Annual Scientific Report 2015

Ewan Birney
PhD 2000, Wellcome Trust Sanger Institute.
At EMBL since 2000. Joint Associate Director
from 2012 to 2015.
Director since June 2015.
Major achievements
In 2015 our group carried out two major types of
projects: one a series of molecular studies, and the other
a series phenotype-association studies. Working on a
variety of human systems, we explored the association of
molecular events in both normal and diseased samples.
We worked closely with the Stegle research group at
EMBL-EBI for both strands of research, using their new
association methods that can handle both population
confounders and other multiple-phenotype scenarios.
Our molecular studies, in collaboration with MRI
researchers and cardiologists at Imperial College, UK,
focused on the structure and physiology of the human
heart. Our disease-association work is in collaboration
with Francis Collins at the NIH in the US, with whom
we share a student.
We continued to develop the resources around Medaka
fish, and demonstrated that our selected population
would be appropriate for establishing a population
reference panel.
Future projects and goals
In 2016 the Birney group will continue to work on
sequence algorithms and intra-species variation.
Our work with human data will focus on molecular
phenotypes in an induced pluripotent stem cell (iPSC)
panel generated as part of the HipSci consortium, and
on a project based on normal human cardiac data. Our
work in Drosophila will investigate multi-time-point
developmental biology measures. We will also assess
the near isogenic panel in Japanese Rice Paddy fish for a
number of molecular and whole-body phenotypes.
Figure. Region-specific changes in left ventricular
wall thickness depending on SNP genotype for a
locus on chromosome 6. The locus was discovered by
a genome-wide association study of 9 Mio SNPs and
latent factors of heart morpholgy in a cohort of 1000
healthy volunteers (Caucasians).
Selected publications
Birney E, Soranzo N. (2015) Human genomics: The end
of the start for population sequencing. Nature 526:52-53
Huang J, Howie B, McCarthy S, et al. (2015) Improved
imputation of low-frequency and rare variants using
the UK10K haplotype reference panel. Nature Commun.
6:8111
We also worked on projects exploring the broader
associations of molecular functional information,
such as information generated by the ENCODE and
Epigenome Roadmap projects, with cancer data (i.e.
the BASIS project on Breast Cancers), and worked
on leveraging human genetics to help improve drug
discovery in the context of a project with Open Targets
(formerly CTTV).
Ip CL, Loose M, Tyson JR, et al. (2015) MinION Analysis
and Reference Consortium: Phase 1 data release and
analysis. F1000Research 4:1075
Taylor PN, Porcu E, Chew S, et al. (2015) Whole-genome
sequence-based analysis of thyroid function. Nature
Commun 6:5681
UK10K Consortium, et al. (2015) The UK10K project
identifies rare variants in health and disease. Nature
526:82-90
Dr Birney engaged in policy-level discussions on
the use of genomic information in human health,
and co-authored a paper on the risks and benefits of
incidental findings in human genomics.
2015 EMBL-EBI Annual Scientific Report 134