Genome Informatics Alliance
The Genome Informatics Alliance (GIA) was an interdisciplinary thought leadership conference started in 2009 to uncover near term challenges to the advancement of Next Generation Sequencing (NGS) as the technology was advancing in terms of quality and quantity (and was reducing in terms of cost). The thesis was that bringing together commercial and academic experts in genomics and in related technological disciplines would result in an acceleration in the application of NGS to precision medicine, life sciences research, and in any field in which some aspect of -omics data could extend understanding. The format was built around framing questions to guide short expert presentation each followed by active Q&A for the presenter.
The basic format of the two day meetings were to assemble leading experts - and competitors - to openly discuss pre-competitive areas of need for next generation sequencing. The organizing committee and later the organizer tried to look beyond the current technical capabilities to look beyond the horizon in anticipation of challenges that would be introduced as sequencing technology and its applications became more widespread.
The inaugural framing questions in 2009 were at a time when very few human whole genomes were available, and when the output of a sequencing run was significantly under 10 Gigabases of output. At the time a whole human DNA sequence required 30x representation or 100G of data. With this in mind, the initial questions were:
- What data models are required on which to build a foundation?
- How will genomes need to be compared?
- How will collaboration and data sharing evolve?
All four GIA meetings were sponsored by Illumina, and were initially organized by committee.
The 2009 GIA meeting was held in Healdsburg, California at the Hotel Healdsburg on 17-18 March 2009; the organizing committee was comprised of David Dooling Elaine Mardis of Washington University in St. Louis (WUStL), and Scott Kahn of Illumina.
Introduction Meeting Overview Elaine Mardis WUStL
- Why this is important?
- How will the concepts of a common reference evolve?
- How does this impact ‘omics and research beyond the genomics lab.
Session 1 Challenges at Genome Centers Session Chair: Scott Kahn
- What are the challenges that the large genome centers are currently facing that the typical researcher will be facing soon?
Session 2 Challenges with Users and Analysts Session Chair: Dirk Evers
- How is analysis being changed by the increased availability of data from multiple genomes and rapid turnaround of experiments?
Session 3 Challenges from a High Data Volume Perspective Session Chair: David Dooling
- What can we learn from groups that handle high volumes of analytical data?
Session 4 Challenges with Data Management Session Chair: Elaine Mardis
- How do the platforms manage the current data load and what will data management look like if the platform yield increases by 10X?
- What are the data structures and QC measures that will be needed for effective data transport and integration?
Round Table Discussion: Framing Issues Moderator: Jacques Retief
- What is preventing the reduction in data storage and processing?
- What are the most critical missing applications?
- Sequence analysis challenges, specific to different applications
- Action items?
Session 5 Framing Solutions Session Chair: Jordan Stockton
- What potential solutions already exist and what is on the horizon?
- What are the obstacles to their adoption?
Session 6 Framing Data Structure Solutions Session Chair: Jacques Retief
- Do current ways of storing data make sense?
- What challenges remain unsolved?
Session 7 Framing the Tool and Service Solutions Session Chair: Gavin Sherlock
- How can software help to transform genomic data into biological insight?
Round Table Discussion Moderators: Elaine and Scott
- How do we break free from old perspectives on data?
- Universal data structures for sequence transfer and storage
- How can the data analysis pipeline be streamlined?
- Action items?
The 2010 GIA meeting was held in Woodinville, Washington at the Willows Lodge on 6-7 May 2010; the organizing committee was comprised of David Dooling of WUStL and Scott Kahn of Illumina.
The 2011 GIA meeting was held in Verona, Italy at the Byblos Art Hotel - Villa Amista on 9-10 June 2011; the meeting was organized by Scott Kahn of Illumina.
Introduction Scott Kahn (Illumina) Genomics and the Importance of Annotation
Session 1 Evolution of the human reference genome Session Chair. Scott Kahn
Session 2 Tools, methods and best practices for genomic annotation Session Chair. Jacques Retief
Session 3 State-of-art in database curation and aggregation Session Chair. Gary Schroth
Session 4 Communication and visualization of genomic annotations Session Chair. Jordan Stockton
Session 5 Tools, methods and best practices for genomic annotation (continued) Session Chair. Jordan Stockton
Session 6 State-of-art in database curation and aggregation (continued) Session Chair. John MacPherson
Session 7 Communication and visualization of genomic annotations (continued) Session Chair. Dirk Evers
The 2012 GIA meeting was held in Newberg, Oregon at the Allison Inn and Spa on 29-30 March 2012; the meeting was organized by Scott Kahn of Illumina.
Scott Kahn Illumina Welcome
David Bentley Illumina Meeting Overview
The One Million Genome Challenge Session Chair: Jordan Stockton
- What are the challenges in trying to aggregate one million human whole genome sequences?
- Are there collaboration mechanisms that would support this?
- Are there database frameworks that are applicable?
- Would this change the definition of "raw data"?
- Are there analysis and visualization tools that are needed?
- How would it advance science?
Tools, methods and best practices for genomic annotation Session Chair: Semyon Kruglyak
- How is context included in annotation to support use and re-use?
- How will transitioning from single genomes to multi-sample studies impact tools?
- What are the content-centric interdependencies that must be resolved?
- How do/will social media methods impact this area?
Sequencing unplugged Session Chair: Scott Kahn
- If sequencing technology was not bounded by current sequencer form factors and technological limitations, what would be the ultimate application?
- What technologies exist in other marker segments that we can re-purpose?
- What are interesting convergences that can be foreseen?
Information communication challenges Session Chair: Jacques Retief
- How are truly large amounts of data communicated in biology and outside of biology.
- What will be needed to support research, clinical applications, applied technology applications (e.g., forensics), and ultimately personal use?
Clinical applications Session Chair: David Bentley
- How can the world-wide accumulated genomic information be used to improve the diagnosis of an individual patient?
- Will there ever be an exhaustive library of cancer mutations? How big a cohort will it take to build it?
- What will be required to build a comprehensive set of rules/mechanisms that can describe the acquisition of genomic aberrations and disease progression in cancer?
More than DNA Session Chair: Gary Schroth
- What are the unique opportunities and challenges presented by metagenomics, epigenomics, RNA, and their integration.
- Will we ever achieve wholeomics, a completely integrated view of the genome, epigenome and biology?
Round Table Discussion Moderator Scott Kahn
- Summary of meeting and discussion of where to explore next
- Are there topics that would be fruitfully be brought into scope for GIA?
- Are there next steps that we should take away from this meeting?
References
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