Genome BC Signals Summer 2014

SIGNALS Genome BC News | Summer 2014

ContentsFeature Story | Message from the President & CEO | Profile | Special Feature | News & Announcements

The human genome project, completed in April of 2003, allowed us the first opportunity to read nature’s complete genetic blueprint for a human being. The knowledge uncovered by the research set the stage for a new era of genomics and insight into genomes of all living organisms.

In November 2007, 23andMe – a California based private company challenged “Pandora’s Box” by allowing individuals to access their personal genetic information using genomics technology. By simply sending a saliva sample through the mail, people were able to trace their ancestry beyond the traditional family tree, learn about their history and even find ‘relatives across continents or across the street’.

In 2014 the market for direct-to-consumer genetic testing is still growing as more individuals want to know about the potential of certain genetic diseases, take a more proactive role in their healthcare and learn about their ancestral origins.

These direct-to-consumer genetic tests, however, do have significant risks and limitations. Consumers are vulnerable to being misled by the results of unproven or invalid tests. Private company websites suggest

that they offer consumers information — and that this information should not be used to make diagnoses. Without guidance from a licensed healthcare provider, individuals may make important decisions about treatment or prevention based on inaccurate, incomplete, or misunderstood information about their health. Consumers also raise questions around genetic privacy and how their genetic information could or will be used in the future.

As professionals in the genomics field, they wanted to understand more about the results delivered by direct-to-consumer genetic testing.

In the last two years, four Genome BC staff members decided to pursue personal genome testing. Drs. Marcia MacDonald, Agnes Baross and Aniko Takacs-Cox chose 23andMe to genotype their approximately one million known single nucleotide variant positions. Chief Scientific Officer Dr. Brad Popovich took an even more fulsome approach and used Illumina to navigate his personal genomics path—you can read more about his journey in the Special Feature section in this issue of Signals.

Marcia, Agnes and Aniko had similar reasons for wanting the information: as professionals in the genomics field, they wanted to understand more about the results delivered by direct-to-consumer genetic testing. They also understand that the more genetic data made accessible for research, the more meaningful individual results will become.

NO.47

www.genomebc.ca

CONSUMER GENOMICS: HOW MUCH DO WE REALLY WANT TO KNOW?

Agnes Baross Marcia MacDonald Anikó Takács-Cox

So what did they gain by doing this? Marcia now has her own dataset for personal use in testing new tools for population genetics. She was surprised to link up with an unknown second cousin, learned she had a significant number of relatives in Australia, and confirmed her First Nations ancestry.

Aniko, meanwhile, was not surprised by the many variants in her health related genes. In fact, her variants linked to conditions that are more related to lifestyle rather than genetics so the results reaffirmed choices she is already making. And while her ancestry was predictable, she did make contacts with a few potential relatives in an attempt to find a common ancestor and plans to spend a lot more time on genealogy databases to get even more detailed information.

So what can we conclude from this? Consumer genomics offers individuals new insights into ancestry and lineage beyond the family tree and hints at some potential health concerns in the future. As for the risks—the ability to know (or not know) presents a moral dilemma. How much do we really want to know and what are we to do with the information if and when we receive it?

Do you have thoughts or comments about direct-to-consumer genetic testing? Feel free to add them to our Facebook or Twitter pages.

Marcia, Agnes and Aniko also contributed their anonymized data to further general research. Marcia took an extra step and made her genotypes openly available through OpenSNP.org, which allows users of direct-to-customer genetic tests to make their test results public. She also confirms she would make her whole genome and most health information available if she were selected to participate in the Personal Genome Project.

This initiative believes that individuals from the general public have a vital role to play in making the data from personal genome sequencing useful for research purposes in order to advance our understanding of genetic and environmental contributions to human health.

Consumers also raise questions... how their genetic information could be used in the future.

Agnes was interested in learning about her health and drug response risks based on genetic profile, even though she knows that most results are based on research and have not been fully clinically validated. For her, the ancestry piece was fun and interesting to review but it wasn’t the primary driver behind taking the test. Agnes may consider more fulsome whole genome sequencing in the future.

CONSUMER GENOMICS: HOW MUCH DO WE REALLY WANT TO KNOW?Cont’d from cover

MESSAGE FROM THE PRESIDENT & CEO

USHERING IN THE GENOMICS ERA

The ‘genomics era’ is well and truly upon us. The price of sequencing—either the whole genome or selected genes—is quickly becoming affordable to the average consumer. Consumer genomics, the focus of this issue, is no longer an intangible but rather something we hear and learn about on a daily basis. At Genome BC the advent of consumer genomics and the corresponding reduction in the cost of sequencing tells us that genomics is no longer something reserved solely for scientists and academics. We have moved from a time of genomic scarcity to a time of genomic abundance.

Consumer genomics have a major impact on three areas. First of all, on the medical side we are learning that the cost of whole genome sequencing will be cheaper than a battery of one-off tests. A whole genome sequence offers a much more comprehensive view of a person’s genomic health, and the steadily decreasing cost is set to revolutionize the laboratory business. Second, we are getting better and better at establishing the link between a genotype and a phenotype in a relatively cost-effective way. Genomic testing is quickly becoming the standard of care in guiding targeted cancer therapies.

And finally, research has been deeply impacted by the advent of cheaper sequencing methods—and not just in human health. Re-sequencing genomes to look for associations and links for a particular phenotype and disease in fish or a dairy cow could be commonplace in just a few short years. Individuals are clearly also impacted by the reduction in sequencing costs as they are now able to pay for these sequencing tests in order to discover or dive deeper into information about ancestry and personal health. Genetic linkages to family members have an impact on health as it relates to predispositions for disease as well.

In the longer term, digital health promises to be the way of the future—the combination of electronic apps allows health monitoring to happen in real-time and the genome provides the context for that. Consumer interests will lead this sphere and determine where priorities lie be it diabetes, heart conditions or more generic health monitoring.

Full of promise and opportunity the genomics era will be a future that leads to unprecedented understanding of living organisms and how they adapt to their environments.

Alan E. WinterPresident & CEO, Genome British Columbia

With the proliferation of direct-to-consumer genomic tests now available via the Internet, and the marketing hype surrounding many of them, it can be hard for consumers to make informed decisions. Deciding whether to pay for genomic testing, determining the reliability of a company offering these products and validating the scientific evidence on which the test is based is daunting; interpreting the results is often even harder. This challenge can be further exacerbated by the fact that most healthcare professionals are unfamiliar with these new kinds of tests and often cannot help their patients contextualize and understand their results.

Genetic counsellors are health professionals trained to help people consider the benefits, limitations and

meaning of genetic tests. However, they are in short supply: in fact, there are just 46 genetic counsellors in BC, almost all of whom work in the public healthcare system, which does not currently pay for consumer genetic testing.

The biggest concern is how to support people who receive unexpected or unwanted results. Genomic testing is very complex, as it involves looking at many (or all) of a person’s genes at the same time. Incidental findings include genetic information uncovered during a genetic test that may be of value or concern to a person, but unrelated to the original purpose of the test. Incidental findings are similar to side effects of prescription medication: they can be bad, good, or indifferent, but regardless, they can provide consumers with information they are ill-equipped to understand. And while Incidental findings may have important medical implications for relatives, as well as the person tested, they can also generate unexpected information about family relationships or ancestry, affect one’s ability to get insurance, or cause anxiety or additional worries for the family.

An informed consumer is a well-prepared consumer. Those considering undergoing genetic testing on their own should do research and consider how and what they really want to find out. Current, accurate and convenient online education geared both to the consumer and to clinical community can help people get the most value from genomic testing, and also help counteract inaccurate or biased marketing by some consumer genomics companies. Genomic testing can be valuable, but can also be a waste of money and create more problems. Like a powerful medication, today it needs to be used alongside a healthcare professional, such as a genetic counsellor, who can help people fully understand its potential benefits and risks.

PROFILE:SHELIN ADAM CLINICAL ASSISTANT PROFESSOR - DEPARTMENT OF MEDICAL GENETICS, UBC

THE ROLE OF GENETIC COUNSELLORS AND PRIVATELY-PURCHASED GENOMIC TESTS

Dr. Brad Popovich, Genome BC’s Chief Scientific Officer, is a genomics pioneer. He has been working in the field his entire career — doing translational research, testifying as an expert scientist in courtrooms and starting and managing biotech companies. Throughout all this time, he did not know the full sequence of his genome and the information that may be of benefit or cause alarm.

Earlier this year Brad decided to “take the plunge” and begin his personal genome journey. He opted to go beyond analysis provided by groups such as 23andMe and chose Illumina’s Understand Your Genome program. For $5,000 his whole genome was sequenced, his DNA analyzed and the information interpreted by a medical professional.

SPECIAL FEATURE: PERSONAL GENOME SEQUENCING: AN INDUSTRY PIONEER TAKES THE PLUNGE

INTERFACE Digital Health Summit 2014Sept 29 & 30, Vancouver. Details & discount code here:

https://www.eventbrite.ca/e/interface-2014-tickets-

11755058697?discount=GBC14

Brad’s curiosity and desire to pursue personal genome sequencing has professional origins. He wanted to know if he had his own detailed genetic information, would it change the way he lived his life?

Technology and bioinformatics are key components in genomics testing and analysis. Brad, and many of his contemporaries including Dr. Eric Topol (the 2013 Don Rix Distinguished Keynote Speaker) can access their results via an electronic device. In fact, Brad’s fully sequenced genome from Illumina was presented to him on an iPad Mini, a necessity given the huge amount of data being delivered. The human genome is made up of 3 billion base pairs and, of this, 3.4 million variations were detected. Within those variations approximately 1.3 million were present in the one to two per cent of his genetic sequence that provides instructions for biological processes.

There’s a path being paved leading towards the use of genomic information to make better and more informed healthcare decisions.

Dr. Brad Popovich

Both professionally and personally Brad believes that he reaped significant benefit from the experience and helped solidify his vision for the future of personalized medicine. “There’s a path being paved leading towards the use of genomic information to make better and more informed healthcare decisions,” he says, but adds that he doesn’t think these activities will replace visits to your family physician any time soon.

In order to make personalized medicine and the personal genome a tool accessible to everyone, much more data is required to establish baseline information create a strong foundation for comparison. Brad and some of his Genome BC colleagues are helping to accomplish this. Three staff members have participated in direct-to-consumer genetic testing (see their stories in the cover story of this newsletter). They are three of the one million participants who are helping to build genetic resources for researchers to draw upon and further personalized medicine research.

As a certified clinical molecular geneticist, Brad was able to understand much of his information and good comparative data exists for well-known genetic variations for diseases like Cystic Fibrosis, Huntington’s or breast cancer. However, for something like cardiac arrhythmia, for which his sequencing detected a variant, there are not enough people with a similar finding to reach a firm conclusion regarding the medical importance.

SPECIAL FEATURE: PERSONAL GENOME SEQUENCING: AN INDUSTRY PIONEER TAKES THE PLUNGE Cont’d

Example of an anonymous genetic test report

NEWS & ANNOUNCEMENTS

Genome BC held its 12th Annual Genome BC Genomics Forum at UBC on May 9th. The theme was Genomics: Driving BC’s Bioeconomy and the speakers covered topics including the “Landscape of Biotechnology in Canada and BC” and “The Future of Agri-Food/Genomics Innovations.” Thank you to the Student Biotech Network for organizing the annual poster competition as part of the event.

Congratulations to Dr. Elizabeth M. Simpson, Senior Scientist, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, and Professor, Department of Medical Genetics at UBC for winning the Genome British Columbia Award for Scientific Excellence at the 16th Annual LifeSciences BC Gala on April 23rd.

Dr. Brad Popovich, Genome BC’s Chief Scientific Officer spoke at the “Let’s Get Personal!” breakfast event hosted by LifeSciences BC on May 1st. Along with Dr. James Taylor, Precision Nanosystems and Dr. Steven Jones, Canada’s Michael Smith Genome Sciences Centre, Brad spoke about personal genome sequencing.

As part of the International Cooperation to Sequence the Atlantic Salmon Genome (ICSASG), Genome BC announced completion of a fully mapped and openly accessible salmon genome at the 2nd International Conference on Integrative Salmonid Biology held in Vancouver June 9-12.

•

Genome British ColumbiaSuite 400575 West 8th AvenueVancouver, BC V5Z 0C4Tel: 604 738 8072

[email protected]

lan de la RocheChair

Ida GoodreauVice Chair

Alan WinterGenome BC

Neena L. ChappellUniversity of Victoria

Jock Finlayson BC Business Council

Joseph Garcia Blake, Cassels & Graydon LLP

Janet HalliwellJ.E. Halliwell Associates Inc.

Victor LingTerry Fox Research Institute

Alan PelmanPast Chair

Edward SafarikOcean Fisheries Ltd.

John ShepherdUniversity of British Columbia

John F.H. ThompsonPetraScience Consultants Inc.

BOARD MEMBERS

We welcome your comments and input.Please send comments to: [email protected]

Genome BC is supported by the Province of British Columbia, the Government of Canada through Genome Canada and Western Economic Diversification Canada and more than 300 international public and private co-funding partners.

Printed on 100% recyclable paper.

DID YOU KNOW?

Genome BC currently has five open funding competitions available to BC-based researchers. Our funding programs support a wide range of opportunities from large-scale applied genomics projects to accelerating the commercialization process for genomics-related innovations to supporting collaborative research institution/industry partnerships in finding research solutions to the needs of BC’s key sectors. Details can be found on our website:

www.genomebc.ca/opportunities/current-funding-competitions.

At the Annual General Meeting on June 6th, Genome BC thanked Ken Galbraith and Peter O’Callaghan for their invaluable contributions over many years as board members. Two new members have joined the board: Jock Finlayson, Executive Vice President and Chief Policy Officer at the Business Council of British Columbia and Joseph Garcia, Partner at Blake, Cassels and Graydon LLP.

Genome BC recently released its 2013-2014 Annual Report. There are “many good reasons”why you should read it. Find it online at:

www.genomebc.ca/about/publications/annual-report/