Working Group Meeting September 26-27, 2011
EGAPP Working Group members present:
Al Berg, MD, MPH; Ned Calonge, MD, MPH, chair; Doug Campos-Outcalt, MD, MPA; Ben Djulbegovic, MD; Ted Ganiats, MD; Roger D. Klein, MD, JD; Don Lyman, MD, DTPH; Ken Offit, MD, MPH; Stephen Pauker, MD, MACP, FACC, ABMH; Margaret Piper, PhD, MPH; Ora Strickland, PhD; Sean Tunis, MD, MSc; and David L. Veenstra, PharmD, PhD
Opening Statement and Welcome
Ned Calonge welcomed all the EGAPP Working Group (EWG) members to Atlanta and to the meeting. He also welcomed Sheri Schully and Jim Evans, invited guests, to the meeting. Meeting participants introduced themselves to meeting attendees.
Dave Dotson provided a brief overview of the current status of various EGAPP projects. These updates include a review of current evidence reviews and recommendations underway, web site statistics and updating reviews for National Guidelines Clearinghouse (due December 2012).
The FY2012 Activities will be focused on: submitting the methods update and lessons learned manuscripts, WGS binning, updating reviews, peer review and recommendations for T2D and KRAS, and potential recommendations for fecal DNA, CYP clopidogrel, PCA3/prostate cancer & Prostate cancer SNPs.
Developing Priorities for Public Health Genomics: 2012-2017
Dr. Khoury presented an update on the status of CDC’s Office of Public Health Genomics (OPHG), and the EGAPP Initiative. The presentation included a report from the 2011 external stakeholder event which focused on the past, promise and future potential, Public Health Essential functions and services, and support to keep EGAPP going at the least through September 2012. The top priorities for the office are:
- Priority 1: maintain CDCs public health genomics “honest broker” role.
- Priority 2: implement a public health messaging and networking function
- Priority 3: Promote the use of data and databases for public health action in genomics and family history
Knowledge Synthesis Center Issue Framing
Katrina Goddard, Kaiser Permanente Center for Health Research, presented a brief outline from the KSC in regards to framing the issues around WGS from their perspective. The larger context involves many organizations who each have a part or project with WGS. These include WGS and FDA & CAP recommendations/checklists for inspection, IOM roundtable on clinical validity, and NHGRI & EGAPP in the clinical validity/utility arena.
The focus of specific WGS and EGAPP contextual matters are pre-conception, prenatal, newborn screening, childhood & adult screening, diagnostic, and treatment/monitoring. False negative and false positive issues (sensitivity and specificity).
The beginning of the project on WGS should focus on case studies based on various topics previously presented to the EWG for review. Development of the project is an iterative process of refining, trial criteria, working examples and repeating these to create final criteria.
Framing the questions should take into consideration template preparation, assembly method and sequencing platform for Whole Genome Sequencing.
Overview – Whole Genome Sequence binning
Jim Evans was invited to give a presentation on his perspective of Whole Genome Sequencing (WGS). His presentation was entitled “Cutting up the cow – implementing the NGS in clinical medicine and public health.”
Technology is the driver of sequencing DNA. Sequencing DNA can be done by a variety of approaches each with their own pros and cons. Sanger sequencing is slow but is considered the gold standard. Now, next generation sequencing can do 10 million reactions quickly but the read accuracy can be less accurate.
Some polymorphisms are meaningless, some influencing traits, and some are medically important mutations. Occasionally, rare mutations are detected.
Genomics in the Clinic
Diagnostics – guiding prognosis, treatment, and medical progress
- Provides a real benefit
- Ends the diagnostic odyssey
- Informing patients and providers about natural history
- Reproductive decisions
Whole genome sequencing
- Target the correct patients
- Rare diseases is key target
- most rare diseases are caused by something in the genome
- Chronic diseases is likely limited utility for WGS
- Genetic component is only a portion of the “cause”
Improving the population’s public health
- Conflating relative and absolute risk
- Few data suggest that knowledge of genomic status is effective in changing behavior
- Common disease….what does it really mean to be at “relatively reduced risk”?
- Identifying HIGHLY penetrant mutations
- Knowledge of risk allows prevention (ex. Lynch syndrome)
- Pre-conception carrier screening
- Screening for a bad mutation in an embryo vs. designer babies (e.g. traits)
The central challenges in WGS are: dealing with lots of data, quantitatively very difficult to deal with 4 million variants, and the unknown significance of the variants and dealing with surprises. The analytical validity can be poor and vary by platform. There is a need to confirm using Sanger sequencing any informative mutation/deletion, etc. prior to reporting to patient.
The binning of data/results should be consistent and evidence-based. There is a need to facilitate analysis, reporting, storage and patient choice in a common manner. Challenges to realizing genomic medicine include: how to formulate the bin structure, should be based on clinical actionability, personal utility is not an argument for disclosure in the clinical setting.
When formulating the bins, the focus needs to be on:
- Too big of a job for a lab director or practitioner
- Focus on utility and actionability
- Evidence-based criteria
- Needs to be iterative
- Can guide research, clinical practice, public health and patient education
- Define the genes, then variants
- New knowledge can change the bin location of the gene/variant
Key points in the classification scheme by bins in terms of evidence of clinical utility
- BIN 1: actionable
- Obligatory reported
- BIN 2: not necessilary actionable
- Clinical validity only
- May be reportable to patient
- BIN3 : no known significance
- Not reportable
WGS Binning Discussion
Operationalization of the process needs to be led by the EWG representatives and the KSC team. There is a need to have a small group of representatives to put together a framework of bins. The data to look at in developing the framework include:
- What are people’s attitudes towards bins?
- What to do before you get the data?
- What genes?
- Same gene can be in two different bins (variants)
- Before reporting a variant, how to verify the result.
- There is a need to generalize EGAPP methods to handle WGS.
- The informed consent process must include the process of notifying the patient with their results.
The Topics SC work and the work that EGAPP has done can be used to inform the “binning process.” Examples to start with could include Lynch syndrome (EGAPP) and BRCA1/2 form AHRQ
Modeling Return on Investment (ROI) for EGAPP
Dave Dotson, Dave Veenstra and Scott Grosse have started an ad hoc group to discuss a manuscript on ROI for Lynch Syndrome. ROI for a topic that OPHG and EGAPP are involved in has monetary and health implications from EGAPP.
Steve Pauker, Scott Grosse and Dave Veenstra to conduct modeling and hope to publish the results in Health Affairs or American Journal of Managed Care.
Complete presentation is available on the final meeting CD.
Type 2 Diabetes review/recommendation
Michael Douglas presented an update on the Type 2 Diabetes review. The focus of the report was on the items completed since the last meeting. These include the introduction, methods, results and appendix B describing the genes, genotype/allele frequencies, literature search and clinical validity evidence. The items to be completed are the clinical utility and discussion; as well as, peer review and submission to the journal for publication. The recommendation statement has been completed. However, the recommendation manuscript still needs to be completed. The recommendation team leader will be Ted Ganiants, and Doug Campos-Outcalt, Maggie Piper, and Ned Calonge will be involved in the review manuscript and recommendation manuscript draft.
Dave Dotson presented the KRAS/BRAF recommendation statement to the EWG. The EWG suggested edits and they were made to the recommendation statement during the meeting.
Lessons Learned Manuscript
Ned Calonge presented the Lessons Learned Manuscript to the EWG. The first impression was there was too much history up front without getting to lessons learned. The expectation was to get into the lessons learned fairly quickly in the manuscript; the history of EGAPP and other information regarding OPHG. Reorganization is needed to target the lessons learned upfront.
The section on the evidence-based practice center/KSC should describe the KSC in more of a direction relationship/partnership role.
There is a need to rearrange the manuscript so there doesn’t look like a death of EGAPP and OPHG at the end; but rather put a more positive spin or call to action at this point.
There is not a need to put the context of EGAPP in terms of other evidence-based organizations or history. However, EGAPP relationships to other federal organizations/projects should be included.
The need to include the EGAPP steering committee in some format in the manuscript would be be appropriate since they have been in the process from the beginning.
Overall, we need to clearly define the audience and keep the manuscript focused to the audience.
Methods Update Manuscript
Dave Veenstra presented the methods update manuscript. He requested comments to focus on two areas, the last part of abstract and the organization and flow of direction of the manuscript.
Ned Calonge thanked all the meeting participants and the meeting was adjorned at 11:50am.
The next EGAPP Working Group Meeting is scheduled for Monday & Tuesday,
January 30 -31, 2012 in Atlanta, GA.