredited laboratory.
  • Board certified genetics experts, such as clinical geneticists, or genetic counselors should be available to assist with test interpretation
  • DTC genetic tests should incorporate family history and patient-specific information into result reports, which should be presented in a manner that is comprehensible by the consumer.
  • Consumers should be informed of the possibility of incidental findings and of the implications of these incidental findings for relatives.
  • The scientific evidence underlying the validity and utility of a genetic test should be explicitly stated. 
  • Consumers should be made aware of where test results will be stored, as well as the identities of the parties that will have access to the test results. 

Read the revised ACMG position statement.

Thursday, December 17, 2015

DIGITizE Suggests Implementing 2 CPIC Guidelines in CDS

The DIGITizE Action Collaborative has suggested that Clinical Decision Support (CDS) be implemented based on CPIC's TPMT/azathioprine and HLA-B/abacavir guidelines.  DIGITizE (Displaying and Integrating Genetic Information Through the EHR) is a collaborative group of the Institute of Medicine consisting of key stakeholders interested in integrating genomic information into electronic health records (EHR).  As part of their efforts to create support for a few very specific use cases, they have chosen to focus on the impact of (1) HLA-B*57:01 on abacavir hypersensitivity and (2) TPMT alleles on azathioprine dosing, consistent with the CPIC guidelines.  They recommend having patient genotypes in the EHR before prescribing these medications.

CPIC guidelines can be found on PharmGKB for TPMT/azathioprine and HLA-B/abacavir.

Friday, December 11, 2015

Combining large PGx datasets from cancer cell lines

Testing cancer cell lines in vitro for drug sensitivity is a cornerstone of preclinical drug development. Large publically available datasets can be found at The Genomics of Drug Sensitivity in Cancer Project (GDSE) and The Cancer Cell Line Encyclopedia (CCLE).

Studies attempting to combine large public datasets and analyzing for correlation questioned the reliability of the data due to limited concordance, reported in [PMID: 24284626], discussed in [PMID:24284624] and a confirmation study here.

A new report in Nature describes different methods to analyze the data from CCLE and GDSE and concludes that “data from either study yields similar predictors of drug response” [PMID:26570998].

These papers demonstrate the continuing difficulty trying to compare across large datasets. Such problems include comparing different experimental protocols and measurements for drug sensitivity across studies, trouble matching the drug and cell line names to ensure like comparison, discordance in the genotyping data, and drugs that had few examples of cell lines that were drug sensitive.  As always, attention to detail in the documentation and description of the experiments can help mitigate some of these difficulties. While development of standard testing protocols and data curation and reporting frameworks may lead to better validation of drug response predictors going forward there will always be the need for methods to filter the noise that is inevitable in large datasets.

Wednesday, December 9, 2015

ASHP Foundation Recognizes Clinical Implementation of PGx

The University of Illinois (UI) Personalized Medicine Program led by Dr. Edith Nutescu, is one of three finalists for the 2015 Award for Excellence in Medication-Use Safety, which is given by the American Society of Health-Systems Pharmacists (ASHP) Foundation. The program at the UI Hospital and Health Sciences System has genotyped over 1,500 patients to help guide warfarin and clopidogrel dosing. According to Dr. Nutescu, the program has led to significant decreases in hospital readmission rates due to drug-related adverse events, while simultaneously saving UI health an estimated $600,000 annually. 

Read the UIC press release: 

The Clinical Pharmacogenetics Implementation Consortium (CPIC) dosing guidelines are available for warfarin and clopidogrel

Interactive pharmacokinetic (PK) and pharmacodynamic (PD) pathway summaries for warfarin (PD and PK) and clopidogrel (PK and PD ) are also available on PharmGKB.

CPIC Upcoming Meetings - Save the Date!

The Clinical Pharmacogenetics Implementation Consortium is holding a meeting for members in 2016 and an open meeting in 2017.

CPIC Luncheon Meeting (open to CPIC members)
Thursday March 10th, 2016 Noon-1:30 PM
Hilton Bayfront Hotel, San Diego, CA
Email: to attend

CPIC Meeting (a specialty meeting of the PGRN)
Wednesday March 15th, 2017
Marriott Wardman Park Hotel,  Washington DC
Further details pending

Monday, December 7, 2015

Framework Published to Guide Development of PGx Public Policy, Applied in Canada

The paper, “The 3-I framework: a framework for developing public policies regarding pharmacogenomics (PGx) testing in Canada” was published last week in NRC Research Press. It presents a political science framework of considering ideas, interests, and institutions to identify challenges and needs for PGx implementation. The analysis is presented as a tool to guide policy development, with the goal of increasing PGx usage in clinical care. The article gives a review of the status of PGx policy and needs in Canada now, and compares it to key policies in other countries. These policies include the Genetic Information Nondiscrimination Act in the US and the contracts to prevent the disclosure of direct-to-consumer testing results to insurers in the UK.  We present this article as an example of conversations and tools around PGx policy development, and of how different countries are approaching the increasing usage of PGx in clinical care. If you are interested in learning more about implementation guidelines in the US, see the Clinical Pharmacogenetics Implementation Consortium (CPIC) at