March 12, 2019

Developing best practices for benchmarking: The quiet but crucial work behind sequencing today

The Global Alliance for Genomics and Health publishes new guidelines for comparing a patient’s test results to a reference human genome

Finding the difference between a patient’s DNA sequence and a reference sequence – also known as variant calling – is central to cancer research, but approaches to variant calling differ from lab to lab. Comparing – or benchmarking – one lab’s approach to another lab is important to the development of new sequencing and analysis tools, yet there are no widely-accepted standards for benchmarking variant calls.

To develop these standards and address common benchmarking challenges, a group of stakeholders from government agencies, academic bioinformatics groups, sequencing technology developers and other organizations around the world gathered to create the Global Alliance for Genomics and Health (GA4GH) Benchmarking Team. They’ve recently published their best practices for benchmarking genome sequencing results in Nature Biotechnology.

“Technology is improving rapidly, but we’ve lacked ways to know the strengths and weaknesses of new sequencing and genome analysis methods,” says Dr. Justin Zook, lead author of the study from the National Institute of Standards and Technology. “This paper gives people tools to develop accurate sequencing tests for precision medicine.”

The adoption of these practices – and their continual improvement – can also help facilitate collaboration between research and clinical laboratories while improving the performance of shared tools and methods.

The framework was developed in part by Dr. Paul Boutros and his lab members at OICR, who have used crowdsourcing to develop benchmarking foundations for individual variants as well as broader genetic variation.

Read more about this benchmarking work on Genome Web.

November 21, 2018

The buzz about Beacon: A look into the Global Alliance’s newest standards for the Beacon API

 

Beacon logo resembling a lighthouse

GA4GH releases its latest standards for genomics search engines, a project co-led by OICR Associate, Dr. Marc Fiume

While we are generating genomic data at an unprecedented rate, it is collected and studied in academic and clinical settings around the world with different data privacy requirements, making it difficult to share this knowledge. Researchers must undergo a lengthy process to request access to data and until now there has been no way to know if a data set contains information that is relevant to the research being conducted.

Continue reading – The buzz about Beacon: A look into the Global Alliance’s newest standards for the Beacon API

October 23, 2018

Updates and highlights from Global Alliance’s 6th Plenary Meeting

The Global Alliance for Genomics and Health (GA4GH) held its 6th Plenary Meeting in Basel, Switzerland earlier this month. The meeting brought together more than 430 participants from 25 countries, making it the biggest GA4GH event yet. Attendees of the meeting learned about GA4GH Connect – a strategic phase focused on connecting GA4GH development work to the immediate data sharing needs of the community.

Peter Goodhand, CEO of GA4GH, introducing GA4GH Connect

At the meeting, Peter Goodhand, Chief Executive Officer of GA4GH, announced a call for new real-world genomic data initiatives – Driver Projects – with a specific focus on global collaboration and scientific merit. The Steering Committee will announce the accepted Driver Projects in February 2019.

Also at the meeting, Dr. Marc Fiume, Chief Executive Officer of DNAstack and OICR Associate, presented on the recent progress of the Beacon Project – an international collaborative initiative that has developed a realtime discovery platform for genetic mutations. The Beacon Project has released Beacon API V1.0.0 on Friday – the first genomic data interoperability standard from the GA4GH 2018 Strategic Roadmap.

“It was a fantastic meeting and an eye-opening experience to learn about how the field of precision medicine is linking genomic tools with clinical databases and patient outcomes to drive a patient-centered, learning healthcare model,” says Dr. Laszlo Radvanyi, President and Scientific Director of OICR. “GA4GH continues to play a critical role in establishing standards for genomic data acquisition, quality, interpretation, integrity, security, and sharing that many national genomic health initiatives are beginning to embrace around the world.”

Access highlights and updates from the Plenary Meeting online, or read a PDF of the meeting report here.

August 21, 2018

Leader in data access and CEO of DNAstack, Dr. Marc Fiume, joins OICR as its newest Associate

Dr. Marc Fume poses for a photo in an atrium

Formalizing his longstanding relationship with OICR, Dr. Marc Fiume joins the Institute as an Associate to turn big data into a cure

“We know there are valuable – potentially life-saving – genomics and clinical data that are locked away in the sever rooms in hospital basements,” says Dr. Marc Fiume, CEO of DNAstack, Adjunct Professor at the University of Toronto, and OICR’s newest Associate. “We’re working to make these data more findable, accessible and useful to help researchers find cures for diseases faster than ever before.”

Continue reading – Leader in data access and CEO of DNAstack, Dr. Marc Fiume, joins OICR as its newest Associate

February 9, 2018

Global Alliance for Genomics and Health launches 2018 Strategic Roadmap

The Global Alliance for Genomics and Health (GA4GH) has laid out its plans for the next five years as it continues to align its activities with meeting the key needs of the genomics data community. The Strategic Roadmap encompasses the standards and frameworks that will be developed by GA4GH and will be updated with new deliverables annually. OICR is a GA4GH Host Institution.

Continue reading – Global Alliance for Genomics and Health launches 2018 Strategic Roadmap

October 18, 2017

GA4GH Strikes Formal Collaborations with 15 International Genomic Data Initiatives

Orlando, Florida (October 17, 2017) – The Global Alliance for Genomics and Health (GA4GH) has struck formal collaborations with 15 international genomic data initiatives as 2017 Driver Projects, including Genomics England, Australian Genomics and the U.S. All of Us Research Program. The announcement, made at the GA4GH 5th Plenary Meeting, comes as part of the launch of GA4GH Connect: A 5-year Strategic Plan. GA4GH Connect aims to drive uptake of standards and frameworks for genomic data sharing within the research and healthcare communities in order to enable responsible sharing of clinical-grade genomic data by 2022.

Continue reading – GA4GH Strikes Formal Collaborations with 15 International Genomic Data Initiatives

October 17, 2017

Global Alliance for Genomics and Health charts path to the future of genomic data sharing

Technology and DNA

The Global Alliance for Genomics and Health (GA4GH) has launched a new five-year strategic plan to develop international standards that will enable the responsible and secure sharing of genomic data for both scientific and clinical purposes. The plan, known as GA4GH Connect, was launched at the organization’s 5th Plenary Meeting in Orlando, Florida.  

Continue reading – Global Alliance for Genomics and Health charts path to the future of genomic data sharing

May 8, 2017

Interview: Mr. Peter Goodhand, President of OICR

Peter Goodhand

OICR is pleased to announce that Mr. Peter Goodhand is OICR’s new President for a one-year term. Goodhand served as Interim President of OICR over the past 10 months, in addition to his role as Executive Director of the Global Alliance for Genomics and Health (GA4GH). We spoke to Goodhand about why he took on the new, expanded job, how it differs from his previous role, what this means for the search for a permanent OICR President and Scientific Director and what he’s planning for the next year at OICR.

Continue reading – Interview: Mr. Peter Goodhand, President of OICR

January 10, 2017

Partnership to expand genomic data sharing in Europe

The Global Alliance for Genomics and Health’s (GA4GH) Beacon Project has partnered with ELIXIR, the body that organizes Europe’s infrastructure for life science data, to make genomic data in that continent more easily discoverable by researchers. The Beacon Project is a demonstration project that enables genomic data centres to make their data more easily discoverable to users by allowing them to use simple queries to explore a dataset’s contents.

Continue reading – Partnership to expand genomic data sharing in Europe

October 25, 2016

From our Annual Report: Constructing the cloud

Illustration showing clouds

OICR’s reputation as leader in managing and analyzing big data has grown over the past year as the Institute has worked with private and public partners to bring more genomic and health data to the cloud.

Continue reading – From our Annual Report: Constructing the cloud

June 9, 2016

GA4GH presents vision, model for genomic and clinical data sharing

Global Alliance for Genomics and Health

TORONTO, CANADA (June 9, 2016) — In today’s Science, the Global Alliance for Genomics and Health (GA4GH) calls for a federated data ecosystem for sharing genomic and clinical data. The authorship, which includes Canadian leaders as well as a diverse team of international leaders in academia, research, medicine, and industry, argues that a common framework of principles, protocols, and interoperable technical systems are necessary to enable responsible and effective data sharing.

Continue reading – GA4GH presents vision, model for genomic and clinical data sharing

November 20, 2015

OICR’s Tom Hudson named Chair of Global Alliance for Genomics and Health Steering Committee

Global Alliance LogoOn October 6, at the 2015 Annual Meeting of the American Society of Human Genetics, Dr. Tom Hudson, President and Scientific Director of the Ontario Institute for Cancer Research, assumed the role of Chair of the Global Alliance for Genomics and Health (GA4GH) Steering Committee, succeeding Dr. David Altshuler. Altshuler has served as Chair since GA4GH was established in 2013, and will remain as a member of the Steering Committee.

“Just over two years ago, a group of leaders from around the globe came together to enable the responsible sharing of genomic and clinical data. Tom was a key contributor from the start, and with his help, GA4GH has made substantial progress,” Altshuler said. “I cannot think of a better person to lead the Steering Committee.”

The role of the Steering Committee is to make high-level decisions about the direction, values, and working products from the GA4GH. GA4GH is a community of individuals and world-leading organizations working together to create interoperable tools and approaches to enable genomic and clinical data sharing. More information about GA4GH can be found at www.genomicsandhealth.org.

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