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Whole Genome Sequencing

genome sequencingPatients with complex, undiagnosed medical conditions are being recruited by the Geisinger Genomic Medicine Institute to participate in a new clinical whole genome sequencing program that has the potential to diagnose their condition and improve their care. 

WGS is an emerging technology that allows analysis of all the genes at one time. This testing has the ability to detect numerous rare and previously unidentified changes that could be responsible for the patient’s disease.

The Geisinger Genomic Medicine Institute’s WGS program will sequence the genomes of patients and their parents and perform a personalized analysis of results as we seek to end the diagnostic odyssey.

Geisinger's Genomic Medicine Institute named one of four grand prize winners for Best Practices at the 2013 Bio-IT World Conference & Expo
The Genomic Medicine Institute at Geisinger used SimulConsult’s Genome-Phenome Analyzer to analyze the genomes of three family trios. Investigators correctly predicted 100% of the relevant genes in all three families and reduced the time required to do clinical interpretation for symptomatic patients by up to 90%. Click for story.

Genome Best Practices Award

Description and pilot results from a novel method for evaluating return of incidental findings from next-generation sequencing technologies
Katrina A.B. Goddard PhD, Evelyn P. Whitlock MD, MPH, Jonathan S. Berg MD, PhD, Marc S. Williams MD, Elizabeth M. Webber MS, Jennifer A. Webster MS, Jennifer S. Lin MD, MCR, Kasmintan A. Schrader MBBS, Doug Campos-Outcalt MD, MPA, Kenneth Offit MD, MPH, Heather Spencer Feigelson PhD and Celine Hollombe MPH
Genet Med advance online publication, April 4, 2013; doi:10.1038/gim.2013.37
Abstract | Full Text | PDF | Supplementary information
Marc Williams, Director, Genomic Medicine Institute, is a co-author on this journal publication.

The American College of Medical Genetics and Genomics (ACMG) has released the widely-anticipated "ACMG Recommendations for Reporting of Incidental Findings in Clinical Exome and Genome Sequencing” (.pdf) report at its 2013 Annual Clinical Genetics Meeting in Phoenix, AZ. The recommendations of its task force included those of Marc Williams, MD, Director, Geisinger Genomic Medicine Institute.

Marc S. Williams, MD, director of the Genomic Medicine Institute, spoke to an audience at Northwestern University recently about how whole genome sequencing will impact the future of medicine. Click for story.

Geisinger honored in CLARITY Challenge

Geisinger, in collaboration with Simulconsult, was one of eight winners in Boston Children’s Hospital’s Clarity Challenge that looked at analyzing DNA sequencing results and generating reports that can help guide potential treatment. 

The Geisinger-Simulconsult team was one of five honorable mentions among the 23 groups that completed the challenge. The results were announced at the recent American Society of Human Genetics meetings in San Francisco. Simulconsult is a Boston-based company that uses databases and software to aid clinicians in making diagnostic decisions.

The team included Marc S. Williams, MD, Director of the Genomic Medicine Institute at Geisinger, Dr. Gerard Tromp, who led the sequencing informatics analysis, along with Mickey Segal, founder of Simulconsult, and Lynn Feldman, Simulconsult CEO.  Dr. Williams had high praise for Geisinger’s David Gehrum, IT support director, and his team for their contributions to the project, as well as the Whole Genome Sequencing Committee and Dr. Anne Moon, who provided invaluable input. The Oversight Committee of the Whole Genome Sequencing project provided input on the laboratory report. 

“This was a tremendous team effort that allowed us to test out ideas about analysis and reporting of whole genome sequencing results. The lessons learned from our participation will benefit all of the families that are participating in our Whole Genome Sequencing project. To have been recognized for our innovation given the quality of the other teams was a great honor, and reinforced some of our innovative ideas,” said Dr. Williams. 

Each team was provided with the whole genome and whole exome sequencing results from three patients and their families, and asked to identify genes and variants that could be related to the clinical problems suffered by the patients. 

One child suffered from muscle weakness and hearing impairment; another had heart rhythm problems and structural heart defects that caused his death just 12 days after his birth; and a third suffered from a muscle-weakening disease.  Causal mutations were identified by the Clarity Team in the first two families. The Geisinger-Simulconsult team correctly identified that the first family had two different genes involved—one for hearing loss and one for the muscle weakness. The team correctly identified the gene involved in the hearing loss, but a software glitch discovered after the submission led to missing the muscle weakness gene. 

In family 2, the Geisinger-Simulconsult team identified a mutation in the gene that was determined to be causal by the Clarity Challenge team, but were convinced that this gene would only explain the rhythm problem. A second gene was identified that could cause the structural heart lesions and the Clarity team noted that they will take this under consideration.  

For the third family, the Geisinger-Simulconsult team identified a mutation in a gene that could potentially cause the muscle weakness that will be further explored by the child’s clinicians.  Dr. Williams noted, “The fact that we were able to identify causal mutations from the information provided gives us confidence that our analytic approach is sound and can be successfully applied to our patients.”

Dr. Williams, who is leading Geisinger’s Whole Genome Sequencing project, said the challenge “was important to be able to test our ideas. What was most gratifying was our honorable mention for the innovation using a software tool to collect patient signs and symptoms, family history, information from physical and neurologic examinations and laboratory and radiology reports to narrow the potential list of genes to a manageable number while not eliminating any of the candidates. Many if not most of the other teams consisted of 20-50 team members, while the bulk of the analytic work for our project was done by three people, myself and Drs. Tromp and Segal. That we were able to compete against these high-powered teams not only reinforces the soundness of our approach, but also makes the point that the use of intelligent analytic tools can reduce the work required to do the analysis that will ultimately make this a sustainable clinical approach.”

clarity challenge

From left: Alan Beggs, Clarity Co-Organizer; Lynn Feldman, Simulconsult CEO; Marc Williams, Director of the Genomic Medicine Institute; Mickey Segal, Simulconsulat Founder

Recent publications on Whole Genome Sequencing