Reflections with Ewan Birney - how far have we come in 20 years?
Director General of EMBL, Director of EMBL-EBI and Senior Scientist
As the annual Genome Informatics conference approaches its 20th year, we reflect on how the field of genome biology has developed over the past two decades, with Ewan Birney, Director of EMBL-EBI, Joint Head of Research and Senior Scientist.
Ewan shares his experiences from both attending and speaking at this conference, since its inception in 2001 – when he was also a key member of the first organising committee.
Having alternated between Wellcome Genome Campus Advanced Courses and Scientific Conferences and Cold Spring Harbour, in the USA – since the beginning, 2020 will see Ewan take part as keynote speaker of its first presentation as a virtual conference, delivered by ACSC in September.
Here’s how the feel and focus of Genome Informatics has evolved over the last 20 years, through the eyes of Ewan Birney.
Significant changes in genomes informatics over the past 20 years
The last 20 years has seen a rapid drop in genome sequencing prices, making the possibility of wide-scale personalised medicine an emerging reality for future societies.
Ewan Birney highlights how the increased affordability of sequencing technology has spurred on many aspects of genome informatics, both in genetics of diseases but also by enabling the scaling of assays that could shift to a DNA readout – hence Chip-seq, ATAC-seq and so on.
The innovation continues, he believes, with long read native nucleic acid sequencers:
"I still find it remarkable that we can now directly sequence RNA and sense RNA modifications"
Methods and algorithms have had to keep pace with the depth of data generation. Of the numerous innovations, Birney highlights the importance of both the Burrows-Wheeler transform, which enabled the use of the compressed index string family for short reads, and also the FM-index used in many mapping tools, such as BWA
"Genome informatics would be impossible without them!"
More recently, the rise of neural network architectures for decoding information has revolutionised image analysis and continues to enter genome analysis in a variety of ways.
These vast technological advances in sequencing capabilities are set to define the future of medicine for generations to come, and the impact will be seen greatly across all levels of society.
Growing up with Genome Informatics
As we approach a defining era for rapid technological advancements, and the prospect of widely accessible personalised medicine, it’s easy to forget how far we’ve come since 2001; when informatics was just starting to be acknowledged as a rich topic of scientific discussion in its own right. This new attitude towards informatics set in motion a level of momentum and investment in this field that eventually saw the possibility of a human genome sequencing project.
“This makes me feel very lucky to have grown up with this field, at such an interesting time when it has been possible to be actively involved in a turning point of the field. From 1992, when I published my first paper on computational biology and going on to become part of the public human genome sequencing project I’ve loved being part of the computational biology community"
The evolution of informatics into a revered field of its own, also helped establish the foundation of the Genome Informatics meeting, held in 2001. Birney appeared on the very first organising committee, and has since been involved in speaking and presenting across its 20 year dominance as a popular meeting for its broadening community of researchers.
His involvement has helped cement his passion for global information sharing – a feature becoming increasingly more important to the field.
“I’ve gotten so much out of the international data sharing and international perspective – I find it hard to think of any other way of working”
This has been greatly influenced by the ability of the informatics community to be able to come together annually at the Genome Informatics conference, to share data and form an international mind-set, as well as valuable international connections and collaborations.
Benefits to modern medicine that have evolved as a result
The current biggest practical benefit to modern medicine in Birney’s opinion has been the routine diagnosis of rare genetic diseases often from the genome or exome sequencing in the first year of life. For almost all, this stops the continued testing of the child to understand their condition and allows for care planning. For a small percentage, it provides direct treatment options which can have a profound impact. A confident genomic-based diagnosis also enables parents to make more informed choices about having further children and offers particularly reassurance when the genetic changes are shown to be de novo mutations.
“Whilst the development of non-invasive pregnancy tests may be an unexpected practical health benefit of sequencing, they are nevertheless a milestone event made possible by informatics technology”
Sampling fragmented DNA from the foetus that is present in the pregnant mother’s blood allows identification of chromosomal abnormalities. The result is as accurate as the previous invasive tests, but instead taken from a simple blood test ’ – removing the risk to the foetus and the discomfort for the patient.
“This is defining stuff for the improvement of patient healthcare and clinical practice”
The list of the significant benefits of genome informatics to health goes on. In cancer care, identification of patient-specific genomic biomarkers facilitates the tailoring of therapeutics and drug choice, and oncogene sequencing can identify drug sensitising mutations. Rapid DNA or RNA sequencing of infectious diseases can provide information on antibiotic resistance or help us understand patterns that exist behind outbreaks – RNA sequencing of virus RNA has been critical in the current COVID-19 crisis!
“The impact of genomics is just starting to reach into broad common disease, such as heart attacks or Type II diabetes – but expect wide ranging advances in the next 20 years!”
Many milestones have been achieved since the inception of the Genome Informatics conference, in 2001. However, new technology and pace bring brand new challenges to the fore.
Birney views bioinformatics as being at the frontline, battling the deluge of new data from an expanding and diverse information landscape.
“Fortunately, new toolkits, such as Machine Learning/Deep Neural Networks, are being developed that can be deployed against particular datasets”
These innovations will all contribute in their own way to the management of the increasing demands emerging from the increase in digital data.
How has the genome informatics research community changed over the years?
Just as the genome informatics field has moved from DNA sequencing to embrace more methods, more algorithms and over broader data types; the community has broadened to become more gender-balanced and internationally diverse.
“This broadening community can also be seen at the Genome Informatics conference – evident in the growing diversity of our conference attendees and speakers”
But now is not the time to rest on our laurels, Birney continues:
“We need to continue to provide a broad and welcoming community, and ensure that the many unconscious biases present, are challenges, and wherever possible, removed!”
You can hear more from Ewan Birney at our Genome Informatics 2020 conference.
With the first Genome Informatics conference being held back in 2001, 20 years later Advanced Courses and Scientific Conferences are delighted to be hosting the first virtual Genome Informatics meeting in 2020, with Ewan Birney as keynote speaker.
Abstracts are being accepted until 21 July.
Please submit your research for an opportunity to feature as party of this milestone programme.