|
2013 ISCB OVERTON PRIZE: GONCALO ABECASIS
By Christiana N. Fogg, Freelance
Science Writer, Kensington, MD
ISCB recognizes the achievements of an early or mid-career scientist
annually with the Overton Prize. The Overton Prize honors the memory
of G. Christian Overton, a prominent bioinformatics researcher and
founding ISCB Board member who died suddenly in 2000. Winners of the
Overton Prize are up-and-coming independent scientists honored for
their significant contributions to computational biology through
research, teaching, and service.
ISCB is thrilled to recognize Dr.
Goncalo Abecasis, Felix E. Moore Collegiate Professor of
Biostatistics at the University of Michigan, as the 2013 winner of
the Overton Prize. Goncalo Abecasis was drawn to biology ever
since he was a child. "From a young age, I have always been
fascinated with understanding how life works," said Abecasis. He
fondly recalls spending Sundays at a bookstore with his parents and
collecting a small library of books.
But it was
his experiences in a high school computer programming club that
opened his eyes to an entirely different field. "Although I didn't
know it at the time, a key skill that later contributed to my
success in genetics was my interest in computer programming," recalled Abecasis.
"The club was meant to keep us busy and out of trouble, but they did
encourage us to try programming and point us in the direction of
very useful techniques, like object oriented programming and the
like."
Human genetics appealed to
Abecasis as he pursued his undergraduate studies at the
University of Leeds, and he landed a position in the lab of Dr. Mary
Anne Shaw studying "how genetic variation in the interleukin-1 gene
cluster, a set of immune genes where variation was easy to measure
with then available techniques, was related to infection by
Leishmania and other tropical parasites." This experience proved
invaluable for helping Abecasis to receive funding for his Ph.D.
training in the lab of Dr. William Cookson at the University of
Oxford. Cookson's lab was studying genes that contribute to
asthma susceptibility at the Wellcome Trust Center for Human
Genetics at Oxford. In the late 1990's and early 2000's, Abecasis
described this Center as "a mecca for human geneticists at the time,
with great support from the Wellcome Trust, and lots of smart people
trying new ways to run genetic studies and looking to make rapid
progress in many different traits." Abecasis also recalled that, "as
we pushed the limits of the sequencing and genotyping technologies
of the time, we were soon generating datasets that were beyond the
reach of existing analysis tools and methods."
Abecasis saw
that, "It was easy to realize that new analysis methods and computer
software were needed -- and being in Oxford, working at the Wellcome
Trust Center was just the right place to be." With Cookson's
support, and under the comentorship of statistical geneticist Dr.
Lon Cardon, Abecasis developed software to tackle the analysis of
large genetic datasets. Abecasis remembered dealing with many
software bugs along the way, but then, as now, he repeated the
mantra to himself that "all software is buggy, and this is no
exception!" Abecasis was pursuing his Ph.D. at the same time as the
race to sequence the first human genome was wrapping up. As the
field of genomics was emerging, he realized that several of the
methods he had developed could be used to look at how Abecasis's
research, and the field of human population genetics in general,
have been transformed by the advent of high-throughput genetics. "We
now have very clear answers about the degree and structure of
genetic variation in the world today, but have also gained a lot of
detail on human population history -- including very ancient events,
like admixture with Neanderthals," said Abecasis.
Abecasis's lab
is now focused primarily on identifying genetic variants relevant to
human disease. They look at linkage disequilibrium within human
genomes in order to describe, "how groups of variants are shared
among individuals." One of the observations that Abecasis's group
and others made several years ago that he recalled as being
surprising was "that much of the genetic variation in any individual
could be recovered very accurately by comparing each individual to a
reference set of individuals and, more recently, we have used the
process to make it relatively inexpensive to sequence large
numbers of individuals. At our last count, >30,000 human
genomes had been sequenced using our "low-coverage" linkage
disequilibrium based approach."
One of the
highlights of Abecasis's career was being invited to the White House
in 2010. "I was thrilled. I remember I had very short notice
(perhaps a couple of days) and had to rush and find something to
wear, recalled Abecasis. Although it is cheesy, it is really amazing
to live in a country that functions so much like a meritocracy. I
didn't have to write a check, join a committee, vote - anything. I
had a good idea about how to sequence a lot of genomes more rapidly,
proposed it, and not only did I get funded to try it out (it worked,
by the way), but my work was selected as one of the highlights for
Vice President Biden's speech on the important of technology
development and biomedical research."
Abecasis described the
importance of collaborations to his research and is a strong
proponent of sharing data and software tools. "So many great
discoveries and advances come from bringing in insights, ideas and
approaches from a different field," said Abecasis. But
Abecasis also agreed that data sharing is not without challenges.
"There are legitimate concerns about protecting the identity and
privacy of research subjects and, once in a while, people do use
data you share pre-publication to gain an advantage," said Abecasis.
"Still, there is no doubt we are moving in the right direction --
expectations for data sharing and collaboration are so much more
open than when I started."
Abecasis has felt fortunate to
work with so many great collaborators. One of his most interesting
collaborations has been his work with Drs. David Schlessinger,
Francesco Cucca, and Serena Sanna and many others on the "SardiNIA
project." "When I first met David, and he described the idea of
conducting a thorough genetic study in an isolated valley in
Sardinia, I never thought it would happen," remembered Abecasis.
"It seemed so ambitious. But David and our Sardinian
colleagues have boundless energy and real dedication, and the study
probably accounts for most of my highly cited papers!" "The work
of Goncalo underscores the importance of the theoretical
developments and their implementation in computational method for
the progress in current biomedical research, bringing genomic
information closer to the study of the complex genetic basis of
common diseases," said Alfonso Valencia, chair of the ISCB's Awards
committee.
Abecasis feels truly honored and humbled to be
the 2013 recipient of the Overton Prize. Abecasis also hopes that,
"If this award encourages members of the ISCB to bring some of their
considerable expertise to bear on the big open problems in genetics,
that would be an amazing outcome."
This article is excerpted
from the June 28, 2013, issue of Bioinformatics. A transcript
of the full interview with Dr. Abecasis can be found at http://genome.sph.umich.edu/wiki/Goncalo_Abecasis:_Interview_with_Christiana_Fogg.
 |