2009 Vienna - European Society of Human Genetics

Genomics, Genomic technology and Epigenetics
netic diversity of autosomal disorders. Genetic diversity of HDs in the
investigated populations was revealed 454 disorders (6800 affected):
215 AD, 183 AR and 56 X-linked recessive. It is established, that 57.39
% of patients for all types of inheritance concern to the common forms
of the HDs causing only 6 % of all revealed nozological forms. These
28 disorders meet with high frequencies in all investigated populations
(15 with AD, 8 with AR and 5 with X-linked inheritance). However, besides
these 28 diseases which frequencies also varied between regions,
specific common diseases are revealed in each population. It
has been demonstrated that the genes of HDs are a promising tool for
characteristic ethnogenetic processes in populations.
P11.047
HGVbaseG2P: an advanced database for the integration of
genetic association datasets
R. C. Free, R. K. Hastings, O. Lancaster, G. A. Thorisson, A. J. Brookes;
University of Leicester, Leicester, United Kingdom.
The reporting of genetic association studies is far from optimal since in
many cases (especially negative findings) results are not made publically
available. Consequently, it is very difficult to determine what signals
should be believed, or to integrate the results of different studies.
To improve on this situation, the Human Genome Variation Genotype-
Phenotype database (HGVbaseG2P: www.hgvbaseg2p.org) has been
constructed to provide a new publication medium for association study
results - including large-scale, small-scale, GWAS, candidate gene,
positive, and negative findings. HGVbaseG2P focuses upon summary-level
information, and work is underway to orchestrate the control of
access to such datasets globally, to overcome concerns about identifying
study participants from such information.
HGVbaseG2P aims to combine the best features of a database and a
scientific journal, and in that respect a partnership has been established
with HUGO and Springer to explore awarding DOIs and PubMed IDs
to studies submitted to HGVbaseG2P. Additionally, curators actively
gather and collate data from all relevant public data resources.
The latest version of HGVbaseG2P provides a highly-innovative set of
new genome browser options for visually comparing and contrasting
genetic association datasets - both at genome wide and region specific
levels.
To disseminate these technologies more widely, a blank ‘HGVbaseG2P-in-a-box’
will shortly be made available so that others can
create compliant databases to report their own compilations of research
findings. All such databases will automatically be interoperable,
enabling pan-database searches.
Acknowledgements: GEN2PHEN is funded by the European Community’s
Seventh Framework Programme (FP7/2007-2013) under grant
agreement 200754.
P11.048
GEN2PHEN Knowledge centre: a virtual centre of excellence for
the genotype-to-phenotype community
A. J. Webb, A. J. Brookes;
University of Leicester, Leicester, United Kingdom.
The GEN2PHEN project aims to help establish increasingly holistic
access to Genotype- Phenotype (G2P) information. This goal involves
promoting a federated network of G2P resources, and enabling the bidirectional
flow of knowledge between public G2P databases to G2P
researchers. To this end, we are constructing the ‘GEN2PHEN Knowledge
Centre’ (GEN2PHEN-KC: www.gen2phen.org).
The GEN2PHEN-KC will be much more than a simple informational
website, as it will provide: i) increasingly comprehensive searches of
broad segments of the G2P domain, ii) systems by which researchers
can add comments onto records in public databases, allied to various
modes for the community to discuss small or large topics in the G2P
field, iii) access to software, tools and resources created by the GEN-
2PHEN Project, iv) latest news and updates on the G2P field, including
an extensive diary of relevant events, v) training resources, such as
tutorials, screencasts and instructional videos.
Such features will equip researchers with an easy-to-use and effective
central outlet to promote their research, to network and establish collaborations,
and to assess the value of G2P datasets and resources.
Researchers will also be able to rate and comment on articles, blog
posts and resources, edit wiki-type pages, and engage in debates with
peers.
The first version of the website provides an introduction to the GEN-
2PHEN project, and this will evolve into the fully functional GEN-
2PHEN-KC during the first few months of 2009, with ongoing development
thereafter.
Acknowledgements: GEN2PHEN is funded by the European Community’s
Seventh Framework Programme (FP7/2007-2013) under grant
agreement 200754.
P11.049
UGt1A1(tA)n promoter polymorphism in spanish patients with
a clinical diagnosis of Gilbert syndrome
M. Pico 1 , L. Peña 2 , E. del Rio 3 , A. Lasa 3 , M. Cornet 3 , M. Baiget 3 ;
1 H. U. de Gran Canaria Dr. Negrín, Las Palmas de Gran canaria, Spain, 2 Hospital
Materno-Infantil, Las Palmas de Gran canaria, Spain, 3 Hospital Sant Pau,
Barcelona, Spain.
Gilbert’s syndrome is a mild hereditary unconjugated hyperbilirubinemia
caused by mutations in the UDP-glucuronosyltransferase gene
(UGT1A1). The causative mutation in Caucasians is almost exclusively
a TA dinucleotide insertion in the TATA box of the UGT1A1 promoter.
The vast majority of affected individuals are homozygous for the variant
promoter and have 7 instead of 6 TA repeats.
The aim of the present study was to determine the genotypes of
UGT1A1(TA)n promoter in 686 cases referred to our laboratory with
clinical diagnosis of Gilbert Syndrome.
To determine the number of TA repeats, we performed a fluorescencelabelled
PCR. The PCR products were separated by an automated
capillary electrophoresis and analyzed using the ABI GeneScan programme
(Applied Biosystems).
We have identified the following genotypes: TA 5 /TA 6 (n:1); TA 6 /TA 6
(n:58); TA 6 /TA 7 (n:147); TA 6 /TA 8 (n: 5); TA 7 /TA 7 (n: 472); TA 7 /TA 8 (n: 2)
and TA 8 /TA 8 (n:1)
The TA 8 allele was first described by Beutler in subjects with African
ancestry and is very rare in Caucasians. Four cases out of five with a
TA 6 /TA 8 genotype were first degree relatives of the boy with a homozygous
TA 8 /TA 8 genotype. This is, to our knowledge, the first homozygous
case of this rare allele.
P11.050
complete sequencing of the cFtR gene using next-generation
Gs-FLX sequencing technology
L. Vliegen, J. Cassiman, H. Cuppens;
Center for Human Genetics, Leuven, Belgium.
Next generation sequencing technologies have been recently introduced.
However, this technology was initially developed for whole genome
sequencing purposes.
We have adopted this technology for complete sequence analysis of
the CFTR coding region.
For a 50x coverage, only half a million nucleotides are needed for
CFTR sequence analysis of one patient. Therefore, 100-200 samples
should be pooled in order to use the full capacity of the GS-FLX system.
We have developed an economically feasible universal sample
tagging approach allowing the pooling of 100 samples with one set of
260 primers (60 amplicon-specific primers and 200 tagging primers).
This compares to 6000 primers if amplicon-specific primers are tagged
as such.
Normally, each amplicon should be amplified individually and purified.
Then, the concentration of each solution is accurately determined in
order to pool all amplicons in equimolar concentrations. The universal
tagging approach resulted in a less dynamic range of the yield of the
different amplicons, so that the time-consuming preparation of equimolar
solutions could be simplified.
We are even further simplifying the PCR steps through the development
of robust multiplex PCR reactions. Indeed, 30 amplicons should
be analyzed for the CFTR gene, and this can ultimately be only economically
feasible if amplified in one, or a limited number, of multiplex
PCR reaction(s). Specifically, we have developed a robust multiplex
amplification assay in which biotinylated amplicon-specific primers are
locally restricted through streptavidin/biotin crosslinking.
We thus developed an assay for routine sequencing of the CFTR gene
in a diagnostic setting using next generation sequencing.